paragraph_ref_data_revision.json

{"1. MRPS21 (Mitochondrial Ribosomal Protein S21) is a component of the small 28S subunit of the mitochondrial ribosome. It is involved in the assembly of the ribosomal subunit and is essential for mitochondrial protein synthesis, which is crucial for the production of proteins that are part of the oxidative phosphorylation (OXPHOS) system.": {"keywords": "(\"MRPS21\") AND (\"mitochondrial protein synthesis\" OR \"ribosomal assembly\" OR \"oxidative phosphorylation\") AND (hasabstract[text])", "references": []}, "2. MRPS23 (Mitochondrial Ribosomal Protein S23) is another constituent of the small 28S subunit of the mitochondrial ribosome. Similar to MRPS21, it plays a role in the assembly and stability of the mitochondrial ribosome, facilitating the synthesis of mitochondrial-encoded proteins.": {"keywords": "(\"MRPS23\" OR \"MRPS21\") AND (\"mitochondrial ribosome\" OR \"protein synthesis\" OR \"ribosomal assembly\") AND (hasabstract[text])", "references": []}, "3. MRPS28 (Mitochondrial Ribosomal Protein S28) is also a part of the small 28S subunit of the mitochondrial ribosome. It contributes to the proper assembly and function of the mitochondrial ribosome, which is necessary for the translation of the 13 proteins encoded by the mitochondrial genome that are integral to the OXPHOS system.": {"keywords": "(\"MRPS28\") AND (\"mitochondrial ribosome\" OR \"translation\" OR \"OXPHOS\") AND (hasabstract[text])", "references": []}, "4. MRPS35 (Mitochondrial Ribosomal Protein S35) is a component of the small 28S subunit of the mitochondrial ribosome as well. It is implicated in the assembly of the ribosomal subunit and is involved in mitochondrial protein synthesis, particularly in the translation process of mitochondrial DNA-encoded proteins.": {"keywords": "(\"MRPS35\") AND (\"mitochondrial protein synthesis\" OR \"ribosomal assembly\" OR \"translation\") AND (hasabstract[text])", "references": []}, "1. The majority of the proteins listed, including MRPL10, MRPL11, MRPL13, MRPL14, MRPL16, MRPL17, MRPL18, MRPL19, MRPL22, MRPL23, MRPL24, MRPL27, MRPL2, MRPL33, MRPL35, MRPL36, MRPL37, MRPL38, MRPL39, MRPL3, MRPL41, MRPL42, MRPL43, MRPL44, MRPL4, MRPL50, MRPL51, MRPL53, MRPL55, MRPL9, and MRPS18A, are components of the mitochondrial ribosome (mitoribosome). These proteins are integral to the structure and function of the mitoribosome, which is responsible for synthesizing proteins encoded by the mitochondrial genome.": {"keywords": "(\"MRPL10\" OR \"MRPL11\" OR \"MRPL13\" OR \"MRPL14\" OR \"MRPL16\" OR \"MRPL17\" OR \"MRPL18\" OR \"MRPL19\" OR \"MRPL22\" OR \"MRPL23\" OR \"MRPL24\" OR \"MRPL27\" OR \"MRPL2\" OR \"MRPL33\" OR \"MRPL35\" OR \"MRPL36\" OR \"MRPL37\" OR \"MRPL38\" OR \"MRPL39\" OR \"MRPL3\" OR \"MRPL41\" OR \"MRPL42\" OR \"MRPL43\" OR \"MRPL44\" OR \"MRPL4\" OR \"MRPL50\" OR \"MRPL51\" OR \"MRPL53\" OR \"MRPL55\" OR \"MRPL9\" OR \"MRPS18A\") AND (\"mitochondrial ribosome\" OR \"protein synthesis\" OR \"mitochondrial genome\") AND (hasabstract[text])", "references": ["Box, Jodie M, Kaur, Jasvinder, Stuart, Rosemary A. \"MrpL35, a mitospecific component of mitoribosomes, plays a key role in cytochrome <i>c</i> oxidase assembly.\" Molecular biology of the cell, 2017, pp. 3489-3499.", "Gruschke, Steffi, Gr\u00f6ne, Kerstin, Heublein, Manfred, H\u00f6lz, Stefanie, Israel, Lars, Imhof, Axel, Herrmann, Johannes M, Ott, Martin. \"Proteins at the polypeptide tunnel exit of the yeast mitochondrial ribosome.\" The Journal of biological chemistry, 2010, pp. 19022-8.", "Gan, Xiang, Kitakawa, Madoka, Yoshino, Ken-Ichi, Oshiro, Noriko, Yonezawa, Kazuyoshi, Isono, Katsumi. \"Tag-mediated isolation of yeast mitochondrial ribosome and mass spectrometric identification of its new components.\" European journal of biochemistry, 2002, pp. 5203-14.", "Amarasekera, Sumudu S C, Hock, Daniella H, Lake, Nicole J, Calvo, Sarah E, Gr\u00f8nborg, Sabine W, Krzesinski, Emma I, Amor, David J, Fahey, Michael C, Simons, Cas, Wibrand, Flemming, Mootha, Vamsi K, Lek, Monkol, Lunke, Sebastian, Stark, Zornitza, \u00d8stergaard, Elsebet, Christodoulou, John, Thorburn, David R, Stroud, David A, Compton, Alison G. \"Multi-omics identifies large mitoribosomal subunit instability caused by pathogenic MRPL39 variants as a cause of pediatric onset mitochondrial disease.\" Human molecular genetics, 2023, pp. 2441-2454.", "Wessels, Hans J C T, Vogel, Rutger O, Lightowlers, Robert N, Spelbrink, Johannes N, Rodenburg, Richard J, van den Heuvel, Lambert P, van Gool, Alain J, Gloerich, Jolein, Smeitink, Jan A M, Nijtmans, Leo G. \"Analysis of 953 human proteins from a mitochondrial HEK293 fraction by complexome profiling.\" PloS one, 2013, pp. e68340.", "Horga, Alejandro, Manole, Andreea, Mitchell, Alice L, Bugiardini, Enrico, Hargreaves, Iain P, Mowafi, Walied, Bettencourt, Concei\u00e7\u00e3o, Blakely, Emma L, He, Langping, Polke, James M, Woodward, Catherine E, Dalla Rosa, Ilaria, Shah, Sachit, Pittman, Alan M, Quinlivan, Ros, Reilly, Mary M, Taylor, Robert W, Holt, Ian J, Hanna, Michael G, Pitceathly, Robert D S, Spinazzola, Antonella, Houlden, Henry. \"Uniparental isodisomy of chromosome 2 causing MRPL44-related multisystem mitochondrial disease.\" Molecular biology reports, 2021, pp. 2093-2104.", "Di Nottia, Michela, Marchese, Maria, Verrigni, Daniela, Mutti, Christian Daniel, Torraco, Alessandra, Oliva, Romina, Fernandez-Vizarra, Erika, Morani, Federica, Trani, Giulia, Rizza, Teresa, Ghezzi, Daniele, Ardissone, Anna, Nesti, Claudia, Vasco, Gessica, Zeviani, Massimo, Minczuk, Michal, Bertini, Enrico, Santorelli, Filippo Maria, Carrozzo, Rosalba. \"A homozygous MRPL24 mutation causes a complex movement disorder and affects the mitoribosome assembly.\" Neurobiology of disease, 2020, pp. 104880."]}, "2. Proteins such as MALSU1 (Mitochondrial Assembly of Ribosomal Large Subunit 1) are directly involved in the assembly of the mitoribosome, particularly the large subunit, indicating a specialized role in the biogenesis of the mitochondrial translation machinery.": {"keywords": "(\"MALSU1\") AND (\"mitoribosome\" OR \"biogenesis\" OR \"mitochondrial translation\") AND (hasabstract[text])", "references": []}, "3. Aminoacyl-tRNA synthetases including AARS2 (Alanyl-tRNA Synthetase 2, Mitochondrial), NARS2 (Asparaginyl-tRNA Synthetase 2, Mitochondrial), TARS2 (Threonyl-tRNA Synthetase 2, Mitochondrial), VARS2 (Valyl-tRNA Synthetase 2, Mitochondrial), and YARS2 (Tyrosyl-tRNA Synthetase 2, Mitochondrial) are responsible for charging tRNAs with their respective amino acids, a critical step in the translation process within mitochondria.": {"keywords": "(\"AARS2\" OR \"NARS2\" OR \"TARS2\" OR \"VARS2\" OR \"YARS2\") AND (\"aminoacyl-tRNA synthetase\" OR \"translation\" OR \"mitochondria\") AND (hasabstract[text])", "references": ["Vanlander, Arnaud V, Menten, Bj\u00f6rn, Smet, Jo\u00e9l, De Meirleir, Linda, Sante, Tom, De Paepe, Boel, Seneca, Sara, Pearce, Sarah F, Powell, Christopher A, Vergult, Sarah, Michotte, Alex, De Latter, Elien, Vantomme, Lies, Minczuk, Michal, Van Coster, Rudy. \"Two siblings with homozygous pathogenic splice-site variant in mitochondrial asparaginyl-tRNA synthetase (NARS2).\" Human mutation, 2015, pp. 222-31.", "Diodato, Daria, Melchionda, Laura, Haack, Tobias B, Dallabona, Cristina, Baruffini, Enrico, Donnini, Claudia, Granata, Tiziana, Ragona, Francesca, Balestri, Paolo, Margollicci, Maria, Lamantea, Eleonora, Nasca, Alessia, Powell, Christopher A, Minczuk, Michal, Strom, Tim M, Meitinger, Thomas, Prokisch, Holger, Lamperti, Costanza, Zeviani, Massimo, Ghezzi, Daniele. \"VARS2 and TARS2 mutations in patients with mitochondrial encephalomyopathies.\" Human mutation, 2014, pp. 983-9."]}, "4. DHX30 and GFM1 are associated with the translation process, with DHX30 likely involved in RNA processing or ribosome assembly based on its helicase activity, and GFM1 (Elongation Factor G1, Mitochondrial) playing a role in the translocation step during mitochondrial protein synthesis.": {"keywords": "(\"DHX30\" OR \"GFM1\") AND (\"translation\" OR \"ribosome assembly\" OR \"mitochondrial protein synthesis\") AND (hasabstract[text])", "references": []}, "5. HMGB3 (High Mobility Group Box 3) is a non-histone chromosomal protein that can bind to DNA and may have a role in the organization of the mitochondrial genome, thus indirectly influencing mitochondrial protein synthesis.": {"keywords": "(\"HMGB3\") AND (\"mitochondrial genome\" OR \"DNA binding\" OR \"protein synthesis\") AND (hasabstract[text])", "references": []}, "6. PTCD1 (Pentatricopeptide Repeat Domain 1), RPUSD4 (RNA Pseudouridylate Synthase Domain Containing 4), and other proteins with less clear roles may contribute to the regulation of mitochondrial gene expression or the stability of mitochondrial RNAs, further supporting the process of mitochondrial protein synthesis.": {"keywords": "(\"PTCD1\" OR \"RPUSD4\") AND (\"mitochondrial gene expression\" OR \"mitochondrial protein synthesis\" OR \"RNA stability\") AND (hasabstract[text])", "references": []}, "1. The majority of the proteins listed, such as DDX10, DDX18, DDX21, DDX47, DDX52, DHX33, DHX37, DIMT1, DKC1, ESF1, FBL, IMP4, KRI1, KRR1, LTV1, MPHOSPH10, MRM1, NAF1, NOB1, NOC4L, NOL6, NOP10, PNO1, POP1, POP4, POP5, RCL1, RIOK1, RIOK2, RRP12, RRP7A, RRP9, TSR1, TSR2, UTP11, UTP20, UTP23, UTP6, WDR36, WDR3, WDR46, and components of the small ribosomal subunit such as RPS10, RPS11, RPS12, RPS13, RPS15A, RPS18, RPS19, RPS21, RPS23, RPS24, RPS27, RPS27A, RPS28, RPS29, RPS2, RPS3, RPS3A, RPS4X, RPS5, RPS6, RPS7, RPS9, and RPSA, are directly involved in ribosome biogenesis. This includes the processing of pre-rRNA, assembly of ribosomal proteins, and the maturation of the ribosomal subunits.": {"keywords": "(\"DDX10\" OR \"DDX18\" OR \"DDX21\" OR \"DDX47\" OR \"DDX52\" OR \"DHX33\" OR \"DHX37\" OR \"DIMT1\" OR \"DKC1\" OR \"ESF1\" OR \"FBL\" OR \"IMP4\" OR \"KRI1\" OR \"KRR1\" OR \"LTV1\" OR \"MPHOSPH10\" OR \"MRM1\" OR \"NAF1\" OR \"NOB1\" OR \"NOC4L\" OR \"NOL6\" OR \"NOP10\" OR \"PNO1\" OR \"POP1\" OR \"POP4\" OR \"POP5\" OR \"RCL1\" OR \"RIOK1\" OR \"RIOK2\" OR \"RRP12\" OR \"RRP7A\" OR \"RRP9\" OR \"TSR1\" OR \"TSR2\" OR \"UTP11\" OR \"UTP20\" OR \"UTP23\" OR \"UTP6\" OR \"WDR36\" OR \"WDR3\" OR \"WDR46\" OR \"RPS10\" OR \"RPS11\" OR \"RPS12\" OR \"RPS13\" OR \"RPS15A\" OR \"RPS18\" OR \"RPS19\" OR \"RPS21\" OR \"RPS23\" OR \"RPS24\" OR \"RPS27\" OR \"RPS27A\" OR \"RPS28\" OR \"RPS29\" OR \"RPS2\" OR \"RPS3\" OR \"RPS3A\" OR \"RPS4X\" OR \"RPS5\" OR \"RPS6\" OR \"RPS7\" OR \"RPS9\" OR \"RPSA\") AND (\"ribosome biogenesis\" OR \"pre-rRNA processing\" OR \"ribosomal proteins\") AND (hasabstract[text])", "references": ["Doherty, Leana, Sheen, Mee Rie, Vlachos, Adrianna, Choesmel, Valerie, O'Donohue, Marie-Fran\u00e7oise, Clinton, Catherine, Schneider, Hal E, Sieff, Colin A, Newburger, Peter E, Ball, Sarah E, Niewiadomska, Edyta, Matysiak, Michal, Glader, Bertil, Arceci, Robert J, Farrar, Jason E, Atsidaftos, Eva, Lipton, Jeffrey M, Gleizes, Pierre-Emmanuel, Gazda, Hanna T. \"Ribosomal protein genes RPS10 and RPS26 are commonly mutated in Diamond-Blackfan anemia.\" American journal of human genetics, 2010, pp. 222-8.", "Wang, RuNan, Yoshida, Kenichi, Toki, Tsutomu, Sawada, Takafumi, Uechi, Tamayo, Okuno, Yusuke, Sato-Otsubo, Aiko, Kudo, Kazuko, Kamimaki, Isamu, Kanezaki, Rika, Shiraishi, Yuichi, Chiba, Kenichi, Tanaka, Hiroko, Terui, Kiminori, Sato, Tomohiko, Iribe, Yuji, Ohga, Shouichi, Kuramitsu, Madoka, Hamaguchi, Isao, Ohara, Akira, Hara, Junichi, Goi, Kumiko, Matsubara, Kousaku, Koike, Kenichi, Ishiguro, Akira, Okamoto, Yasuhiro, Watanabe, Kenichiro, Kanno, Hitoshi, Kojima, Seiji, Miyano, Satoru, Kenmochi, Naoya, Ogawa, Seishi, Ito, Etsuro. \"Loss of function mutations in RPL27 and RPS27 identified by whole-exome sequencing in Diamond-Blackfan anaemia.\" British journal of haematology, 2015, pp. 854-64.", "Suzuki, Masayoshi, Tezuka, Kenta, Handa, Takumi, Sato, Risa, Takeuchi, Hina, Takao, Masaki, Tano, Mitsutoshi, Uchida, Yasuo. \"Upregulation of ribosome complexes at the blood-brain barrier in Alzheimer's disease patients.\" Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism, 2022, pp. 2134-2150.", "Ameismeier, Michael, Cheng, Jingdong, Berninghausen, Otto, Beckmann, Roland. \"Visualizing late states of human 40S ribosomal subunit maturation.