New GTEx eQTL 44 tissues and summary tracks on hg19
31 views
Skip to first unread message
Cath Tyner
Oct 18, 2017, 8:01:20 PM10/18/17
to Genome Browser Announcements
We are pleased to announce two new GTEx eQTL tracks in the GRCh37/hg19 browser within the "Regulation" track category. These tracks show genetic variants associated with and likely causal for differences in gene expression in 44 human tissues from the Genotype-Tissue Expression (GTEx) V6 data release. The data items displayed are gene expression quantitative trait loci within 1MB of gene transcription start sites (cis-eQTLs), significantly associated with gene expression and in the credible set of variants for the gene at a high confidence level (95%).
hg19: GTEx Combined eQTL
This "all in one" track displays all cis-eQTL's from the 44 tissues, collapsed into a single track for a summary view in the browser display. Gene/variant pairs occurring in multiple tissues are combined into a single item in the display. The item label shows the number of tissues where the eQTL was identified, or the tissue name and the GTEx-convention tissue color if the eQTL was identified solely in one tissue. Mouseover lists all tissues affected and the effect size. The item color reflects the largest effect size in any tissue (red for positive, blue for negative). Click-through on a combined eQTL shows for each tissue the significance of the association, effect size on gene expression, and the probability the eQTL belongs to the the 95% credible set. Track configuration supports filtering by gene, effect size, or probability. Tissues can be selected via checkboxes or from the UCSC GTEx Body Map graphic.
hg19: GTEx Tissue eQTL
This track is a composite track containing 44 subtracks representing the GTEx eQTL tissues. Each subtrack contains all eQTLs identified for that tissue. Filtering is available for all 44 subtracks.
These two tracks join the previously released GTEx data tracks and track hubs in the UCSC Genome Browser:
Please see the related October 11, 2017 publication in Nature, "Genetic effects on gene expression across human tissues" for an in-depth article about these data.
Acknowledgements to UCSC Genome Browser engineer, Kate Rosenbloom, for creating these tracks.
* Unsubscribe: Email genome-announce+unsubscri...@soe.ucsc.edu
hg19: GTEx Combined eQTL
This "all in one" track displays all cis-eQTL's from the 44 tissues, collapsed into a single track for a summary view in the browser display. Gene/variant pairs occurring in multiple tissues are combined into a single item in the display. The item label shows the number of tissues where the eQTL was identified, or the tissue name and the GTEx-convention tissue color if the eQTL was identified solely in one tissue. Mouseover lists all tissues affected and the effect size. The item color reflects the largest effect size in any tissue (red for positive, blue for negative). Click-through on a combined eQTL shows for each tissue the significance of the association, effect size on gene expression, and the probability the eQTL belongs to the the 95% credible set. Track configuration supports filtering by gene, effect size, or probability. Tissues can be selected via checkboxes or from the UCSC GTEx Body Map graphic.
hg19: GTEx Tissue eQTL
This track is a composite track containing 44 subtracks representing the GTEx eQTL tissues. Each subtrack contains all eQTLs identified for that tissue. Filtering is available for all 44 subtracks.
These two tracks join the previously released GTEx data tracks and track hubs in the UCSC Genome Browser:
- GTEx Gene
- GTEx Transcript
- GTEx RNA-Seq Signal Hub on hg19 and hg38.
- GTEx Analysis Hub: Allele-Specific Expression on hg19 and hg38.
Please see the related October 11, 2017 publication in Nature, "Genetic effects on gene expression across human tissues" for an in-depth article about these data.
Acknowledgements to UCSC Genome Browser engineer, Kate Rosenbloom, for creating these tracks.
UCSC Genome Browser Announcements List (low volume email alerts, new data & software):
* Subscribe: Email genome-announce+subscribe...@soe.ucsc.edu * Unsubscribe: Email genome-announce+unsubscri...@soe.ucsc.edu
Cath
. . .
Cath Tyner. . .
UCSC Genome Browser, Software QA & User Support
UC Santa Cruz Genomics InstituteReply all
Reply to author
Forward
0 new messages