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README.md
coefficients.tsv
create-markdown-previews.ipynb
disease-localization.tsv
diseases.tsv
expression.tsv.gz
features.tsv.gz
figures.zip
gene-associations.tsv
genes.tsv
loci-associations.tsv
network-tables.zip
network.json.gz
predictions.tsv.gz
protein-interactions.tsv.gz

README.md

Disease-Associated Genes Prediction Downloads

This directory contains datasets related to the study:

Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes
Daniel S. Himmelstein, Sergio E. Baranzini
PLOS Computational Biology (2015-07-09) https://doi.org/98q
DOI: 10.1371/journal.pcbi.1004259 · PMID: 26158728 · PMCID: PMC4497619

Previousely, these downloads were described at https://het.io/disease-genes/downloads/. In August 2019, we moved the downloads documentation to this README.

Many of these downloads are also available as Supporting Information files from PLOS Computational Biology, as indicated by the corresponding DOI links. Where the Supporting Information files use as .txt extension, the downloads here have switched to .tsv when appropriate for better GitHub previewing.

The first two rows are shown below for each TSV download. These previews were generated by create-markdown-previews.ipynb.

Predictions

  • Predictionspredictions.tsv.gz
    Predicted probabilities of association between all genes (rows) and diseases (columns).
    PLOS S1 Data at https://doi.org/10.1371/journal.pcbi.1004259.s013

    gene_symbol age related macular degeneration Alzheimer's disease ankylosing spondylitis asthma atopic dermatitis bipolar disorder breast carcinoma celiac disease chronic lymphocytic leukemia coronary artery disease Crohn's disease Graves' disease lung carcinoma metabolic syndrome X migraine multiple sclerosis obesity Parkinson's disease primary biliary cirrhosis prostate carcinoma psoriasis refractive error rheumatoid arthritis schizophrenia systemic lupus erythematosus type 1 diabetes mellitus type 2 diabetes mellitus ulcerative colitis vitiligo
    A1BG 0.000902865316849012 0.000843094981697786 0.000865232781366083 0.000831379132325189 0.000911703492360143 0.000808922207291462 0.000959152333696821 0.000863317239021426 0.000883366400989101 0.000860652442140361 0.00101527849738045 0.000834690712259122 0.000836175784541967 0.000890262249489595 0.000910202482110256 0.000942966382621634 0.000885761201398873 0.00108242243839361 0.000877403291771053 0.000955266902171645 0.000836837597339859 0.000867033176122321 0.000913629510226676 0.000900995771178386 0.00088691653115335 0.000925299177993949 0.000918381930484204 0.000894170209705782 0.000883307183575619
    A1CF 0.000957085997890059 0.000931608757521376 0.000846946668196247 0.000896742727312265 0.000885461144158393 0.000880761040241341 0.00118376663378837 0.000937125303326467 0.0010001122696522 0.00103019822337742 0.00115055855886886 0.000884716707004226 0.000961631136752842 0.00108022768862733 0.000942302096046314 0.00107627566455975 0.000966189226666171 0.000871368013059514 0.000955566329246775 0.00103882600872266 0.000926214620214113 0.000865329148260458 0.000976980091510641 0.000976109228605849 0.000937952065921 0.00100576569571365 0.00116644271736648 0.000945200666696613 0.000906560576575734
  • Featuresfeatures.tsv.gz
    The features (columns) computed for each gene-disease pair (rows). Column names with beginning with 'XB' refer to standardized features.