\" Nature, 2018, pp. 249-253.", "Arthurs, Callum, Murtaza, Bibi Nazia, Thomson, Calum, Dickens, Kerry, Henrique, Rui, Patel, Hitendra R H, Beltran, Mariana, Millar, Michael, Thrasivoulou, Christopher, Ahmed, Aamir. \"Expression of ribosomal proteins in normal and cancerous human prostate tissue.\" PloS one, 2017, pp. e0186047.", "Montellese, Christian, van den Heuvel, Jasmin, Ashiono, Caroline, D\u00f6rner, Kerstin, Melnik, Andr\u00e9, Jonas, Stefanie, Zemp, Ivo, Picotti, Paola, Gillet, Ludovic C, Kutay, Ulrike. \"USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit.\" eLife, 2020, pp.  .", "D'Allard, Diane L, Liu, Johnson M. \"Toward RNA Repair of Diamond Blackfan Anemia Hematopoietic Stem Cells.\" Human gene therapy, 2016, pp. 792-801.", "Lumsden, Thomas, Bentley, Amber A, Beutler, William, Ghosh, Arnab, Galkin, Oleksandr, Komar, Anton A. \"Yeast strains with N-terminally truncated ribosomal protein S5: implications for the evolution, structure and function of the Rps5/Rps7 proteins.\" Nucleic acids research, 2010, pp. 1261-72.", "P\u00e9rez-Fern\u00e1ndez, Jorge, Mart\u00edn-Marcos, Pilar, Dosil, Mercedes. \"Elucidation of the assembly events required for the recruitment of Utp20, Imp4 and Bms1 onto nascent pre-ribosomes.\" Nucleic acids research, 2011, pp. 8105-21.", "Kan, Guangyan, Wang, Ziyang, Sheng, Chunjie, Chen, Gong, Yao, Chen, Mao, Yizhi, Chen, Shuai. \"Dual Inhibition of DKC1 and MEK1/2 Synergistically Restrains the Growth of Colorectal Cancer Cells.\" Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2021, pp. 2004344.", "Zheng, Sanduo, Lan, Pengfei, Liu, Ximing, Ye, Keqiong. \"Interaction between ribosome assembly factors Krr1 and Faf1 is essential for formation of small ribosomal subunit in yeast.\" The Journal of biological chemistry, 2014, pp. 22692-22703.", "Chen, Cheng, Huang, Haigen, Yan, Ruibin, Lin, Shuo, Qin, Wei. \"Loss of <i>rps9</i> in Zebrafish Leads to <i>p53</i>-Dependent Anemia.\" G3 (Bethesda, Md.), 2019, pp. 4149-4157.", "Jiao, Jianqin, Kavdia, Kanisha, Pagala, Vishwajeeth, Palmer, Lance, Finkelstein, David, Fan, Yiping, Peng, Junmin, Demontis, Fabio. \"An age-downregulated ribosomal RpS28 protein variant regulates the muscle proteome.\" G3 (Bethesda, Md.), 2021, pp.  ."]}, "2. Several DEAD-box proteins (DDX) and DHX proteins are RNA helicases that participate in the remodeling of RNA-protein complexes, which is a critical step in the maturation of ribosomal RNA and ribosome assembly.": {"keywords": "(\"DDX\" OR \"DHX\") AND (\"RNA helicases\" OR \"ribosome assembly\" OR \"rRNA maturation\") AND (hasabstract[text])", "references": ["Tian, Changxu, Tan, Suxu, Bao, Lisui, Zeng, Qifan, Liu, Shikai, Yang, Yujia, Zhong, Xiaoxiao, Liu, Zhanjiang. \"DExD/H-box RNA helicase genes are differentially expressed between males and females during the critical period of male sex differentiation in channel catfish.\" Comparative biochemistry and physiology. Part D, Genomics & proteomics, 2017, pp. 109-119."]}, "3. Proteins such as DIMT1, DKC1, and NOP10 are involved in the modification of rRNA, which is essential for proper ribosome function.": {"keywords": "(\"DIMT1\" OR \"DKC1\" OR \"NOP10\") AND (\"rRNA modification\" OR \"ribosome function\" OR \"proteins\") AND (hasabstract[text])", "references": ["Walne, Amanda J, Dokal, Inderjeet. \"Advances in the understanding of dyskeratosis congenita.\" British journal of haematology, 2009, pp. 164-72."]}, "4. The PeBoW complex, consisting of proteins such as BOP1 (not listed but related to the process), WDR36, and PES1 (not listed but related to the process), is crucial for the maturation of the 60S ribosomal subunit.": {"keywords": "(\"BOP1\" OR \"WDR36\" OR \"PES1\") AND (\"ribosome maturation\" OR \"PeBoW complex\" OR \"60S subunit\") AND (hasabstract[text])", "references": ["Kellner, Markus, Rohrmoser, Michaela, Forn\u00e9, Ignasi, Voss, Kirsten, Burger, Kaspar, M\u00fchl, Bastian, Gruber-Eber, Anita, Kremmer, Elisabeth, Imhof, Axel, Eick, Dirk. \"DEAD-box helicase DDX27 regulates 3' end formation of ribosomal 47S RNA and stably associates with the PeBoW-complex.\" Experimental cell research, 2015, pp. 146-59."]}, "5. Proteins like FBL (fibrillarin) are involved in rRNA methylation, a modification necessary for the proper structure and function of the ribosome.": {"keywords": "(\"FBL\") AND (\"rRNA methylation\" OR \"ribosome\" OR \"fibrillarin\") AND (hasabstract[text])", "references": []}, "6. The assembly factors such as NOB1, PNO1, and RRP12 are implicated in the final steps of 40S ribosomal subunit maturation.": {"keywords": "(\"NOB1\" OR \"PNO1\" OR \"RRP12\") AND (\"ribosomal assembly\" OR \"40S subunit\" OR \"maturation\") AND (hasabstract[text])", "references": ["Zemp, Ivo, Wandrey, Franziska, Rao, Sanjana, Ashiono, Caroline, Wyler, Emanuel, Montellese, Christian, Kutay, Ulrike. \"CK1\u03b4 and CK1\u03b5 are components of human 40S subunit precursors required for cytoplasmic 40S maturation.\" Journal of cell science, 2014, pp. 1242-53."]}, "7. Proteins like IMP4 and UTP20 are components of the small subunit (SSU) processome, which is involved in the early stages of 18S rRNA processing.": {"keywords": "(\"IMP4\" OR \"UTP20\") AND (\"rRNA processing\" OR \"SSU processome\" OR \"proteins\") AND (hasabstract[text])", "references": ["P\u00e9rez-Fern\u00e1ndez, Jorge, Mart\u00edn-Marcos, Pilar, Dosil, Mercedes. \"Elucidation of the assembly events required for the recruitment of Utp20, Imp4 and Bms1 onto nascent pre-ribosomes.\" Nucleic acids research, 2011, pp. 8105-21."]}, "8. The presence of ribosomal proteins (RPS and RPL families) indicates that these proteins are also involved in the actual structure of the ribosome, which is the site of mRNA translation.": {"keywords": "(\"RPS\" OR \"RPL\") AND (\"ribosome\" OR \"translation\" OR \"ribosomal proteins\") AND (hasabstract[text])", "references": ["Moin, Mazahar, Bakshi, Achala, Saha, Anusree, Dutta, Mouboni, Madhav, Sheshu M, Kirti, P B. \"Rice Ribosomal Protein Large Subunit Genes and Their Spatio-temporal and Stress Regulation.\" Frontiers in plant science, 2016, pp. 1284."]}, "9. A few proteins, such as ZCCHC9, ZNF236, C1orf131, ZNF84, ZNHIT6, CCDC59, AATF, CPEB1, and GLB1, do not have a direct known connection to ribosome biogenesis but may be involved in related processes such as RNA binding, transcriptional regulation, or other cellular processes.": {"keywords": "(\"ZCCHC9\" OR \"ZNF236\" OR \"C1orf131\" OR \"ZNF84\" OR \"ZNHIT6\" OR \"CCDC59\" OR \"AATF\" OR \"CPEB1\" OR \"GLB1\") AND (\"ribosome biogenesis\" OR \"RNA binding\" OR \"transcriptional regulation\") AND (hasabstract[text])", "references": []}, "1. The majority of the proteins listed, including RPL10A, RPL10, RPL11, RPL13, RPL14, RPL17, RPL19, RPL21, RPL23A, RPL23, RPL24, RPL26, RPL27A, RPL30, RPL31, RPL32, RPL34, RPL36, RPL37A, RPL37, RPL38, RPL4, RPL5, RPL6, RPL7, RPL8, and RPL9, are ribosomal proteins that are integral components of the ribosome. These proteins are essential for the structure and function of ribosomes, which are the cellular machines responsible for protein synthesis.": {"keywords": "(\"RPL10A\" OR \"RPL10\" OR \"RPL11\" OR \"RPL13\" OR \"RPL14\" OR \"RPL17\" OR \"RPL19\" OR \"RPL21\" OR \"RPL23A\" OR \"RPL23\" OR \"RPL24\" OR \"RPL26\" OR \"RPL27A\" OR \"RPL30\" OR \"RPL31\" OR \"RPL32\" OR \"RPL34\" OR \"RPL36\" OR \"RPL37A\" OR \"RPL37\" OR \"RPL38\" OR \"RPL4\" OR \"RPL5\" OR \"RPL6\" OR \"RPL7\" OR \"RPL8\" OR \"RPL9\") AND (\"ribosomal proteins\" OR \"protein synthesis\" OR \"ribosome structure\") AND (hasabstract[text])", "references": ["Suzuki, Masayoshi, Tezuka, Kenta, Handa, Takumi, Sato, Risa, Takeuchi, Hina, Takao, Masaki, Tano, Mitsutoshi, Uchida, Yasuo. \"Upregulation of ribosome complexes at the blood-brain barrier in Alzheimer's disease patients.\" Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism, 2022, pp. 2134-2150.", "Devis, Deborah, Firth, Sue M, Liang, Zhe, Byrne, Mary E. \"Dosage Sensitivity of RPL9 and Concerted Evolution of Ribosomal Protein Genes in Plants.\" Frontiers in plant science, 2015, pp. 1102.", "Fancello, Laura, Kampen, Kim R, Hofman, Isabel J F, Verbeeck, Jelle, De Keersmaecker, Kim. \"The ribosomal protein gene RPL5 is a haploinsufficient tumor suppressor in multiple cancer types.\" Oncotarget, 2017, pp. 14462-14478.", "Ramu, Vemanna S, Dawane, Akashata, Lee, Seonghee, Oh, Sunhee, Lee, Hee-Kyung, Sun, Liang, Senthil-Kumar, Muthappa, Mysore, Kirankumar S. \"Ribosomal protein QM/RPL10 positively regulates defence and protein translation mechanisms during nonhost disease resistance.\" Molecular plant pathology, 2020, pp. 1481-1494.", "Genuario, R R, Kelley, D E, Perry, R P. \"Comparative utilization of transcription factor GABP by the promoters of ribosomal protein genes rpL30 and rpL32.\" Gene expression, 1993, pp. 279-88.", "Marygold, Steven J, Coelho, Carmen M A, Leevers, Sally J. \"Genetic analysis of RpL38 and RpL5, two minute genes located in the centric heterochromatin of chromosome 2 of Drosophila melanogaster.\" Genetics, 2005, pp. 683-95.", "Blitvich, B J, Rayms-Keller, A, Blair, C D, Beaty, B J. \"Molecular cloning and complete cDNA sequences of the ribosomal proteins rpl34 and rpl44 from Aedes triseriatus mosquitoes.\" DNA sequence : the journal of DNA sequencing and mapping, 2000, pp. 451-5.", "Luan, Yizhao, Tang, Nan, Yang, Jiaqi, Liu, Shuting, Cheng, Chichi, Wang, Yan, Chen, Congying, Guo, Ya-Nan, Wang, Hongwei, Zhao, Wenxue, Zhao, Qian, Li, Wei, Xiang, Mengqing, Ju, Rong, Xie, Zhi. \"Deficiency of ribosomal proteins reshapes the transcriptional and translational landscape in human cells.\" Nucleic acids research, 2022, pp. 6601-6617."]}, "2. Proteins such as BOP1, WDR12, and PES1 are part of the PeBoW complex, which is crucial for the maturation of the 60S ribosomal subunit. Their interaction is necessary for the processing of the 28S rRNA, a component of the large ribosomal subunit.": {"keywords": "(\"BOP1\" OR \"WDR12\" OR \"PES1\") AND (\"ribosome maturation\" OR \"PeBoW complex\" OR \"rRNA processing\") AND (hasabstract[text])", "references": ["Kellner, Markus, Rohrmoser, Michaela, Forn\u00e9, Ignasi, Voss, Kirsten, Burger, Kaspar, M\u00fchl, Bastian, Gruber-Eber, Anita, Kremmer, Elisabeth, Imhof, Axel, Eick, Dirk. \"DEAD-box helicase DDX27 regulates 3' end formation of ribosomal 47S RNA and stably associates with the PeBoW-complex.\" Experimental cell research, 2015, pp. 146-59."]