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
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