    gene_code gene_symbol disease_code disease_name status status_int percentile part PC_s|G-a-D PC_t|G-a-D DWPC_0.4|G-e-T-l-D DWPC_0.4|G-i-G-a-D DWPC_0.4|G-m-C5.B-m-G-a-D DWPC_0.4|G-m-C2.CP.K-m-G-a-D DWPC_0.4|G-m-C2.CP.B-m-G-a-D DWPC_0.4|G-m-C3.T-m-G-a-D DWPC_0.4|G-m-C1-m-G-a-D DWPC_0.4|G-m-C3.M-m-G-a-D DWPC_0.4|G-m-C4.CG-m-G-a-D DWPC_0.4|G-m-C4.CM-m-G-a-D DWPC_0.4|G-a-D-a-G-a-D DWPC_0.4|G-a-D-m-P-m-D DWPC_0.4|G-a-D-l-T-l-D DWPC_0.4|G-m-C5.M-m-G-a-D DWPC_0.4|G-m-C2.CG-m-G-a-D DWPC_0.4|G-m-C2.CP.R-m-G-a-D DWPC_0.4|G-m-C7-m-G-a-D DWPC_0.4|G-m-C6-m-G-a-D DWPC_0.4|G-e-T-e-G-a-D DWPC_0.4|G-i-G-e-T-l-D DWPC_0.4|G-i-G-i-G-a-D DWPC_0.4|G-m-C5.C-m-G-a-D disease_pathophys ridge lasso XB|PC_s|G-a-D XB|PC_t|G-a-D XB|DWPC_0.4|G-e-T-l-D XB|DWPC_0.4|G-i-G-a-D XB|DWPC_0.4|G-m-C5.B-m-G-a-D XB|DWPC_0.4|G-m-C2.CP.K-m-G-a-D XB|DWPC_0.4|G-m-C2.CP.B-m-G-a-D XB|DWPC_0.4|G-m-C3.T-m-G-a-D XB|DWPC_0.4|G-m-C1-m-G-a-D XB|DWPC_0.4|G-m-C3.M-m-G-a-D XB|DWPC_0.4|G-m-C4.CG-m-G-a-D XB|DWPC_0.4|G-m-C4.CM-m-G-a-D XB|DWPC_0.4|G-a-D-a-G-a-D XB|DWPC_0.4|G-a-D-m-P-m-D XB|DWPC_0.4|G-a-D-l-T-l-D XB|DWPC_0.4|G-m-C5.M-m-G-a-D XB|DWPC_0.4|G-m-C2.CG-m-G-a-D XB|DWPC_0.4|G-m-C2.CP.R-m-G-a-D XB|DWPC_0.4|G-m-C7-m-G-a-D XB|DWPC_0.4|G-m-C6-m-G-a-D XB|DWPC_0.4|G-e-T-e-G-a-D XB|DWPC_0.4|G-i-G-e-T-l-D XB|DWPC_0.4|G-i-G-i-G-a-D XB|DWPC_0.4|G-m-C5.C-m-G-a-D
    HGNC:5 A1BG DOID:10286 prostate carcinoma negative 0 0.10572593 train 0 34 0 0 0 0 0 0.00155245904597262 0 0 0 0.0020210045278042 0 0 0 0 0.00121789583242957 0 0 0 0.00089748671759056 0.0019959656678926 0 0.00411933832386317 neoplastic 0.000955266902171645 0.000904602830537589 0 0.0578418829928233 0 0 0 0 0 0.0220756680131442 0 0 0 0.0289325302452683 0 0 0 0 0.0400509738187678 0 0 0 0.00401721262818795 0.00350152338505844 0 0.0405191297120283
    HGNC:24086 A1CF DOID:10286 prostate carcinoma negative 0 0.59621654 train 0 34 0.00590021447147218 0 0.00619975385355829 0 0 0 0 0 0 0 0 0 0 0 0.000645118666484247 0 0.00111228506784582 0 0.00483938065794723 0.00469503472779078 0 0.00268768008923857 neoplastic 0.00103882600872266 0.000846424494832754 0 0.0578418829928233 0.0173638829936915 0 0.0974203041285678 0 0 0 0 0 0 0 0 0 0 0 0.0212149759719727 0 0.030702468640466 0 0.0216614025708436 0.00823650133740952 0 0.0264368812654755
  • Model Coefficientscoefficients.tsv
    Standardized and unstandardized coefficients from the ridge and lasso logistic regression models.