}, "3. EIF6 (eukaryotic translation initiation factor 6) is involved in the biogenesis of the 60S ribosomal subunit and also acts to prevent premature association of the 40S and 60S ribosomal subunits.": {"keywords": "(\"EIF6\") AND (\"ribosome biogenesis\" OR \"translation initiation\" OR \"ribosomal subunits\") AND (hasabstract[text])", "references": []}, "4. NVL, a member of the AAA ATPase family, is implicated in ribosome biogenesis, specifically in the processing of the 60S subunit.": {"keywords": "(\"NVL\") AND (\"ribosome biogenesis\" OR \"AAA ATPase\" OR \"60S subunit\") AND (hasabstract[text])", "references": []}, "5. Several DEAD-box proteins, including DDX24, DDX51, and DDX56, are RNA helicases that participate in various stages of rRNA processing and ribosome assembly.": {"keywords": "(\"DDX24\" OR \"DDX51\" OR \"DDX56\") AND (\"RNA helicases\" OR \"rRNA processing\" OR \"ribosome assembly\") AND (hasabstract[text])", "references": []}, "6. MDN1 is a large AAA ATPase essential for the final steps of 60S ribosomal subunit maturation, functioning in the release of biogenesis factors from mature subunits.": {"keywords": "(\"MDN1\") AND (\"ribosome biogenesis\" OR \"AAA ATPase\" OR \"maturation\") AND (hasabstract[text])", "references": []}, "7. Nucleolar proteins such as NOP16, MYBBP1A, and NOL8 are involved in the processing of pre-rRNA and the assembly of ribosomal subunits.": {"keywords": "(\"NOP16\" OR \"MYBBP1A\" OR \"NOL8\") AND (\"ribosome assembly\" OR \"nucleolar proteins\" OR \"pre-rRNA processing\") AND (hasabstract[text])", "references": []}, "8. RRS1 and RSL1D1 are ribosome biogenesis factors that are required for the maturation of the 40S ribosomal subunit.": {"keywords": "(\"RRS1\" OR \"RSL1D1\") AND (\"ribosome biogenesis\" OR \"40S subunit\" OR \"maturation\") AND (hasabstract[text])", "references": []}, "9. Proteins like MAK16, NIP7, and LSG1 are also associated with ribosome biogenesis, contributing to the processing of pre-rRNAs and the assembly of ribosomal subunits.": {"keywords": "(\"MAK16\" OR \"NIP7\" OR \"LSG1\") AND (\"ribosome biogenesis\" OR \"pre-rRNA processing\" OR \"ribosomal assembly\") AND (hasabstract[text])", "references": []}, "10. CARF, CCDC86, ABCF1, GNL2, NLE1, PPAN, RBM28, and SDAD1, while not as directly linked to ribosome biogenesis as the other proteins mentioned, are involved in cellular processes that can intersect with ribosome assembly, such as cell cycle regulation, RNA processing, and stress responses.": {"keywords": "(\"CARF\" OR \"CCDC86\" OR \"ABCF1\" OR \"GNL2\" OR \"NLE1\" OR \"PPAN\" OR \"RBM28\" OR \"SDAD1\") AND (\"ribosome biogenesis\" OR \"cell cycle regulation\" OR \"RNA processing\") AND (hasabstract[text])", "references": []}, "1. ABCA1 and ABCB8 are members of the ATP-binding cassette (ABC) transporters involved in lipid transport and homeostasis. ABCA1 plays a crucial role in the efflux of cholesterol and phospholipids to apolipoproteins, a process essential for HDL formation, while ABCB8 is implicated in mitochondrial iron homeostasis.": {"keywords": "(\"ABCA1\" OR \"ABCB8\") AND (\"lipid transport\" OR \"cholesterol efflux\" OR \"mitochondrial iron homeostasis\") AND (hasabstract[text])", "references": []}, "2. ACAA2, ACADL, ACADM, and ACADS are enzymes involved in the beta-oxidation of fatty acids, a process that breaks down fatty acids to generate acetyl-CoA, which enters the citric acid cycle for energy production.": {"keywords": "(\"ACAA2\" OR \"ACADL\" OR \"ACADM\" OR \"ACADS\") AND (\"beta-oxidation\" OR \"fatty acids\" OR \"energy production\") AND (hasabstract[text])", "references": ["Song, Yu-Feng, Tan, Xiao-Ying, Pan, Ya-Xiong, Zhang, Li-Han, Chen, Qi-Liang. \"Fatty Acid \u03b2-Oxidation Is Essential in Leptin-Mediated Oocytes Maturation of Yellow Catfish Pelteobagrus fulvidraco.\" International journal of molecular sciences, 2018, pp.  ."]}, "3. ACLY is ATP citrate lyase, which converts citrate to acetyl-CoA, pivotal for both energy production and biosynthesis of fatty acids and cholesterol.": {"keywords": "(\"ACLY\") AND (\"energy metabolism\" OR \"acetyl-CoA\" OR \"fatty acid synthesis\") AND (hasabstract[text])", "references": []}, "4. ACO2 and ACOX1 are involved in the citric acid cycle and peroxisomal beta-oxidation, respectively, both essential for energy production and fatty acid metabolism.": {"keywords": "(\"ACO2\" OR \"ACOX1\") AND (\"citric acid cycle\" OR \"beta-oxidation\" OR \"energy production\") AND (hasabstract[text])", "references": []}, "5. ADIPOQ and ADIPOR2 are adiponectin and its receptor, which play significant roles in glucose regulation and fatty acid oxidation.": {"keywords": "(\"ADIPOQ\" OR \"ADIPOR2\") AND (\"adiponectin\" OR \"glucose regulation\" OR \"fatty acid oxidation\") AND (hasabstract[text])", "references": ["Bag, Susmita, Anbarasu, Anand. \"Revealing the Strong Functional Association of adipor2 and cdh13 with adipoq: A Gene Network Study.\" Cell biochemistry and biophysics, 2015, pp. 1445-56."]}, "6. AGPAT3 is involved in the biosynthesis of glycerophospholipids, important components of cell membranes and signaling molecules.": {"keywords": "(\"AGPAT3\") AND (\"glycerophospholipid biosynthesis\" OR \"cell membranes\" OR \"signaling molecules\") AND (hasabstract[text])", "references": []}, "7. AIFM1, AK2, and ALDH2 are involved in maintaining mitochondrial integrity and function, which is crucial for energy production.": {"keywords": "(\"AIFM1\" OR \"AK2\" OR \"ALDH2\") AND (\"mitochondrial integrity\" OR \"energy production\" OR \"apoptosis\") AND (hasabstract[text])", "references": []}, "8. ALDOA is an enzyme in the glycolytic pathway, which is the initial step in glucose metabolism.": {"keywords": "(\"ALDOA\") AND (\"glycolysis\" OR \"enzyme\" OR \"glucose metabolism\") AND (hasabstract[text])", "references": []}, "9. ANGPT1, ANGPTL4, and APOE are involved in angiogenesis and lipid metabolism, with APOE being critical for the normal catabolism of triglyceride-rich lipoprotein constituents.": {"keywords": "(\"ANGPT1\" OR \"ANGPTL4\" OR \"APOE\") AND (\"angiogenesis\" OR \"lipid metabolism\" OR \"triglyceride catabolism\") AND (hasabstract[text])", "references": []}, "10. CPT2, CRAT, and CS are involved in the transport and metabolism of fatty acids within the mitochondria and the citric acid cycle, respectively.": {"keywords": "(\"CPT2\" OR \"CRAT\" OR \"CS\") AND (\"fatty acid metabolism\" OR \"mitochondrial transport\" OR \"citric acid cycle\") AND (hasabstract[text])", "references": ["Alaedin, M, Ghaffari, M H, Sadri, H, Meyer, J, D\u00e4nicke, S, Frahm, J, Huber, K, Grindler, S, Kersten, S, Rehage, J, Mur\u00e1ni, E, Sauerwein, H. \"Effects of dietary l-carnitine supplementation on the response to an inflammatory challenge in mid-lactating dairy cows: Hepatic mRNA abundance of genes involved in fatty acid metabolism.\" Journal of dairy science, 2021, pp. 11193-11209."]}, "11. CYP4B1 is a member of the cytochrome P450 family, which is involved in the oxidation of fatty acids.": {"keywords": "(\"CYP4B1\") AND (\"cytochrome P450\" OR \"fatty acid oxidation\" OR \"enzymes\") AND (hasabstract[text])", "references": []}, "12. DGAT1 is involved in the final step of triglyceride synthesis, which is crucial for storing energy.": {"keywords": "(\"DGAT1\") AND (\"triglyceride synthesis\" OR \"DGAT1\" OR \"energy storage\") AND (hasabstract[text])", "references": []}, "13. ECH1, ECHS1, and ENPP2 are involved in fatty acid metabolism and signaling.": {"keywords": "(\"ECH1\" OR \"ECHS1\" OR \"ENPP2\") AND (\"fatty acid metabolism\" OR \"signaling\" OR \"enzymes\") AND (hasabstract[text])", "references": []}, "14. FABP4 is a fatty acid-binding protein that plays a role in intracellular transport of fatty acids and their targeting to specific metabolic pathways.": {"keywords": "(\"FABP4\") AND (\"fatty acid-binding\" OR \"metabolic pathways\" OR \"intracellular transport\") AND (hasabstract[text])", "references": []}, "15. GPAM and GPAT4 are involved in glycerolipid biosynthesis, contributing to the storage of energy.": {"keywords": "(\"GPAM\" OR \"GPAT4\") AND (\"glycerolipid biosynthesis\" OR \"energy storage\") AND (hasabstract[text])", "references": ["Yu, Haibin, Iqbal, Ambreen, Fang, Xibi, Jiang, Ping, Zhao, Zhihui. \"Transcriptome analysis of CRISPR/Cas9-mediated GPAM<sup>-/-</sup> in bovine mammary epithelial cell-line unravelled the effects of GPAM gene on lipid metabolism.\" Gene, 2022, pp. 146574."]}, "16. IDH1, IDH3A, and IDH3G are isocitrate dehydrogenases involved in the citric acid cycle, important for energy production.": {"keywords": "(\"IDH1\" OR \"IDH3A\" OR \"IDH3G\") AND (\"citric acid cycle\" OR \"isocitrate dehydrogenase\" OR \"energy production\") AND (hasabstract[text])", "references": ["Fattal-Valevski, Aviva, Eliyahu, Hila, Fraenkel, NItai D, Elmaliach, Ganit, Hausman-Kedem, Moran, Shaag, Avraham, Mandel, Dror, Pines, Ophry, Elpeleg, Orly. \"Homozygous mutation, p.Pro304His, in IDH3A, encoding isocitrate dehydrogenase subunit is associated with severe encephalopathy in infancy.\" Neurogenetics, 2017, pp. 57-61."]}, "17. LPL is lipoprotein lipase, which hydrolyzes triglycerides in lipoproteins, such as those found in chylomicrons and very low-density lipoproteins (VLDL), into free fatty acids and glycerol.": {"keywords": "(\"LPL\") AND (\"lipoprotein lipase\" OR \"triglycerides\" OR \"hydrolysis\") AND (hasabstract[text])", "references": []}, "18. PPARG is a nuclear receptor that regulates fatty acid storage and glucose metabolism.": {"keywords": "(\"PPARG\") AND (\"nuclear receptor\" OR \"fatty acid\" OR \"glucose metabolism\") AND (hasabstract[text])", "references": []}, "19. SLC27A1 is a fatty acid transporter involved in the uptake of long-chain fatty acids.": {"keywords": "(\"SLC27A1\") AND (\"fatty acid transport\" OR \"long-chain fatty acids\" OR \"SLC27A1\") AND (hasabstract[text])", "references": []}, "20. UCP2 is an uncoupling protein that can dissipate the proton gradient across the mitochondrial membrane, thus regulating energy metabolism and heat production.": {"keywords": "(\"UCP2\") AND (\"mitochondrial membrane\" OR \"energy metabolism\" OR \"heat production\") AND (hasabstract[text])", "references": []}, "1. The proteins CD4, CD8A, CD8B, CD28, CD40, CD40LG, and the T-cell receptor components CD3D, CD3E, CD3G, and CD247 are critical in T-cell activation and function. CD4 and CD8 are co-receptors that enhance the signal from the T-cell receptor (TCR) upon antigen recognition. CD28 provides a co-stimulatory signal necessary for T-cell activation and survival. CD40 and its ligand CD40LG are essential for B-cell activation and T-cell-dependent immune responses.": {"keywords": "(\"CD4\" OR \"CD8A\" OR \"CD8B\" OR \"CD28\" OR \"CD40\" OR \"CD40LG\" OR \"CD3D\" OR \"CD3E\" OR \"CD3G\" OR \"CD247\") AND (\"T-cell activation\" OR \"co-stimulatory signals\" OR \"B-cell activation\") AND (hasabstract[text])", "references": ["Liu, Zhicui, Liu, Shuai, Zhang, Yan, Zeng, Weihong, Wang, Shujun, Ji, Ping, Pan, Meng, Zhu, Cheng, Wang, Ying. \"Distinct roles of ICOS and CD40L in human T-B cell adhesion and antibody production.\" Cellular immunology, 2021, pp. 104420.", "Zhou, Ying, Yuan, Jun, Pan, Yujun, Fei, Yiping, Qiu, Xiangning, Hu, Nan, Luo, Yongqi, Lei, Wenzhi, Li, Yaping, Long, Hai, Sawalha, Amr H, Richardson, Bruce, Lu, Qianjin. \"T cell CD40LG gene expression and the production of IgG by autologous B cells in systemic lupus erythematosus.\" Clinical immunology (Orlando, Fla.), 2009, pp. 362-70.", "Pinto, Mariana Tomazini, Malta, Tathiane Maistro, Rodrigues, Evandra Strazza, Takayanagui, Osvaldo Massaiti, Tanaka, Yuetsu, Covas, Dimas Tadeu, Kashima, Simone. \"T cell receptor signaling pathway is overexpressed in CD4(+) T cells from HAM/TSP individuals.\" The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases, 2015, pp. 578-84.", "Kheirolomoom, Azadeh, Kare, Aris J, Ingham, Elizabeth S, Paulmurugan, Ramasamy, Robinson, Elise R, Baikoghli, Mo, Inayathullah, Mohammed, Seo, Jai W, Wang, James, Fite, Brett Z, Wu, Bo, Tumbale, Spencer K, Raie, Marina N, Cheng, R Holland, Nichols, Lisa, Borowsky, Alexander D, Ferrara, Katherine W. \"In situ T-cell transfection by anti-CD3-conjugated lipid nanoparticles leads to T-cell activation, migration, and phenotypic shift.\" Biomaterials, 2022, pp. 121339."]}, "2. Cytokines such as IL2, IL4, IL6, IL10, IL12A, IL12B, IL18, and TNF, and their respective receptors, including IL2RA, IL2RB, IL2RG, IL4R, IL6R, IL10RA, IL12RB1, and TNFRSF1A, play pivotal roles in immune cell communication, differentiation, and effector functions. These cytokines mediate various immune responses, including inflammation, cell-mediated immunity, and humoral responses.": {"keywords": "(\"IL2\" OR \"IL4\" OR \"IL6\" OR \"IL10\" OR \"IL12A\" OR \"IL12B\" OR \"IL18\" OR \"TNF\" OR \"IL2RA\" OR \"IL2RB\" OR \"IL2RG\" OR \"IL4R\" OR \"IL6R\" OR \"IL10RA\" OR \"IL12RB1\" OR \"TNFRSF1A\") AND (\"immune response\" OR \"cytokines\" OR \"inflammation\") AND (hasabstract[text])", "references": ["Schulz, Susanne, Immel, Uta Dorothee, Just, Louise, Schaller, Hans-G\u00fcnter, Gl\u00e4ser, Christiane, Reichert, Stefan. \"Epigenetic characteristics in inflammatory candidate genes in aggressive periodontitis.\" Human immunology, 2016, pp. 71-75.", "de Alencar, Josiane Bazzo, Zacarias, Joana Maira Valentini, Tsuneto, Patr\u00edcia Yumeko, Souza, Victor Hugo de, Silva, Cl\u00e9verson de Oliveira E, Visentainer, Jeane Eliete Laguila, Sell, Ana Maria. \"Influence of inflammasome NLRP3, and IL1B and IL2 gene polymorphisms in periodontitis susceptibility.\" PloS one, 2020, pp. e0227905.", "Han, Jisoo, Yoo, Inkyu, Lee, Soohyung, Cheon, Yugyeong, Yun, Cheol-Heui, Ka, Hakhyun. \"Interleukin-10 and its receptors at the maternal-conceptus interface: expression, regulation, and implication for T helper 2 cytokine predominance and maternal immune tolerance in the pig, a true epitheliochorial placentation species\u2020.