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Brian Haas edited this page Apr 3, 2019 · 18 revisions

CTAT_HumanFusionLib

Collections of fusion transcripts from various sources including those below. These data are leveraged by FusionAnnotator as integrated into the Trinity Cancer Transcriptome Analysis Toolkit Fusion-finding modules including STAR-Fusion and FusionInspector.

CTAT_HumanFusionLib currently integrates the following resources to help with identifying fusions known to be relevant to cancer biology as well as those that are more likely to be not relevant - known artifacts or fusions that tend to show up in normal samples.

Fusions relevant to cancer biology

Label Source Info
Mitelman Known fusions from the Mitelman database
chimerdb_omim, chimerdb_pubmed Fusions in OMIM and identified in Pubmed, as catalogued by ChimerDB2
ChimerKB represents a knowledgbase of fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences, derived from http://ercsb.ewha.ac.kr/fusiongene
ChimerPub includes fusion genes obtained from text mining of PubMed abstracts, derived from http://ercsb.ewha.ac.kr/fusiongene
ChimerSeq fusion candidates from TCGA as per FusionScan and TopHat-Fusion, derived from http://ercsb.ewha.ac.kr/fusiongene
Cosmic Fusions listed in Cosmic
YOSHIHARA_TCGA Fusion genes identified in cancer cell lines in The Cancer Genome Atlas based on previously published work by Yoshihara et al.
Klijn_CellLines Fusions reported in Klijn et al. study of cancer cell lines http://www.ncbi.nlm.nih.gov/pubmed/25485619
Larsson_TCGA Recurrent fusions supported by genomic and transcriptomic data across cancer types, as per http://www.pnas.org/content/113/48/13768#T1
CCLE Fusions identified in cancer cell lines as part of the CCLE project
HaasMedCancer Cancer-relevant fusions reported in the literature, as a last-ditch supplement to other resources (ie. ChimerPub) and populated by yours truly (B. Haas)
GUO2018CR_TCGA Fusions identified in TCGA data sets as reported in Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep. 2018 Apr 3;23(1):227-238.e3.
TumorFusionsNAR2018 Tumor fusions reported in TumorFusions: an integrative resource for cancer-associated transcript fusions. Nucleic Acids Res. 2018
TCGA_StarF2019 Fusions found by STAR-Fusion (v1.5.0) across corresponding TCGA data sets
CCLE_StarF2019 Fusions identified in the Cancer Cell Line Encyclopedia RNA-seq data sets

Individual genes of cancer relevance, which may show up in fusions

Label Source Info
Oncogene The oncogene label is applied to individual genes that are found in the list of oncogenes provided at http://www.bushmanlab.org/links/genelists
ArcherDX_panel Gene is included in the Archer® FusionPlex® Solid Tumor Kit
FoundationOne_panel Gene's included on Foundation Medicine's cancer gene listing.
OncocartaV1_panel Genes on the OncoCarta v1 Panel
OncomapV4_panel Genes on the OncoMap v4 Panel as described in PLoS One. 2012; 7(6): e38892.

Red Herrings: Fusion pairs that may not be relevant to cancer, and potential false positives.

Label Source Info
GTEx_recurrent_StarF2019 Fusions found recurrently in GTEx as mined using STAR-Fusion v1.5.0
BodyMap Fusions found by STAR-Fusion as applied to the Illumina Human Body Map reference data
DGD_PARALOGS Duplicated genes as per the Duplicated Genes Database
HGNC_GENEFAM HGNC gene family membership as per ftp://ftp.ebi.ac.uk/pub/databases/genenames/genefam_list.txt.gz
Greger_Normal Fusion transcripts (mostly from tandem genes) detected based on analysis of RNA-Seq from 1000 genomes project samples. List derived from Greger et al. PLOS One, 2014
Babiceanu_Normal Recurrent chimeric fusion RNAs in non-cancer tissues and cells as per Babiceanu et al. NAR, 2016
ConjoinG Fused transcripts derived from the Conjoined Gene Database

Other fusion-related resources, including many that overlap with the above are provided by Daniel Nicorici as part of FusionCatcher and described here.

** Contributions and pointers to additional resources to include are welcomed! **

Contact us at our Google forum: https://groups.google.com/forum/#!forum/trinity_ctat_users

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