Schema for Gene Interactions - Protein Interactions from Curated Databases and Text-Mining
  Database: hg38    Primary Table: interactions Data last updated: 2017-08-05
Big Bed File: /gbdb/hg38/bbi/interactions.bb
Item Count: 16,786
Format description: Browser Extensible Data
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart166839456Start position in chromosome
chromEnd166856344End position in chromosome
namePOGK: UCHL3,ZNF331,ZNF250,ZNF8,RBAK,ZNF124,ZFP1,C1QBP,HSP90AB1,ZNF552Name of item.
score23Score (0-1000)
strand.+ or - for strand
thickStart166839456Start of where display should be thick (start codon)
thickEnd166856344End of where display should be thick (stop codon)
reserved0,0,128Used as itemRgb as of 2004-11-22

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreserved
chr1166839456166856344POGK: UCHL3,ZNF331,ZNF250,ZNF8,RBAK,ZNF124,ZFP1,C1QBP,HSP90AB1,ZNF55223.1668394561668563440,0,128
chr1166856509166876327TADA1: SUPT3H,TAF5L,TADA3,KAT2A,TAF12,TAF10,TAF6L,TAF9,USP22,TADA2B105.1668565091668763270,0,0
chr1166918865166975482ILDR2: SFN,UBC2.166918865166975482173,216,230
chr1166989088167022210MAEL: DDX4,TDRD1,PIWIL2,PIWIL14.166989088167022210173,216,230
chr1167052835167090631GPA33: POT11.167052835167090631173,216,230
chr1167094849167129165DUSP27: EPHB2,MAPK4,MAPK3,MAPK14,MAPK15,MAPK1,MAPK10,MAPK11,MAPK12,MAPK1330.1670948491671291650,0,128
chr1167220890167427342POU2F1: HIST2H2BE,POU2F1,NFYA,SNAPC4,POU2AF1,NR3C1,AR,RXRA,MNAT1,NPAT169.1672208901674273420,0,0
chr1167430639167518610CD247: ZAP70,SYK,CD3E,CD8B,FYN,CD3D,CSK,LCK,NCR1,SHC1217.1674306391675186100,0,0
chr1167541012167553767CREG1: RB1,CAPN1,RBL1,IGF2R,RBL2,TBP,NEUROD2,NEUROD1,NEUROD6,NEUROD4153.1675410121675537670,0,0
chr1167630092167706249RCSD1: ACTC1,ARHGAP6,CORO1A,MYO9B,MYO3A,ACTA1,ESPN,MIR4329,FMN1,MYO1A41.1676300921677062490,0,128

Gene Interactions (interactions) Track Description
 

Description

The Pathways and Gene Interactions track shows a summary of gene interaction and pathway data collected from two sources: curated pathway/protein-interaction databases and interactions found through text mining of PubMed abstracts.

Display Conventions and Configuration

Track Display

The track features a single item for each gene loci in the genome. On the item itself, the gene symbol for the loci is displayed followed by the top gene interactions noted by their gene symbol. Clicking an item will take you a gene interaction graph that includes detailed information on the support for the various interactions.

Items are colored based on the number of documents supporting the interactions of a particular gene. Genes with >100 supporting documents are colored black, genes with >10 but <100 supporting documents are colored dark blue, and those with >10 supporting documents are colored light blue.

Pathway and Gene Interaction Display

See the help documentation accompanying this gene interaction graph for more information on its configuration.

Methods

The pathways and gene interactions were imported from a number of databases and mined from millions of PubMed abstracts. More information can be found in the "Data Sources and Methods" section of the help page for the gene interaction graph.

Data Access

The underlying data for this track can be accessed interactively through the Table Browser or Data Integrator. The data for this track is spread across a number of relational tables. The best way to export or analyze the data is using our public MySQL server. The list of tables and how they are linked together are described in the documentation linked at the bottom of the gene interaction viewer.

The genome annotation is just a summary of the actual interactions database and therefore often not of interest to most users. It is stored in a bigBed file that can be obtained from the download server. The data underlying the graphical display is in bigBed formatted file named interactions.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed. Instructions for downloading source code and precompiled binaries can be found here. The tool can also be used to obtain only features within a given range, for example:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/interactions.bb -chrom=chr6 -start=0 -end=1000000 stdout

Credits

The text-mined data for the gene interactions and pathways were generated by Chris Quirk and Hoifung Poon as part of Microsoft Research, Project Hanover.

Pathway data was provided by the databases listed under "Data Sources and Methods" section of the help page for the gene interaction graph. In particular, thank you to Ian Donaldson from IRef for his unique collection of interaction databases.

The short gene descriptions are a merge of the HPRD and PantherDB gene/molecule classifications. Thanks to Arun Patil from HPRD for making them available as a download.

The track display and gene interaction graph were developed at the UCSC Genome Browser by Max Haeussler.

References

Poon H, Quirk C, DeZiel C, Heckerman D. Literome: PubMed-scale genomic knowledge base in the cloud Bioinformatics. 2014 Oct;30(19):2840-2. PMID: 24939151