\" Biology of reproduction, 2022, pp. 1159-1174.", "Liu, Q, Hua, M, Yan, S, Zhang, C, Wang, R, Yang, X, Han, F, Hou, M, Ma, D. \"Immunorelated gene polymorphisms associated with acute myeloid leukemia.\" Clinical and experimental immunology, 2020, pp. 266-278."]}, "3. HLA class I molecules (HLA-A, HLA-E, HLA-G) and class II molecules (HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DQA1, HLA-DRA) are involved in antigen presentation to T cells. These molecules are essential for the immune system to recognize and respond to pathogens.": {"keywords": "(\"HLA-A\" OR \"HLA-E\" OR \"HLA-G\" OR \"HLA-DMA\" OR \"HLA-DMB\" OR \"HLA-DOA\" OR \"HLA-DOB\" OR \"HLA-DQA1\" OR \"HLA-DRA\") AND (\"antigen presentation\" OR \"immune system\" OR \"pathogens\") AND (hasabstract[text])", "references": ["Neuchel, Christine, F\u00fcrst, Daniel, Tsamadou, Chrysanthi, Schrezenmeier, Hubert, Mytilineos, Joannis. \"Extended loci histocompatibility matching in HSCT-Going beyond classical HLA.\" International journal of immunogenetics, 2021, pp. 299-316.", "Szekeres-Bartho, Julia. \"Immunological relationship between the mother and the fetus.\" International reviews of immunology, 2002, pp. 471-95."]}, "4. The proteins IFNG, IFNAR2, IFNGR1, and IFNGR2 are involved in the interferon-gamma signaling pathway, which is crucial for innate and adaptive immunity against viral and intracellular bacterial infections and for tumor control.": {"keywords": "(\"IFNG\" OR \"IFNAR2\" OR \"IFNGR1\" OR \"IFNGR2\") AND (\"interferon-gamma\" OR \"innate immunity\" OR \"adaptive immunity\") AND (hasabstract[text])", "references": ["D\u00f6ffinger, R, Altare, F, Casanova, J L. \"Genetic heterogeneity of Mendelian susceptibility to mycobacterial infection.\" Microbes and infection, 2000, pp. 1553-7."]}, "5. Signal transduction molecules such as AKT1, JAK2, LCK, LYN, MAP3K7, MAP4K1, PRKCB, PRKCG, and ZAP70 are involved in various signaling pathways that lead to immune cell activation, proliferation, and survival.": {"keywords": "(\"AKT1\" OR \"JAK2\" OR \"LCK\" OR \"LYN\" OR \"MAP3K7\" OR \"MAP4K1\" OR \"PRKCB\" OR \"PRKCG\" OR \"ZAP70\") AND (\"immune signaling\" OR \"cell activation\" OR \"proliferation\") AND (hasabstract[text])", "references": ["Chen, Muhu, Chen, Xue, Hu, Yingchun, Cai, Xianfu. \"Screening of key genes related to the prognosis of mouse sepsis.\" Bioscience reports, 2020, pp.  .", "Hsueh, R C, Scheuermann, R H. \"Tyrosine kinase activation in the decision between growth, differentiation, and death responses initiated from the B cell antigen receptor.\" Advances in immunology, 2000, pp. 283-316.", "Sampson, Matthew, Zhu, Quan-Sheng, Corey, Seth J. \"Src kinases in G-CSF receptor signaling.\" Frontiers in bioscience : a journal and virtual library, 2007, pp. 1463-74."]}, "6. The proteins FAS and FASLG are involved in the apoptotic pathway, which is a mechanism for the removal of unwanted or damaged cells, including the elimination of immune cells to maintain homeostasis and self-tolerance.": {"keywords": "(\"FAS\" OR \"FASLG\") AND (\"apoptosis\" OR \"FAS\" OR \"FASLG\") AND (hasabstract[text])", "references": ["Chen, Shifeng, Yang, Chunyun, Sun, Chengming, Sun, Yong, Yang, Zongjun, Cheng, Shaoyun, Zhuge, Baozhong. \"miR-21-5p Suppressed the Sensitivity of Hepatocellular Carcinoma Cells to Cisplatin by Targeting FASLG.\" DNA and cell biology, 2019, pp. 865-873."]}, "7. Chemokines and their receptors, including CCL2, CCL4, CCL5, CCL11, CCL13, CCL19, CCL22, CCR1, CCR2, CCR5, CXCL9, CXCL13, and CXCR3, are involved in the chemotactic movement of immune cells to sites of inflammation or injury.": {"keywords": "(\"CCL2\" OR \"CCL4\" OR \"CCL5\" OR \"CCL11\" OR \"CCL13\" OR \"CCL19\" OR \"CCL22\" OR \"CCR1\" OR \"CCR2\" OR \"CCR5\" OR \"CXCL9\" OR \"CXCL13\" OR \"CXCR3\") AND (\"chemotaxis\" OR \"chemokines\" OR \"inflammation\") AND (hasabstract[text])", "references": ["Korbecki, Jan, Kojder, Klaudyna, Barczak, Katarzyna, Simi\u0144ska, Donata, Gutowska, Izabela, Chlubek, Dariusz, Baranowska-Bosiacka, Irena. \"Hypoxia Alters the Expression of CC Chemokines and CC Chemokine Receptors in a Tumor-A Literature Review.\" International journal of molecular sciences, 2020, pp.  .", "Szczuci\u0144ski, Adam, Losy, Jacek. \"Chemokines and chemokine receptors in multiple sclerosis. Potential targets for new therapies.\" Acta neurologica Scandinavica, 2007, pp. 137-46.", "Nanki, Toshihiro. \"[Treatment for rheumatoid arthritis by chemokine blockade].\" Nihon Rinsho Men'eki Gakkai kaishi = Japanese journal of clinical immunology, 2016, pp. 172-80."]}, "8. Proteins involved in antigen processing and presentation, such as TAP1, TAP2, TAPBP, and proteasome subunits like PSMB10, are essential for the generation of peptide antigens that are presented on MHC molecules.": {"keywords": "(\"TAP1\" OR \"TAP2\" OR \"TAPBP\" OR \"PSMB10\") AND (\"antigen processing\" OR \"MHC presentation\" OR \"proteasome\") AND (hasabstract[text])", "references": ["\u017dilionyt\u0117, Karolina, Bagdzevi\u010di\u016bt\u0117, Ugn\u0117, Mlynska, Agata, Urb\u0161tait\u0117, Elena, Paberal\u0117, Emilija, Dobrovolskien\u0117, Neringa, Krasko, Jan Aleksander, Pa\u0161ukonien\u0117, Vita. \"Functional antigen processing and presentation mechanism as a prerequisite factor of response to treatment with dendritic cell vaccines and anti-PD-1 in preclinical murine LLC1 and GL261 tumor models.\" Cancer immunology, immunotherapy : CII, 2022, pp. 2691-2700.", "Palomar, Gemma, Dudek, Katarzyna, Wielstra, Ben, Jockusch, Elizabeth L, Vinkler, Michal, Arntzen, Jan W, Ficetola, Gentile F, Matsunami, Masatoshi, Waldman, Bruce, T\u011b\u0161ick\u00fd, Martin, Zieli\u0144ski, Piotr, Babik, Wies\u0142aw. \"Molecular Evolution of Antigen-Processing Genes in Salamanders: Do They Coevolve with MHC Class I Genes?\" Genome biology and evolution, 2021, pp.  ."]}, "1. ABCC4 (ATP-binding cassette sub-family C member 4) functions as a cellular efflux transporter for various molecules, including lipids and steroid hormones, which can indirectly influence lipid metabolism.": {"keywords": "(\"ABCC4\") AND (\"efflux transporter\" OR \"lipid metabolism\" OR \"steroid hormones\") AND (hasabstract[text])", "references": []}, "2. ACSL3 (Acyl-CoA synthetase long-chain family member 3) is involved in the initial step of fatty acid metabolism, converting free long-chain fatty acids into fatty acyl-CoA esters, which are key components in lipid biosynthesis and degradation.": {"keywords": "(\"ACSL3\") AND (\"fatty acid metabolism\" OR \"lipid biosynthesis\" OR \"acyl-CoA esters\") AND (hasabstract[text])", "references": []}, "3. DHCR24 (24-dehydrocholesterol reductase) and HMGCR (3-hydroxy-3-methylglutaryl-CoA reductase) are critical enzymes in the mevalonate pathway for cholesterol biosynthesis. DHCR24 catalyzes the final step in cholesterol production, while HMGCR is the rate-limiting enzyme in this pathway.": {"keywords": "(\"DHCR24\" OR \"HMGCR\") AND (\"cholesterol biosynthesis\" OR \"mevalonate pathway\" OR \"enzymes\") AND (hasabstract[text])", "references": ["Schroor, Maite M, Mokhtar, Fatma B A, Plat, Jogchum, Mensink, Ronald P. \"Associations between SNPs in Intestinal Cholesterol Absorption and Endogenous Cholesterol Synthesis Genes with Cholesterol Metabolism.\" Biomedicines, 2021, pp.  ."]}, "4. HMGCS1 (3-hydroxy-3-methylglutaryl-CoA synthase 1) also plays a role in the early stages of cholesterol biosynthesis, catalyzing the condensation of acetyl-CoA with acetoacetyl-CoA to form HMG-CoA.": {"keywords": "(\"HMGCS1\") AND (\"cholesterol biosynthesis\" OR \"HMGCS1\" OR \"acetyl-CoA\") AND (hasabstract[text])", "references": []}, "5. INSIG1 (Insulin induced gene 1) is a regulatory protein that helps control cholesterol synthesis by mediating the degradation of HMGCR under sterol-rich conditions.": {"keywords": "(\"INSIG1\" OR \"HMGCR\") AND (\"cholesterol synthesis\" OR \"INSIG1\" OR \"HMGCR degradation\") AND (hasabstract[text])", "references": ["Zhong, Shanshan, Li, Luxiao, Liang, Ningning, Zhang, Lili, Xu, Xiaodong, Chen, Shiting, Yin, Huiyong. \"Acetaldehyde Dehydrogenase 2 regulates HMG-CoA reductase stability and cholesterol synthesis in the liver.\" Redox biology, 2021, pp. 101919."]}, "6. SCD (Stearoyl-CoA desaturase) is a key enzyme in fatty acid metabolism, responsible for the synthesis of monounsaturated fats from saturated fatty acyl-CoAs.": {"keywords": "(\"SCD\") AND (\"fatty acid metabolism\" OR \"monounsaturated fats\" OR \"enzyme\") AND (hasabstract[text])", "references": []}, "7. ELOVL5 (ELOVL fatty acid elongase 5) and FADS1 (Fatty acid desaturase 1) are involved in the elongation and desaturation of fatty acids, respectively, which are crucial steps in the synthesis of long-chain polyunsaturated fatty acids.": {"keywords": "(\"ELOVL5\" OR \"FADS1\") AND (\"fatty acid metabolism\" OR \"elongation\" OR \"desaturation\") AND (hasabstract[text])", "references": ["Castellini, Cesare, Mattioli, Simona, Moretti, Elena, Cotozzolo, Elisa, Perini, Francesco, Dal Bosco, Alessandro, Signorini, Cinzia, Noto, Daria, Belmonte, Giuseppe, Lasagna, Emiliano, Brecchia, Gabriele, Collodel, Giulia. \"Expression of genes and localization of enzymes involved in polyunsaturated fatty acid synthesis in rabbit testis and epididymis.\" Scientific reports, 2022, pp. 2637."]}, "8. IDI1 (Isopentenyl-diphosphate delta isomerase 1) is part of the cholesterol biosynthesis pathway, converting isopentenyl diphosphate to dimethylallyl diphosphate, both precursors for the synthesis of isoprenoids and cholesterol.": {"keywords": "(\"IDI1\") AND (\"cholesterol biosynthesis\" OR \"isoprenoids\" OR \"enzyme activity\") AND (hasabstract[text])", "references": []}, "The proteins listed are significantly involved in the metabolism of lipids and the biosynthesis of cholesterol, with multiple enzymes directly participating in the mevalonate pathway and fatty acid metabolism. The presence of key regulatory proteins such as INSIG1 indicates a system that is not only involved in the synthesis but also the regulation of these processes. The majority of the genes in this system contribute to lipid and cholesterol metabolism, hence the high confidence score. However, the score is not perfect due to the presence of some proteins that may have roles in other unrelated biological processes.": {"keywords": "(\"INSIG1\") AND (\"lipid metabolism\" OR \"cholesterol biosynthesis\" OR \"mevalonate pathway\") AND (hasabstract[text])", "references": []}, "1. COL3A1 and COL5A2 encode for type III and type V collagen, respectively, which are fibrous proteins that are essential components of the extracellular matrix (ECM) and play a critical role in tissue strength and elasticity.": {"keywords": "(\"COL3A1\" OR \"COL5A2\") AND (\"extracellular matrix\" OR \"collagen\" OR \"tissue elasticity\") AND (hasabstract[text])", "references": ["Januchowski, Rados\u0142aw, Zawierucha, Piotr, Ruci\u0144ski, Marcin, Zabel, Maciej. \"Microarray-based detection and expression analysis of extracellular matrix proteins in drug\u2011resistant ovarian cancer cell lines.\" Oncology reports, 2014, pp. 1981-90."]