    feature name ridge_coef ridge_zcoef lasso_coef lasso_zcoef select_coef select_zcoef
    DWPC_0.4|G-a-D-a-G-a-D GaDaGaD 50.1059419658922 2.53778862460897 58.1870914234121 2.94708637179072 57.449958914982 2.90975174796513
    DWPC_0.4|G-a-D-l-T-l-D GaDlTlD 20.5895169007358 2.00413247793486 26.8769993619278 2.61614041700751

Resources

  • Protein-coding Genesgenes.tsv
    Information on the included protein-coding genes, derived from the HGNC database.
    PLOS S3 Data at https://doi.org/10.1371/journal.pcbi.1004259.s015

    hgnc_id symbol name aliases entrez ensembl uniprot chromosome
    HGNC:5 A1BG alpha-1-B glycoprotein 1 ENSG00000121410 P04217 19q13.43
    HGNC:24086 A1CF APOBEC1 complementation factor ACF|ACF64|ACF65|APOBEC1CF|ASP 29974 ENSG00000148584 Q9NQ94 10q21.1
  • Processed GWAS Catalog Lociloci-associations.tsv
    The associated gene-disease loci (regions) derived from the GWAS Catalog.
    PLOS S4 Data at https://doi.org/10.1371/journal.pcbi.1004259.s016

    disease_code disease_name resolved_gene confidence candidate_genes report_counter mapped_genes dapple_genes studies snps mlog_pvals
    DOID:1686 glaucoma CDKN2B HC CDKN2B Counter({CDKN2B: 2}) None|None|None|CDKN2B|None|None CDKN2B|CDKN2A|MTAP 22570617|21532571|22570617|22419738|22428042|22792221 rs2157719|rs4977756|rs2157719|rs1063192|rs7865618|rs523096 17.699|14.000|12.000|10.301|10.046|10.301
    DOID:1686 glaucoma TMCO1 HC TMCO1|ALDH9A1 Counter({TMCO1: 1}) TMCO1 UCK2|MGST3|ALDH9A1|TMCO1 21532571 rs4656461 13.222
  • Gene-Disease Associationsgene-associations.tsv
    All gene-disease associations extracted from the GWAS catalog for the four categories of association.
    PLOS S5 Data at https://doi.org/10.1371/journal.pcbi.1004259.s017

    disease_code disease_name gene_code gene_symbol status
    DOID:10652 Alzheimer's disease HGNC:37 ABCA7 HC_primary
  • Complex Diseasesdiseases.tsv
    All diseases with at least one GWAS-Catalog-extracted association. The manual pathophysiology classification is included.
    PLOS S6 Data at https://doi.org/10.1371/journal.pcbi.1004259.s018

    Disease Code Pathophysiology HC-P HC-S LC-P LC-S
    Crohn's disease DOID:8778 immunologic 67 179 4 2
    multiple sclerosis DOID:2377 immunologic 50 43 38 29
  • Protein-Protein Interactionsprotein-interactions.tsv.gz
    Protein-protein interactions processed from iRefIndex using ppiTrim. ppiTrim converts to gene space, consolidates duplicate interactions, and removes complexes. PLOS S8 Data at ttps://doi.org/10.1371/journal.pcbi.1004259.s020

    source_code source_symbol target_code target_symbol pubmed interaction_type method
    HGNC:5 A1BG HGNC:545 ANXA7 21900206 MI:0407(direct interaction) MI:0018(two hybrid)
    HGNC:5 A1BG HGNC:1784 CDKN1A 21900206 MI:0407(direct interaction) MI:0018(two hybrid)
  • Tissue-specific Gene Expressionexpression.tsv.gz
    A processed version of the GNF BodyMap providing a gene's (row, HGNC symbols) expression value for each of 77 tissues (columns, BRENDA Tissue Ontology IDs).
    PLOS S9 Data at https://doi.org/10.1371/journal.pcbi.1004259.s021