}, "2. LUM encodes for lumican, a keratan sulfate proteoglycan that is involved in the organization of collagen fibers, influencing the tensile strength of the ECM.": {"keywords": "(\"LUM\") AND (\"collagen\" OR \"extracellular matrix\" OR \"tensile strength\") AND (hasabstract[text])", "references": []}, "3. VCAN encodes for versican, a large chondroitin sulfate proteoglycan that is involved in cell adhesion, proliferation, and migration, and is also a critical component of the ECM.": {"keywords": "(\"VCAN\") AND (\"cell adhesion\" OR \"extracellular matrix\" OR \"proliferation\") AND (hasabstract[text])", "references": []}, "4. TIMP1 encodes for tissue inhibitor of metalloproteinases 1, which inhibits the activity of matrix metalloproteinases (MMPs) and is involved in the regulation of ECM turnover.": {"keywords": "(\"TIMP1\") AND (\"matrix metalloproteinases\" OR \"ECM turnover\" OR \"tissue inhibitor\") AND (hasabstract[text])", "references": []}, "5. SPP1 encodes for osteopontin, which is involved in cell-matrix interactions and plays a role in bone remodeling, immune regulation, and cell survival.": {"keywords": "(\"SPP1\") AND (\"cell-matrix interactions\" OR \"bone remodeling\" OR \"immune regulation\") AND (hasabstract[text])", "references": []}, "6. VEGFA encodes for vascular endothelial growth factor A, a signal protein that stimulates vasculogenesis and angiogenesis.": {"keywords": "(\"VEGFA\") AND (\"angiogenesis\" OR \"vasculogenesis\" OR \"growth factor\") AND (hasabstract[text])", "references": []}, "7. FGFR1 encodes for fibroblast growth factor receptor 1, which is a receptor for fibroblast growth factors and is involved in wound healing and angiogenesis.": {"keywords": "(\"FGFR1\") AND (\"angiogenesis\" OR \"wound healing\" OR \"receptor\") AND (hasabstract[text])", "references": []}, "8. PDGFA encodes for platelet-derived growth factor subunit A, which is involved in the regulation of cell proliferation and angiogenesis.": {"keywords": "(\"PDGFA\") AND (\"angiogenesis\" OR \"cell proliferation\" OR \"platelet-derived growth factor\") AND (hasabstract[text])", "references": []}, "9. THBD encodes for thrombomodulin, which is involved in the coagulation system and has anti-inflammatory and cytoprotective properties.": {"keywords": "(\"THBD\") AND (\"coagulation\" OR \"thrombomodulin\" OR \"anti-inflammatory\") AND (hasabstract[text])", "references": []}, "10. CXCL6 encodes for a chemokine that is involved in the recruitment of neutrophils and may play a role in inflammation and wound healing.": {"keywords": "(\"CXCL6\") AND (\"chemokine\" OR \"neutrophil recruitment\" OR \"inflammation\") AND (hasabstract[text])", "references": []}, "11. POSTN encodes for periostin, which is involved in cell adhesion and migration, and plays a role in the development and remodeling of the ECM.": {"keywords": "(\"POSTN\") AND (\"cell adhesion\" OR \"migration\" OR \"ECM development\") AND (hasabstract[text])", "references": []}, "12. JAG1 and JAG2 encode for jagged 1 and jagged 2, which are ligands for the Notch receptor and are involved in cell differentiation, proliferation, and the regulation of gene expression.": {"keywords": "(\"JAG1\" OR \"JAG2\") AND (\"Notch signaling\" OR \"cell differentiation\" OR \"jagged ligands\") AND (hasabstract[text])", "references": ["Katoh, Masaru. \"Dysregulation of stem cell signaling network due to germline mutation, SNP, Helicobacter pylori infection, epigenetic change and genetic alteration in gastric cancer.\" Cancer biology & therapy, 2007, pp. 832-9."]}, "1. ACTA1, ACTB, ACTC1, ACTG1, and ACTG2 are all actin isoforms, which are fundamental components of the cytoskeleton. They play a critical role in maintaining cell shape, enabling cell movement, and facilitating intracellular transport.": {"keywords": "(\"ACTA1\" OR \"ACTB\" OR \"ACTC1\" OR \"ACTG1\" OR \"ACTG2\") AND (\"cytoskeleton\" OR \"cell movement\" OR \"intracellular transport\") AND (hasabstract[text])", "references": ["Suresh, Rahul, Diaz, Roberto J. \"The remodelling of actin composition as a hallmark of cancer.\" Translational oncology, 2021, pp. 101051."]}, "2. ACTN1, ACTN2, ACTN3, and ACTN4 are actinin proteins that function as actin-binding proteins and are involved in the organization of the cytoskeleton and muscle contraction.": {"keywords": "(\"ACTN1\" OR \"ACTN2\" OR \"ACTN3\" OR \"ACTN4\") AND (\"cytoskeleton\" OR \"muscle contraction\" OR \"actin-binding\") AND (hasabstract[text])", "references": ["Shao, Hanshuang, Li, Shaoyan, Watkins, Simon C, Wells, Alan. \"\u03b1-Actinin-4 is required for amoeboid-type invasiveness of melanoma cells.\" The Journal of biological chemistry, 2014, pp. 32717-28.", "Beggs, A H, Byers, T J, Knoll, J H, Boyce, F M, Bruns, G A, Kunkel, L M. \"Cloning and characterization of two human skeletal muscle alpha-actinin genes located on chromosomes 1 and 11.\" The Journal of biological chemistry, 1992, pp. 9281-8."]}, "3. ADAM15, ADAM23, ADAM9, and ADAMTS5 are members of the ADAM (A Disintegrin And Metalloproteinase) family, which are involved in cell adhesion and proteolytic processing of the extracellular matrix, influencing cell migration and signaling.": {"keywords": "(\"ADAM15\" OR \"ADAM23\" OR \"ADAM9\" OR \"ADAMTS5\") AND (\"extracellular matrix\" OR \"cell adhesion\" OR \"proteolytic processing\") AND (hasabstract[text])", "references": ["Mochizuki, Satsuki, Okada, Yasunori. \"ADAMs in cancer cell proliferation and progression.\" Cancer science, 2007, pp. 621-8.", "Evans, J P. \"Fertilin beta and other ADAMs as integrin ligands: insights into cell adhesion and fertilization.\" BioEssays : news and reviews in molecular, cellular and developmental biology, 2001, pp. 628-39."]}, "4. CDH1, CDH11, CDH15, CDH3, CDH4, CDH6, and CDH8 are cadherins, which are calcium-dependent cell adhesion proteins important for the establishment and maintenance of cell-cell junctions in tissues.": {"keywords": "(\"CDH1\" OR \"CDH11\" OR \"CDH15\" OR \"CDH3\" OR \"CDH4\" OR \"CDH6\" OR \"CDH8\") AND (\"cell adhesion\" OR \"cadherins\" OR \"tissue maintenance\") AND (hasabstract[text])", "references": ["Lin, Juntang, Wang, Congrui, Redies, Christoph. \"Restricted expression of classic cadherins in the spinal cord of the chicken embryo.\" Frontiers in neuroanatomy, 2014, pp. 18.", "Xu, Mingfei, Liu, Chaoyue, Pu, Lulan, Lai, Jinrong, Li, Jingjia, Ning, Qianwen, Liu, Xin, Deng, Shishan. \"Systemic analysis of the expression levels and prognosis of breast cancer-related cadherins.\" Experimental biology and medicine (Maywood, N.J.), 2021, pp. 1706-1720."]}, "5. CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CLDN11, CLDN14, CLDN15, CLDN18, and CLDN19 are claudins, which are major constituents of tight junctions and are crucial for maintaining cell polarity and barrier functions.": {"keywords": "(\"CLDN4\" OR \"CLDN5\" OR \"CLDN6\" OR \"CLDN7\" OR \"CLDN8\" OR \"CLDN9\" OR \"CLDN11\" OR \"CLDN14\" OR \"CLDN15\" OR \"CLDN18\" OR \"CLDN19\") AND (\"tight junctions\" OR \"cell polarity\" OR \"barrier function\") AND (hasabstract[text])", "references": ["Hashimoto, Itaru, Oshima, Takashi. \"Claudins and Gastric Cancer: An Overview.\" Cancers, 2022, pp.  .", "Marincola Smith, Paula, Choksi, Yash A, Markham, Nicholas O, Hanna, David N, Zi, Jinghuan, Weaver, Connie J, Hamaamen, Jalal A, Lewis, Keeli B, Yang, Jing, Liu, Qi, Kaji, Izumi, Means, Anna L, Beauchamp, R Daniel. \"Colon epithelial cell TGF\u03b2 signaling modulates the expression of tight junction proteins and barrier function in mice.\" American journal of physiology. Gastrointestinal and liver physiology, 2021, pp. G936-G957.", "Arrojo, Maria Luiza, Oliveira, Katia Klug, Bettim, B\u00e1rbara Beltrame, Kowalski, Luiz Paulo, Carraro, Dirce Maria, Meira, Isabella Tanus Job E, Torrezan, Giovana Tardin, Louren\u00e7o, Silvia Vanessa, Coutinho-Camillo, Cl\u00e1udia Malheiros. \"Tight junction gene expression in salivary gland tumors.\" Pathology, research and practice, 2022, pp. 154113.", "Prot-Bertoye, Caroline, Houillier, Pascal. \"Claudins in Renal Physiology and Pathology.\" Genes, 2020, pp.  ."]}, "6. ITGA2, ITGA3, ITGA9, ITGA10, ITGB1, and ITGB4 are integrins, which are transmembrane receptors that facilitate cell-extracellular matrix adhesion and signal transduction.": {"keywords": "(\"ITGA2\" OR \"ITGA3\" OR \"ITGA9\" OR \"ITGA10\" OR \"ITGB1\" OR \"ITGB4\") AND (\"integrins\" OR \"cell adhesion\" OR \"signal transduction\") AND (hasabstract[text])", "references": ["Park, Hye Jin, Park, Ji Eun, Lee, Hyun, Kim, Seong Jae, Yun, Jung Im, Kim, Minseok, Park, Kyu Hyun, Lee, Seung Tae. \"Integrins functioning in uterine endometrial stromal and epithelial cells in estrus.\" Reproduction (Cambridge, England), 2017, pp. 351-360.", "Wu, Anqi, Zhang, Sai, Liu, Jiaqi, Huang, Yifeng, Deng, Wenyu, Shu, Guang, Yin, Gang. \"Integrated Analysis of Prognostic and Immune Associated Integrin Family in Ovarian Cancer.\" Frontiers in genetics, 2020, pp. 705."]}, "7. VCL (vinculin), TJP1 (ZO-1), and VWF (von Willebrand factor) are additional proteins that play significant roles in cell adhesion and the maintenance of cell integrity.": {"keywords": "(\"VCL\" OR \"TJP1\" OR \"VWF\") AND (\"cell adhesion\" OR \"cell integrity\" OR \"vinculin\") AND (hasabstract[text])", "references": []}, "8. MYH9 and MYH10 are non-muscle myosin heavy chains involved in cellular contractile systems, which are essential for cell motility and cytokinesis.": {"keywords": "(\"MYH9\" OR \"MYH10\") AND (\"cellular contractile systems\" OR \"cell motility\" OR \"cytokinesis\") AND (hasabstract[text])", "references": ["Roy, Anita, Lordier, Larissa, Mazzi, Stefania, Chang, Yunhua, Lapierre, Val\u00e9rie, Larghero, J\u00e9rome, Debili, Najet, Raslova, Hana, Vainchenker, William. \"Activity of nonmuscle myosin II isoforms determines localization at the cleavage furrow of megakaryocytes.\" Blood, 2016, pp. 3137-3145."]}, "9. FLNC (filamin C) and FSCN1 (fascin) are actin-binding proteins that organize filamentous actin into networks and bundles, respectively, contributing to the structural integrity and dynamics of the cytoskeleton.": {"keywords": "(\"FLNC\" OR \"FSCN1\") AND (\"cytoskeleton\" OR \"actin-binding\" OR \"structural integrity\") AND (hasabstract[text])", "references": []}, "10. PTK2 (FAK), SRC, and SYK are kinases that mediate signaling pathways associated with the cytoskeleton and cell adhesion, influencing cell growth, survival, and migration.": {"keywords": "(\"PTK2\" OR \"SRC\" OR \"SYK\") AND (\"cell adhesion\" OR \"signal transduction\" OR \"cell migration\") AND (hasabstract[text])", "references": ["Villari, Giulia, Jayo, Asier, Zanet, Jennifer, Fitch, Briana, Serrels, Bryan, Frame, Margaret, Stramer, Brian M, Goult, Benjamin T, Parsons, Maddy. \"A direct interaction between fascin and microtubules contributes to adhesion dynamics and cell migration.\" Journal of cell science, 2015, pp. 4601-14.", "Chang, Mei-Ying, Huang, Duen-Yi, Ho, Feng-Ming, Huang, Kuo-Chin, Lin, Wan-Wan. \"PKC-dependent human monocyte adhesion requires AMPK and Syk activation.\" PloS one, 2012, pp. e40999."]}, "1. BAX, BCL2L1, BCL2L10, BCL2L11, BCL2L2, BID, BIK, BMF, BNIP3L, CASP1, CASP2, CASP3, CASP4, CASP6, CASP7, CASP8, CASP9, DFFA, DIABLO, FAS, and FASLG are all proteins that play significant roles in the intrinsic and extrinsic pathways of apoptosis. They are involved in the regulation of cell death through various mechanisms such as mitochondrial outer membrane permeabilization, caspase activation, and death receptor signaling.": {"keywords": "(\"BAX\" OR \"BCL2L1\" OR \"BCL2L10\" OR \"BCL2L11\" OR \"BCL2L2\" OR \"BID\" OR \"BIK\" OR \"BMF\" OR \"BNIP3L\" OR \"CASP1\" OR \"CASP2\" OR \"CASP3\" OR \"CASP4\" OR \"CASP6\" OR \"CASP7\" OR \"CASP8\" OR \"CASP9\" OR \"DFFA\" OR \"DIABLO\" OR \"FAS\" OR \"FASLG\") AND (\"apoptosis\" OR \"cell death\" OR \"caspase activation\") AND (hasabstract[text])", "references": ["Wang, Zixiang, Ni, Fubiao, Yu, Fangyi, Cui, Zhonghui, Zhu, Xiandong, Chen, Jicai. \"Prognostic significance of mRNA expression of CASPs in gastric cancer.\" Oncology letters, 2019, pp. 4535-4554.", "Surmiak, M, Hubalewska-Mazgaj, M, Wawrzycka-Adamczyk, K, Musia\u0142, J, Sanak, M. \"Delayed neutrophil apoptosis in granulomatosis with polyangiitis: dysregulation of neutrophil gene signature and circulating apoptosis-related proteins.\" Scandinavian journal of rheumatology, 2020, pp. 57-67.", "Hage-Sleiman, Rouba, Bahmad, Hisham, Kobeissy, Hadile, Dakdouk, Zeinab, Kobeissy, Firas, Dbaibo, Ghassan. \"Genomic alterations during p53-dependent apoptosis induced by \u03b3-irradiation of Molt-4 leukemia cells.\" PloS one, 2017, pp. e0190221.", "G\u00e9recov\u00e1, Gabriela, Kopanicov\u00e1, Jana, Jak\u00e1, Petra, B\u011bhalov\u00e1, Lucia, Juh\u00e1sov\u00e1, Barbora, Bhatia-Ki\u0161\u0161ov\u00e1, Ingrid, Forte, Michael, Pol\u010dic, Peter, Mentel, Marek. \"BH3-only proteins Noxa, Bik, Bmf, and Bid activate Bax and Bak indirectly when studied in yeast model.\" FEMS yeast research, 2013, pp. 747-54.", "Boumela, Imene, Assou, Said, Aouacheria, Abdel, Haouzi, Delphine, Dechaud, Herv\u00e9, De Vos, John, Handyside, Alan, Hamamah, Samir. \"Involvement of BCL2 family members in the regulation of human oocyte and early embryo survival and death: gene expression and beyond.\" Reproduction (Cambridge, England), 2011, pp. 549-61.", "Ji, Guixiang, Gu, Aihua, Hu, Fan, Wang, Shoulin, Liang, Jie, Xia, Yankai, Lu, Chuncheng, Song, Ling, Fu, Guangbo, Wang, Xinru. \"Polymorphisms in cell death pathway genes are associated with altered sperm apoptosis and poor semen quality.\" Human reproduction (Oxford, England), 2009, pp. 2439-46."]}, "2. CDK2, CCNA1, CCND1, CCND2, CDKN1A, CDKN1B, CDC25B, and WEE1 are key regulators of the cell cycle. They are involved in the control of cell cycle progression through different phases by acting as cyclins, cyclin-dependent kinases, and their inhibitors.": {"keywords": "(\"CDK2\" OR \"CCNA1\" OR \"CCND1\" OR \"CCND2\" OR \"CDKN1A\" OR \"CDKN1B\" OR \"CDC25B\" OR \"WEE1\") AND (\"cell cycle\" OR \"cyclins\" OR \"kinase inhibitors\") AND (hasabstract[text])", "references": ["Gayther, Simon A, Song, Honglin, Ramus, Susan J, Kjaer, Susan Kr\u00fcger, Whittemore, Alice S, Quaye, Lydia, Tyrer, Jonathan, Shadforth, Danielle, Hogdall, Estrid, Hogdall, Claus, Blaeker, Jan, DiCioccio, Richard, McGuire, Valerie, Webb, Penelope M, Beesley, Jonathan, Green, Adele C, Whiteman, David C, , , Goodman, Marc T, Lurie, Galina, Carney, Michael E, Modugno, Francesmary, Ness, Roberta B, Edwards, Robert P, Moysich, Kirsten B, Goode, Ellen L, Couch, Fergus J, Cunningham, Julie M, Sellers, Thomas A, Wu, Anna H, Pike, Malcolm C, Iversen, Edwin S, Marks, Jeffrey R, Garcia-Closas, Montserrat, Brinton, Louise, Lissowska, Jolanta, Peplonska, Beata, Easton, Douglas F, Jacobs, Ian, Ponder, Bruce A J, Schildkraut, Joellen, Pearce, C Leigh, Chenevix-Trench, Georgia, Berchuck, Andrew, Pharoah, Paul D P, , . \"Tagging single nucleotide polymorphisms in cell cycle control genes and susceptibility to invasive epithelial ovarian cancer.\" Cancer research, 2007, pp. 3027-35.", "Ma, Hongxia, Chen, Jiaping, Pan, Shiyang, Dai, Juncheng, Jin, Guangfu, Hu, Zhibin, Shen, Hongbing, Shu, Yongqian. \"Potentially functional polymorphisms in cell cycle genes and the survival of non-small cell lung cancer in a Chinese population.\" Lung cancer (Amsterdam, Netherlands), 2011, pp. 32-7.", "Chil\u00e0, Rosaria, Basana, Alessandra, Lupi, Monica, Guffanti, Federica, Gaudio, Eugenio, Rinaldi, Andrea, Cascione, Luciano, Restelli, Valentina, Tarantelli, Chiara, Bertoni, Francesco, Damia, Giovanna, Carrassa, Laura. \"Combined inhibition of Chk1 and Wee1 as a new therapeutic strategy for mantle cell lymphoma.\" Oncotarget, 2015, pp. 3394-408."]}, "3. BRCA1, a protein involved in DNA damage repair, plays a crucial role in maintaining genomic stability and also interacts with cell cycle proteins to halt cell cycle progression in response to DNA damage.": {"keywords": "(\"BRCA1\") AND (\"DNA repair\" OR \"genomic stability\" OR \"cell cycle\") AND (hasabstract[text])", "references": []}, "4. TNF, TNFRSF12A, and TNFSF10 are part of the tumor necrosis factor family and are involved in signaling pathways that can lead to apoptosis, inflammation, and also play roles in immune system regulation.": {"keywords": "(\"TNF\" OR \"TNFRSF12A\" OR \"TNFSF10\") AND (\"apoptosis\" OR \"inflammation\" OR \"immune regulation\") AND (hasabstract[text])", "references": ["Cantarella, Giuseppina, Di Benedetto, Giulia, Puzzo, Daniela, Privitera, Lucia, Loreto, Carla, Saccone, Salvatore, Giunta, Salvatore, Palmeri, Agostino, Bernardini, Renato. \"Neutralization of TNFSF10 ameliorates functional outcome in a murine model of Alzheimer's disease.\" Brain : a journal of neurology, 2015, pp. 203-16.", "Liao, Min, Liao, Junwei, Qu, Jiaquan, Shi, Pan, Cheng, Ying, Pan, Qiong, Zhao, Nan, Zhang, Xiaoxun, Zhang, Liangjun, Tan, Ya, Li, Qiao, Zhu, Jin-Fei, Li, Jianwei, Zhang, Chengcheng, Cai, Shi-Ying, Chai, Jin. \"Hepatic TNFRSF12A promotes bile acid-induced hepatocyte pyroptosis through NF\u03baB/Caspase-1/GSDMD signaling in cholestasis.\" Cell death discovery, 2023, pp. 26."]}, "5. PSEN1 and PSEN2 are part of the gamma-secretase complex, which is involved in the cleavage of several substrates, including amyloid precursor protein (APP), and are implicated in the pathogenesis of Alzheimer's disease through the regulation of apoptosis and cell signaling pathways.": {"keywords": "(\"PSEN1\" OR \"PSEN2\" OR \"APP\") AND (\"gamma-secretase\" OR \"Alzheimer's disease\" OR \"apoptosis\") AND (hasabstract[text])", "references": ["Cohn-Hokke, Petra E, Elting, Mariet W, Pijnenburg, Yolande A L, van Swieten, John C. \"Genetics of dementia: update and guidelines for the clinician.\" American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, 2012, pp. 628-43."]}, "6. Proteins such as JUN, ATF3, DDIT3, and IRF1 are transcription factors that respond to stress signals and can induce apoptosis, cell cycle arrest, or other cellular responses.": {"keywords": "(\"JUN\" OR \"ATF3\" OR \"DDIT3\" OR \"IRF1\") AND (\"transcription factors\" OR \"apoptosis\" OR \"cell cycle arrest\") AND (hasabstract[text])", "references": ["He, Sheng, He, Lili, Yan, Fangran, Li, Junda, Liao, Xiaoting, Ling, Maoyao, Jing, Ren, Pan, Linghui. \"Identification of hub genes associated with acute kidney injury induced by renal ischemia-reperfusion injury in mice.\" Frontiers in physiology, 2022, pp. 951855."]}, "7. Antioxidant enzymes like GPX1, GPX3, GPX4, SOD1, and SOD2 are involved in the cellular response to oxidative stress and can influence cell survival and apoptosis.": {"keywords": "(\"GPX1\" OR \"GPX3\" OR \"GPX4\" OR \"SOD1\" OR \"SOD2\") AND (\"oxidative stress\" OR \"antioxidant enzymes\" OR \"apoptosis\") AND (hasabstract[text])", "references": ["Janicka, Anna, Szyma\u0144ska-Pasternak, Jolanta, Bober, Joanna. \"[Polymorphisms in the oxidative stress-related genes and cancer risk].\" Annales Academiae Medicae Stetinensis, 2013, pp. 18-28.", "Zhang, Min, Zhang, Jiangzhao, Xiong, Yan, Peng, Jiaqing, Wu, Xiaoyan. \"Pyrroloquinoline Quinone Inhibits Oxidative Stress in Rats with Diabetic Nephropathy.\" Medical science monitor : international medical journal of experimental and clinical research, 2020, pp. e924372."]}, "8. Proteins such as MCL1, CFLAR, and XIAP are anti-apoptotic and contribute to the regulation of apoptosis by inhibiting various components of the apoptotic machinery.": {"keywords": "(\"MCL1\" OR \"CFLAR\" OR \"XIAP\") AND (\"apoptosis\" OR \"anti-apoptotic\" OR \"regulation\") AND (hasabstract[text])", "references": ["Werner, Kristin, Lademann, Franziska, Thepkaysone, May-Linn, Jahnke, Beatrix, Aust, Daniela E, Kahlert, Christoph, Weber, Georg, Weitz, J\u00fcrgen, Gr\u00fctzmann, Robert, Pilarsky, Christian. \"Simultaneous gene silencing of KRAS and anti-apoptotic genes as a multitarget therapy.\" Oncotarget, 2016, pp. 3984-92."]}, "1. ATM is a serine/threonine-protein kinase that plays a central role in cell cycle checkpoint control, DNA repair, and apoptosis. It is activated in response to DNA double-strand breaks and phosphorylates several key proteins that initiate the DNA damage checkpoint, leading to cell cycle arrest and DNA repair.": {"keywords": "(\"ATM\") AND (\"DNA repair\" OR \"cell cycle checkpoint\" OR \"apoptosis\") AND (hasabstract[text])", "references": []}, "2. AURKA (Aurora kinase A) is involved in cell cycle regulation, particularly in the entry into mitosis and the formation of the mitotic spindle. It is also implicated in the response to mitotic spindle stress.": {"keywords": "(\"AURKA\") AND (\"cell cycle\" OR \"mitosis\" OR \"spindle stress\") AND (hasabstract[text])", "references": []}, "3. BARD1 forms a heterodimer with BRCA1, acting in tumor suppression and DNA damage repair, particularly in the repair of double-strand breaks by homologous recombination.": {"keywords": "(\"BARD1\" OR \"BRCA1\") AND (\"DNA repair\" OR \"tumor suppression\" OR \"homologous recombination\") AND (hasabstract[text])", "references": ["Irminger-Finger, Irmgard, Leung, Wai Choi. \"BRCA1-dependent and independent functions of BARD1.\" The international journal of biochemistry & cell biology, 2002, pp. 582-7."]}, "4. BLM is a RecQ helicase that helps maintain genomic stability. It is involved in DNA replication, repair, and recombination.": {"keywords": "(\"BLM\") AND (\"genomic stability\" OR \"DNA repair\" OR \"helicase\") AND (hasabstract[text])", "references": []}, "5. BRCA1 and BRCA2 are tumor suppressors that play a critical role in homologous recombination, a mechanism for repairing DNA double-strand breaks. BRCA1 also participates in checkpoint control and ubiquitination.": {"keywords": "(\"BRCA1\" OR \"BRCA2\") AND (\"DNA repair\" OR \"tumor suppressors\" OR \"homologous recombination\") AND (hasabstract[text])", "references": ["Petrovic, Nina, Davidovic, Radoslav, Bajic, Vladan, Obradovic, Milan, Isenovic, R Esma. \"MicroRNA in breast cancer: The association with BRCA1/2.\" Cancer biomarkers : section A of Disease markers, 2017, pp. 119-128."]}, "6. BRIP1 (BACH1) is a DNA helicase associated with BRCA1, involved in DNA repair and the maintenance of genomic stability.": {"keywords": "(\"BRIP1\" OR \"BRCA1\") AND (\"DNA repair\" OR \"genomic stability\" OR \"helicase\") AND (hasabstract[text])", "references": ["Pavanello, Marina, Chan, Isaac Hy, Ariff, Amir, Pharoah, Paul Dp, Gayther, Simon A, Ramus, Susan J. \"Rare Germline Genetic Variants and the Risks of Epithelial Ovarian Cancer.\" Cancers, 2020, pp.  ."]}, "7. BUB1B is a kinase involved in the spindle checkpoint during mitosis, ensuring proper chromosome segregation, and indirectly participates in DNA repair by maintaining genomic stability.": {"keywords": "(\"BUB1B\") AND (\"mitosis\" OR \"spindle checkpoint\" OR \"DNA repair\") AND (hasabstract[text])", "references": []}, "8. CDC73 is a component of the PAF1 complex, involved in transcriptional regulation and modification of histones. It has a role in the response to DNA damage.": {"keywords": "(\"CDC73\") AND (\"transcriptional regulation\" OR \"histone modification\" OR \"DNA damage response\") AND (hasabstract[text])", "references": []}, "9. CHEK1 is a kinase that mediates cell cycle arrest in response to DNA damage. It is a key effector in the DNA damage checkpoint pathway.": {"keywords": "(\"CHEK1\") AND (\"DNA damage checkpoint\" OR \"cell cycle arrest\" OR \"kinase\") AND (hasabstract[text])", "references": []}, "10. FANCA and FANCD2 are part of the Fanconi anemia (FA) core complex, which is essential for the repair of DNA interstrand crosslinks and maintenance of chromosomal stability.": {"keywords": "(\"FANCA\" OR \"FANCD2\") AND (\"DNA repair\" OR \"Fanconi anemia\" OR \"chromosomal stability\") AND (hasabstract[text])", "references": ["Pagano, Giovanni, Talamanca, Annarita Aiello, Castello, Giuseppe, Pallard\u00f3, Federico V, Zatterale, Adriana, Degan, Paolo. \"Oxidative stress in Fanconi anaemia: from cells and molecules towards prospects in clinical management.\" Biological chemistry, 2012, pp. 11-21."]}, "11. MDC1 is a mediator of the DNA damage checkpoint, facilitating the accumulation of repair proteins at the site of damage.": {"keywords": "(\"MDC1\") AND (\"DNA damage checkpoint\" OR \"repair proteins\" OR \"MDC1\") AND (hasabstract[text])", "references": []}, "12. MDM2 is an E3 ubiquitin-protein ligase that negatively regulates the p53/TP53 tumor suppressor, and is involved in DNA damage response.": {"keywords": "(\"MDM2\" OR \"TP53\") AND (\"ubiquitin-ligase\" OR \"p53\" OR \"DNA damage\") AND (hasabstract[text])", "references": ["Timmerman, Dennis M, Remmers, Tessa L, Hillenius, Sanne, Looijenga, Leendert H J. \"Mechanisms of TP53 Pathway Inactivation in Embryonic and Somatic Cells-Relevance for Understanding (Germ Cell) Tumorigenesis.\" International journal of molecular sciences, 2021, pp.  ."]}, "13. MRE11 is part of the MRN complex (together with RAD50 and NBN), which is critical for the detection of DNA double-strand breaks and initiation of their repair.": {"keywords": "(\"MRE11\" OR \"RAD50\" OR \"NBN\") AND (\"DNA repair\" OR \"MRN complex\" OR \"double-strand breaks\") AND (hasabstract[text])", "references": ["Zi\u00f3\u0142kowska-Suchanek, Iwona, Mosor, Maria, Wierzbicka, Ma\u0142gorzata, Rydzanicz, Ma\u0142gorzata, Baranowska, Marta, Nowak, Jerzy. \"The MRN protein complex genes: MRE11 and RAD50 and susceptibility to head and neck cancers.\" Molecular cancer, 2013, pp. 113."]