    BTO:0000038 BTO:0000041 BTO:0000045 BTO:0000047 BTO:0000084 BTO:0000089 BTO:0000141 BTO:0000142 BTO:0000211 BTO:0000232 BTO:0000269 BTO:0000289 BTO:0000293 BTO:0000443 BTO:0000562 BTO:0000614 BTO:0000651 BTO:0000664 BTO:0000671 BTO:0000725 BTO:0000738 BTO:0000755 BTO:0000759 BTO:0000763 BTO:0000776 BTO:0000784 BTO:0000873 BTO:0000876 BTO:0000914 BTO:0000958 BTO:0000961 BTO:0000975 BTO:0000988 BTO:0000991 BTO:0001001 BTO:0001042 BTO:0001067 BTO:0001073 BTO:0001078 BTO:0001101 BTO:0001103 BTO:0001129 BTO:0001154 BTO:0001175 BTO:0001176 BTO:0001203 BTO:0001231 BTO:0001235 BTO:0001253 BTO:0001256 BTO:0001260 BTO:0001264 BTO:0001279 BTO:0001325 BTO:0001355 BTO:0001363 BTO:0001365 BTO:0001374 BTO:0001379 BTO:0001385 BTO:0001387 BTO:0001388 BTO:0001424 BTO:0001539 BTO:0001561 BTO:0002042 BTO:0002246 BTO:0002252 BTO:0002320 BTO:0002417 BTO:0002807 BTO:0002924 BTO:0003335 BTO:0003975 BTO:0004238 BTO:0004730 BTO:0004911
    4 4.05 4.15 4.1 4 4.1 4.1 4 4.2 4.12492424172857 4.05 4 4.1 4.1 3.7 4.05 4.1 4.1 4.1 4.15 4.1 4.05 8898.60000000001 4.05 4 4.1 4.05 4.1 4 4 4.05 4.1 4.1 4.1 4.1 3.9 4.06998771496917 4.1 4.05 4.1 4.1 4.1 3.65 3.95 4.05 4.1 4.05 4.05 4.05 4.05 4.05 4.05 4.1 3.95 4.1 4.05 4.2 4.05 4 4.1 4.1 4.1 4.04969134626332 3.1 4.05 4.1 4.1 4.1 4 4 3.8 4.1 4 4.1 4.05 4.05 4.1
    48.55 63.05 86.1 60.05 92.1 60.7 80.35 40.45 52.6 69.7784350641371 237.25 27.55 37.3 41.15 60.1 64 242.95 39.25 131.65 20.2 39.55 62.85 362.4 53.45 22.05 41.9 40.25 23.1 33.2 39.15 55.9 72.85 215.05 269.9 57.1 52.95 37.207741130039 77.45 52.25 69.1 101.3 51.25 87.4 53.85 28.5 47.15 81.35 50.25 69.85 42.15 45.35 46.75 53.25 107.2 42.4 74.45 46.5 37.6 69.65 79.95 44.85 42.6 63.9411839114666 64.15 63.75 24.45 31.15 37.65 58.2 30.2 44.85 48.9 41.1 58.2 37.3 17.35 31.6
  • Disease Localizationdisease-localization.tsv
    Literature co-occurrence between diseases and tissues calculated using CoPub 5.0.
    PLOS S10 Data at https://doi.org/10.1371/journal.pcbi.1004259.s022

    doid_id doid_name bto_id bto_name r_scaled
    DOID:10652 Alzheimer's disease BTO:0000776 B-lymphocyte 23.0
    DOID:10652 Alzheimer's disease BTO:0000755 Leydig cell 21.0

Network

  • Serialized Networknetwork.json.gz
    A JSON formatted text file storing the complete network. The top level is an JSON object with four pairs (metanodes, metaedges, nodes, edges). The value for each pair is a JSON array containing the corresponding items.

  • Network Tablesnetwork-tables.zip
    A table of network edges (sif format) and a table of node attributes.
    PLOS S2 Data at https://doi.org/10.1371/journal.pcbi.1004259.s014

Visualization

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