}, "14. MSH6 is part of the mismatch repair system, which corrects base-pairing errors that occur during DNA replication.": {"keywords": "(\"MSH6\") AND (\"mismatch repair\" OR \"DNA replication\" OR \"base-pairing errors\") AND (hasabstract[text])", "references": []}, "15. NBN is a component of the MRN complex, involved in the initial recognition of DNA breaks and signaling to the DNA damage response pathways.": {"keywords": "(\"NBN\") AND (\"DNA damage response\" OR \"MRN complex\" OR \"DNA breaks\") AND (hasabstract[text])", "references": []}, "16. PALB2 is a partner and localizer of BRCA2 and is essential for homologous recombination repair of DNA double-strand breaks.": {"keywords": "(\"PALB2\" OR \"BRCA2\") AND (\"homologous recombination\" OR \"DNA repair\" OR \"PALB2\") AND (hasabstract[text])", "references": ["Jacquemont, C\u00e9line, Taniguchi, Toshiyasu. \"The Fanconi anemia pathway and ubiquitin.\" BMC biochemistry, 2007, pp. S10."]}, "17. POLH is a DNA polymerase involved in translesion synthesis, allowing DNA replication to bypass lesions.": {"keywords": "(\"POLH\") AND (\"DNA polymerase\" OR \"translesion synthesis\" OR \"DNA replication\") AND (hasabstract[text])", "references": []}, "18. RAD50, as part of the MRN complex, is involved in DNA double-strand break repair and maintenance of telomere integrity.": {"keywords": "(\"RAD50\") AND (\"DNA repair\" OR \"telomere integrity\" OR \"MRN complex\") AND (hasabstract[text])", "references": []}, "19. RAD51 and its paralogs RAD51B, RAD51C, RAD51D, XRCC2, and XRCC3 are essential for homologous recombination repair of DNA double-strand breaks.": {"keywords": "(\"RAD51\" OR \"RAD51B\" OR \"RAD51C\" OR \"RAD51D\" OR \"XRCC2\" OR \"XRCC3\") AND (\"homologous recombination\" OR \"DNA repair\" OR \"double-strand breaks\") AND (hasabstract[text])", "references": ["Wiese, Claudia, Collins, David W, Albala, Joanna S, Thompson, Larry H, Kronenberg, Amy, Schild, David. \"Interactions involving the Rad51 paralogs Rad51C and XRCC3 in human cells.\" Nucleic acids research, 2002, pp. 1001-8."]}, "20. TOP2A is a DNA topoisomerase that controls and alters the topologic states of DNA during transcription.": {"keywords": "(\"TOP2A\") AND (\"DNA topoisomerase\" OR \"transcription\" OR \"DNA topology\") AND (hasabstract[text])", "references": []}, "21. TP53 (p53) is a tumor suppressor that regulates the expression of a wide range of genes involved in apoptosis, growth arrest, and DNA repair in response to genomic stress.": {"keywords": "(\"TP53\") AND (\"tumor suppressor\" OR \"apoptosis\" OR \"DNA repair\") AND (hasabstract[text])", "references": []}, "22. WRN is a RecQ helicase with exonuclease activity, involved in DNA repair, replication, and telomere maintenance.": {"keywords": "(\"WRN\") AND (\"DNA repair\" OR \"helicase\" OR \"telomere maintenance\") AND (hasabstract[text])", "references": []}, "23. XRCC2 and XRCC3 are involved in homologous recombination repair of DNA double-strand breaks and crosslinks.": {"keywords": "(\"XRCC2\" OR \"XRCC3\") AND (\"homologous recombination\" OR \"DNA repair\" OR \"double-strand breaks\") AND (hasabstract[text])", "references": ["Xu, Zhan, Zhang, Jianxiang, Xu, Meng, Ji, Wen, Yu, Meimei, Tao, Yajun, Gong, Zhiyun, Gu, Minghong, Yu, Hengxiu. \"Rice RAD51 paralogs play essential roles in somatic homologous recombination for DNA repair.\" The Plant journal : for cell and molecular biology, 2018, pp. 282-295."]}, "1. CTNNB1, also known as \u03b2-Catenin, is a central component of the Wnt signaling pathway. It acts as a dual function protein, involved in regulation and coordination of cell\u2013cell adhesion and gene transcription. In the absence of Wnt signaling, \u03b2-Catenin is phosphorylated and targeted for degradation by the proteasome. However, upon Wnt activation, \u03b2-Catenin accumulates in the cytoplasm and translocates into the nucleus, where it acts as a coactivator for transcription factors of the TCF/LEF family, leading to the transcription of Wnt target genes.": {"keywords": "(\"CTNNB1\") AND (\"Wnt signaling\" OR \"\u03b2-Catenin\" OR \"transcription\") AND (hasabstract[text])", "references": []}, "2. BRAF is a protein belonging to the RAF kinase family within the RAS/MAPK signaling pathway. It plays a significant role in directing cell growth, proliferation, and differentiation. Mutations in BRAF can lead to uncontrolled cell growth and are implicated in various forms of cancer. Although BRAF is not directly involved in the Wnt/\u03b2-Catenin pathway, cross-talk between the MAPK pathway and Wnt signaling has been documented, where MAPK can influence the stability and localization of \u03b2-Catenin.": {"keywords": "(\"BRAF\" OR \"RAS\" OR \"MAPK\") AND (\"MAPK signaling\" OR \"cancer\" OR \"BRAF mutation\") AND (hasabstract[text])", "references": ["Wellbrock, Claudia, Arozarena, Imanol. \"The Complexity of the ERK/MAP-Kinase Pathway and the Treatment of Melanoma Skin Cancer.\" Frontiers in cell and developmental biology, 2016, pp. 33."]}, "In summary, CTNNB1 and BRAF are key regulatory proteins within their respective signaling pathways, Wnt/\u03b2-Catenin and RAS/MAPK. The interaction between these proteins suggests a point of cross-talk between these pathways, which can have significant implications for cell fate decisions, proliferation, and oncogenesis. The prominence of CTNNB1 in the Wnt signaling pathway and the known interactions between these pathways justify the high confidence score in naming the process.": {"keywords": "(\"CTNNB1\" OR \"BRAF\") AND (\"Wnt signaling\" OR \"oncogenesis\" OR \"cell proliferation\") AND (hasabstract[text])", "references": []}, "1. NOTCH1 is a transmembrane receptor involved in the Notch signaling pathway, which plays a critical role in cardiac development, particularly in the differentiation of cardiac progenitor cells and the formation of the heart valves. It also influences cell fate decisions and promotes endothelial-to-mesenchymal transition (EndMT), a process essential for heart development.": {"keywords": "(\"NOTCH1\") AND (\"Notch signaling\" OR \"cardiac development\" OR \"EndMT\") AND (hasabstract[text])", "references": []}, "2. TP53, commonly known as p53, is a tumor suppressor protein that regulates the cell cycle and thus functions as a regulator of cell proliferation. In the context of heart development, p53 has been implicated in the control of oxidative stress and the prevention of cardiac hypertrophy. It also plays a role in DNA repair and apoptosis in cardiomyocytes.": {"keywords": "(\"TP53\") AND (\"cell cycle\" OR \"oxidative stress\" OR \"cardiac hypertrophy\") AND (hasabstract[text])", "references": []}, "3. GATA5 is a member of the GATA family of zinc-finger transcription factors, which are known to be crucial for heart formation and function. GATA5, in particular, is involved in the regulation of cardiac morphogenesis and differentiation, as well as in the development of the endocardium and heart valves.": {"keywords": "(\"GATA5\") AND (\"cardiac development\" OR \"transcription factors\" OR \"heart valves\") AND (hasabstract[text])", "references": []}, "4. NKX2-5 is a homeobox transcription factor that is essential for heart development. It is involved in the early specification of cardiac progenitors, heart tube formation, and the development of the conduction system of the heart. Mutations in NKX2-5 are associated with congenital heart defects.": {"keywords": "(\"NKX2-5\") AND (\"heart development\" OR \"transcription factor\" OR \"congenital heart defects\") AND (hasabstract[text])", "references": []}, "5. SMAD6 is an inhibitory SMAD protein that negatively regulates the TGF-\u03b2/BMP signaling pathways. In the context of heart development, SMAD6 is involved in modulating the signaling that controls the differentiation of cardiac cells and the formation of the extracellular matrix, which is important for heart valve development.": {"keywords": "(\"SMAD6\" OR \"TGF-\u03b2\" OR \"BMP\") AND (\"TGF-\u03b2/BMP signaling\" OR \"heart development\" OR \"extracellular matrix\") AND (hasabstract[text])", "references": ["Carreira, Ana Claudia Oliveira, Zambuzzi, Willian Fernando, Rossi, Mariana Correa, Astorino Filho, Renato, Sogayar, Mari Cleide, Granjeiro, Jos\u00e9 Mauro. \"Bone Morphogenetic Proteins: Promising Molecules for Bone Healing, Bioengineering, and Regenerative Medicine.\" Vitamins and hormones, 2015, pp. 293-322."]}, "6. AKT1 is a serine/threonine kinase that is a key regulator of cell growth, proliferation, and survival. In cardiomyocytes, AKT1 signaling promotes cell survival and growth, and it has been implicated in the protection against ischemic injury and the regulation of cardiac hypertrophy.": {"keywords": "(\"AKT1\") AND (\"cell survival\" OR \"cardiomyocytes\" OR \"ischemic injury\") AND (hasabstract[text])", "references": []}, "7. SLC20A1, also known as Pit-1, is a sodium-dependent phosphate transporter. While its direct role in heart development is less clear, phosphate homeostasis is important for energy metabolism and may indirectly influence cardiac function and development.": {"keywords": "(\"SLC20A1\") AND (\"phosphate transport\" OR \"energy metabolism\" OR \"cardiac development\") AND (hasabstract[text])", "references": []}, "1. DISC1 (Disrupted in Schizophrenia 1) is a protein that plays a role in neurodevelopment, particularly in the proper migration and positioning of neurons during brain development. It is implicated in the modulation of various signaling pathways that are critical for neuronal function, including those involving cAMP and GSK3B. DISC1 has been associated with psychiatric disorders such as schizophrenia and depression, suggesting its importance in maintaining mental health.": {"keywords": "(\"DISC1\" OR \"GSK3B\") AND (\"neurodevelopment\" OR \"psychiatric disorders\" OR \"signaling pathways\") AND (hasabstract[text])", "references": ["Kvajo, Mirna, McKellar, Heather, Gogos, Joseph A. \"Molecules, signaling, and schizophrenia.\" Current topics in behavioral neurosciences, 2010, pp. 629-56."]}, "2. SLC6A4 (Solute Carrier Family 6 Member 4), also known as the serotonin transporter, is responsible for the reuptake of serotonin from the synaptic cleft back into the presynaptic neuron. This protein is crucial for regulating serotonin signaling and, by extension, mood, emotion, and sleep. SLC6A4 is a target for many antidepressants, which block the transporter to increase serotonin levels in the synaptic cleft, thereby enhancing neurotransmission.": {"keywords": "(\"SLC6A4\") AND (\"serotonin reuptake\" OR \"antidepressants\" OR \"neurotransmission\") AND (hasabstract[text])", "references": []}, "1. PALB2 (Partner and localizer of BRCA2) is crucial for the repair of DNA double-strand breaks through homologous recombination (HR). It acts as a hub for the recruitment of BRCA2 and RAD51 to DNA damage sites.": {"keywords": "(\"PALB2\" OR \"BRCA2\" OR \"RAD51\") AND (\"DNA repair\" OR \"homologous recombination\" OR \"PALB2\") AND (hasabstract[text])", "references": ["Siaud, Nicolas, Barbera, Maria A, Egashira, Akinori, Lam, Isabel, Christ, Nicole, Schlacher, Katharina, Xia, Bing, Jasin, Maria. \"Plasticity of BRCA2 function in homologous recombination: genetic interactions of the PALB2 and DNA binding domains.\" PLoS genetics, 2011, pp. e1002409."]}, "2. XRCC2 and RAD51D are members of the RAD51 paralog family, which are involved in the HR pathway, stabilizing and promoting the formation of the RAD51 nucleoprotein filament essential for strand invasion.": {"keywords": "(\"XRCC2\" OR \"RAD51D\" OR \"RAD51\") AND (\"homologous recombination\" OR \"DNA repair\" OR \"RAD51 filament\") AND (hasabstract[text])", "references": ["Yard, Brian D, Reilly, Nicole M, Bedenbaugh, Michael K, Pittman, Douglas L. \"RNF138 interacts with RAD51D and is required for DNA interstrand crosslink repair and maintaining chromosome integrity.\" DNA repair, 2016, pp. 82-93."]}, "3. CHEK2 (Checkpoint kinase 2) and ATM (Ataxia telangiectasia mutated) are serine/threonine-protein kinases that respond to DNA damage by phosphorylating several key proteins that initiate cell cycle arrest and DNA repair.": {"keywords": "(\"CHEK2\" OR \"ATM\") AND (\"DNA damage\" OR \"response\" OR \"cell cycle arrest\") AND (hasabstract[text])", "references": ["Nail, Alexandra N, McCaffrey, Lakynkalina M, Banerjee, Mayukh, Ferragut Cardoso, Ana P, States, J Christopher. \"Chronic arsenic exposure suppresses ATM pathway activation in human keratinocytes.\" Toxicology and applied pharmacology, 2022, pp. 116042."]}, "4. BRCA1 and BRCA2 are tumor suppressors that play a critical role in HR repair of DNA double-strand breaks. BRCA1 also participates in DNA damage checkpoint control and ubiquitination processes.": {"keywords": "(\"BRCA1\" OR \"BRCA2\") AND (\"DNA repair\" OR \"tumor suppressor\" OR \"ubiquitination\") AND (hasabstract[text])", "references": ["Cazzaniga, Massimiliano, Bonanni, Bernardo. \"Pharmacoprevention for hereditary breast and ovarian cancer.\" Minerva ginecologica, 2016, pp. 517-35."]}, "5. BARD1 forms a heterodimer with BRCA1, which is essential for BRCA1's tumor suppressor function.": {"keywords": "(\"BARD1\" OR \"BRCA1\") AND (\"tumor suppressor\" OR \"heterodimer\" OR \"BRCA1\") AND (hasabstract[text])", "references": ["Brodie, Kirsty M, Henderson, Beric R. \"Differential modulation of BRCA1 and BARD1 nuclear localisation and foci assembly by DNA damage.\" Cellular signalling, 2010, pp. 291-302."]}, "6. RAD50, NBN (Nibrin), and MRE11 form the MRN complex, which is involved in the detection of DNA double-strand breaks and the initiation of their repair.": {"keywords": "(\"RAD50\" OR \"NBN\" OR \"MRE11\") AND (\"DNA repair\" OR \"MRN complex\" OR \"double-strand breaks\") AND (hasabstract[text])", "references": ["Zi\u00f3\u0142kowska-Suchanek, Iwona, Mosor, Maria, Wierzbicka, Ma\u0142gorzata, Rydzanicz, Ma\u0142gorzata, Baranowska, Marta, Nowak, Jerzy. \"The MRN protein complex genes: MRE11 and RAD50 and susceptibility to head and neck cancers.\" Molecular cancer, 2013, pp. 113."]}, "7. SLX4 is a structure-specific endonuclease that plays a role in the resolution of DNA interstrand cross-links and Holliday junctions, a key step in HR.": {"keywords": "(\"SLX4\") AND (\"DNA repair\" OR \"Holliday junctions\" OR \"endonuclease\") AND (hasabstract[text])", "references": []}, "8. CHEK1 (Checkpoint kinase 1) is involved in cell cycle arrest in response to DNA damage, particularly during the S and G2 phases.": {"keywords": "(\"CHEK1\") AND (\"DNA damage response\" OR \"cell cycle arrest\" OR \"CHEK1\") AND (hasabstract[text])", "references": []}, "9. MLH1, MSH6, and MSH2 are part of the mismatch repair (MMR) system, which corrects base mismatches and insertion-deletion loops in DNA replication.": {"keywords": "(\"MLH1\" OR \"MSH6\" OR \"MSH2\") AND (\"mismatch repair\" OR \"DNA replication\" OR \"base mismatches\") AND (hasabstract[text])", "references": ["Mohni, Kareem N, Mastrocola, Adam S, Bai, Ping, Weller, Sandra K, Heinen, Christopher D. \"DNA mismatch repair proteins are required for efficient herpes simplex virus 1 replication.\" Journal of virology, 2011, pp. 12241-53."]}, "10. MUTYH is involved in base excision repair, recognizing and removing oxidized guanine bases.": {"keywords": "(\"MUTYH\") AND (\"base excision repair\" OR \"DNA repair\" OR \"oxidized guanine\") AND (hasabstract[text])", "references": []}, "11. RAD51C is another RAD51 paralog that participates in HR and is also involved in the repair of DNA cross-links.": {"keywords": "(\"RAD51C\") AND (\"homologous recombination\" OR \"DNA repair\" OR \"cross-links\") AND (hasabstract[text])", "references": []}, "12. RECQL is a DNA helicase that unwinds DNA and is implicated in DNA repair and the maintenance of genomic stability.": {"keywords": "(\"RECQL\") AND (\"DNA repair\" OR \"helicase\" OR \"genomic stability\") AND (hasabstract[text])", "references": []}, "13. MCPH1 (Microcephalin) is involved in DNA damage response and is thought to be important for brain development.": {"keywords": "(\"MCPH1\") AND (\"DNA damage response\" OR \"brain development\" OR \"Microcephalin\") AND (hasabstract[text])", "references": []}, "1. AGPAT2 (1-acylglycerol-3-phosphate O-acyltransferase 2) is an enzyme that catalyzes the acylation of lysophosphatidic acid (LPA) to form phosphatidic acid (PA), a key intermediate in the biosynthesis of triacylglycerols and glycerophospholipids. Mutations in AGPAT2 are associated with congenital generalized lipodystrophy (CGL), a disorder characterized by the near absence of adipose tissue and severe insulin resistance.": {"keywords": "(\"AGPAT2\") AND (\"lipodystrophy\" OR \"acylation\" OR \"insulin resistance\") AND (hasabstract[text])", "references": []}, "2. BSCL2 (Berardinelli-Seip congenital lipodystrophy 2 protein) is involved in the development of adipocytes and is essential for the proper storage of triglycerides. Mutations in BSCL2 lead to a form of congenital generalized lipodystrophy similar to that caused by AGPAT2 mutations, indicating a role in lipid droplet formation and maintenance.": {"keywords": "(\"BSCL2\" OR \"AGPAT2\") AND (\"adipocyte development\" OR \"lipodystrophy\" OR \"triglyceride storage\") AND (hasabstract[text])", "references": ["Ren, Meng, Shi, Jingru, Jia, Jinmeng, Guo, Yongli, Ni, Xin, Shi, Tieliu. \"Genotype-phenotype correlations of Berardinelli-Seip congenital lipodystrophy and novel candidate genes prediction.\" Orphanet journal of rare diseases, 2020, pp. 108."]}, "3. AGPS (alkylglycerone phosphate synthase) is involved in ether lipid synthesis, specifically the formation of alkylglycerone phosphate from dihydroxyacetone phosphate. Ether lipids are important components of cell membranes, with roles in cell signaling and as antioxidants. Defects in ether lipid metabolism are implicated in various human diseases, including peroxisomal disorders.": {"keywords": "(\"AGPS\") AND (\"ether lipid synthesis\" OR \"cell signaling\" OR \"peroxisomal disorders\") AND (hasabstract[text])", "references": []}, "The proteins in this system are involved in the synthesis and storage of lipids, with a particular focus on the pathways that are disrupted in lipodystrophy syndromes. AGPAT2 and BSCL2 are directly involved in the formation and storage of triglycerides, while AGPS contributes to the synthesis of ether lipids. The interaction between these proteins suggests a coordinated regulation of lipid metabolism and adipose tissue function, which is critical for normal energy homeostasis. The dysfunction of these proteins leads to lipodystrophy, highlighting their importance in adipogenesis and lipid storage.": {"keywords": "(\"AGPAT2\" OR \"BSCL2\" OR \"AGPS\") AND (\"lipid metabolism\" OR \"adipogenesis\" OR \"lipodystrophy\") AND (hasabstract[text])", "references": ["Haghighi, A, Kavehmanesh, Z, Haghighi, A, Salehzadeh, F, Santos-Simarro, F, Van Maldergem, L, Cimbalistiene, L, Collins, F, Chopra, M, Al-Sinani, S, Dastmalchian, S, de Silva, D C, Bakhti, H, Garg, A, Hilbert, P. \"Congenital generalized lipodystrophy: identification of novel variants and expansion of clinical spectrum.\" Clinical genetics, 2016, pp. 434-441."]}, "1. UMPS (Uridine Monophosphate Synthetase) is a bifunctional enzyme that catalyzes the last two steps of the de novo pyrimidine biosynthesis pathway. It first converts orotate to orotidine-5'-monophosphate (OMP) via its orotate phosphoribosyltransferase activity, and subsequently decarboxylates OMP to uridine monophosphate (UMP) through its orotidine-5'-phosphate decarboxylase activity. UMP is a precursor for all other pyrimidine nucleotides, which are essential for DNA and RNA synthesis.": {"keywords": "(\"UMPS\") AND (\"pyrimidine biosynthesis\" OR \"enzyme activity\" OR \"nucleotide synthesis\") AND (hasabstract[text])", "references": []}, "2. CAD is a multifunctional protein that has three enzymatic activities required for the de novo synthesis of pyrimidine nucleotides. It includes carbamoyl-phosphate synthetase II, aspartate transcarbamylase, and dihydroorotase activities. These activities are responsible for the first three steps in the pyrimidine biosynthetic pathway, leading to the production of orotate, which is then used by UMPS to produce UMP.": {"keywords": "(\"CAD\" OR \"UMPS\") AND (\"pyrimidine biosynthesis\" OR \"CAD\" OR \"orotate\") AND (hasabstract[text])", "references": ["Yang, Chuanzhen, Zhao, Yiliang, Wang, Liao, Guo, Zihao, Ma, Lingdi, Yang, Ronghui, Wu, Ying, Li, Xuexue, Niu, Jing, Chu, Qiaoyun, Fu, Yanxia, Li, Binghui. \"De novo pyrimidine biosynthetic complexes support cancer cell proliferation and ferroptosis defence.\" Nature cell biology, 2023, pp. 836-847."]}, "Both UMPS and CAD are essential for the de novo synthesis of pyrimidine nucleotides, which are fundamental for cell growth and division. The interaction between these proteins ensures the efficient production of UMP, which is subsequently converted into other pyrimidine nucleotides. Given that both proteins are directly involved in the same metabolic pathway and their activities are sequential steps in pyrimidine biosynthesis, the name \"Pyrimidine Biosynthesis\" accurately reflects the primary biological process performed by this system of interacting proteins.": {"keywords": "(\"UMPS\" OR \"CAD\") AND (\"pyrimidine biosynthesis\" OR \"cell growth\" OR \"UMP production\") AND (hasabstract[text])", "references": ["Yang, Chuanzhen, Zhao, Yiliang, Wang, Liao, Guo, Zihao, Ma, Lingdi, Yang, Ronghui, Wu, Ying, Li, Xuexue, Niu, Jing, Chu, Qiaoyun, Fu, Yanxia, Li, Binghui. \"De novo pyrimidine biosynthetic complexes support cancer cell proliferation and ferroptosis defence.\" Nature cell biology, 2023, pp. 836-847."]}, "1. CBS, or cystathionine beta-synthase, is a key enzyme in the transsulfuration pathway, which converts homocysteine to cystathionine. This enzyme is critical for the regulation of homocysteine levels within the cell and, by extension, in the bloodstream. Elevated levels of homocysteine are associated with cardiovascular diseases and other metabolic disorders. CBS activity is also linked to the production of hydrogen sulfide, a signaling molecule with various physiological functions.": {"keywords": "(\"CBS\") AND (\"transsulfuration\" OR \"homocysteine\" OR \"hydrogen sulfide\") AND (hasabstract[text])", "references": []}, "2. MTRR, or methionine synthase reductase, is an enzyme that plays a crucial role in the remethylation of homocysteine to methionine. It is essential for the regeneration of methionine synthase (MS) to its active form. Methionine synthase is responsible for the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine, thereby producing methionine and tetrahydrofolate. MTRR ensures the proper function of this methylation cycle, which is vital for DNA synthesis and repair, as well as the production of S-adenosylmethionine (SAM), a universal methyl donor for numerous methylation reactions.": {"keywords": "(\"MTRR\" OR \"MS\") AND (\"methylation\" OR \"homocysteine\" OR \"DNA synthesis\") AND (hasabstract[text])", "references": ["Aksoy-Sagirli, Pinar, Erdenay, Ay\u00e7in, Kaytan-Saglam, Esra, Kizir, Ahmet. \"Association of Three Single Nucleotide Polymorphisms in MTR and MTRR Genes with Lung Cancer in a Turkish Population.\" Genetic testing and molecular biomarkers, 2017, pp. 428-432."]}, "1. ETHE1 is a sulfur dioxygenase involved in the catabolism of sulfide, which is a crucial process for detoxification in the mitochondria. It plays a role in cellular response to oxidative stress and is implicated in the disease ethylmalonic encephalopathy, which is characterized by the accumulation of hydrogen sulfide and neurodegeneration.": {"keywords": "(\"ETHE1\") AND (\"sulfur dioxygenase\" OR \"detoxification\" OR \"ethylmalonic encephalopathy\") AND (hasabstract[text])", "references": []}, "1. NBEAL2 (Neurobeachin-like 2) is a protein that has been implicated in the development and function of hematopoietic cells. It is particularly associated with the biogenesis of platelet alpha-granules, cellular organelles that are essential for platelet function. Mutations in NBEAL2 are known to cause Gray Platelet Syndrome, a rare inherited disorder characterized by thrombocytopenia and a lack of alpha-granules in platelets, leading to bleeding complications.": {"keywords": "(\"NBEAL2\") AND (\"hematopoietic development\" OR \"platelet alpha-granules\" OR \"Gray Platelet Syndrome\") AND (hasabstract[text])", "references": []}}