Announcements

PhenoGen v3.3 4/30/2017

Recombinant Inbred Total RNA - Added expression data for reconstructed transcripts across RI Panel in Whole Brain and Liver. Added RNA-Seq based WGCNA for Whole Brain and Liver.

PhenoGen v3.2 11/13/2016

Small RNA - added tracks and detail on all known and novel (predicted by MiRDeep and SNOSeeker) small RNAs in Brain, Heart, and Liver from the BNLx/SHR parental strains.
Merged Total RNA Transcriptome - added a track with the merged transcriptome from the 3 available tissues and assigned new unique PhenoGen IDs to all novel transcripts.

PhenoGen v3.1 6/15/2016

Rn6 - is available in the browser, for gene list analysis, and both RNA-Seq datasets and microarray datasets have been updated.
Rat WGCNA - Heart and Liver have been added to the rn6 data.

PhenoGen v3.0 5/31/2016

Anonymous Gene List - You can now use our gene list analysis tools without registering. We encourage you to link your email so you don't loose access to previous work.
Rn6 (June 2016): Rn6 - Will be available in June 2016. Rn6 and Rn5 will be available in the genome browser, public HXB datasets, and gene list analysis tools.

PhenoGen v2.16.1 11/10/2015

Security Updates - We now require using HTTPS so all of the data transmitted between your browser and our server is encrypted. Update your bookmarks.
Future Update: Rn6 - We are still working on updating the Microarrays and RNA-Seq data to Rn6. Our next major update will include Rn6.

PhenoGen v2.16 7/21/2015

Minor Updates 6/8/2015

We've made a couple of minor updates since the last release.

Workshop Video/Slides 4/16/2015

Watch the workshop:


OR
Download the slides from the Informatics Workshop here.

v2.15 of PhenoGen 3/7/2015


We've added GO term summary and miRNA targeting views to the Weighted Gene Co-expression Network Analysis. Look at what's new for a summary of changes.

HTTPS support 2/9/2015

Thank you for trying the secure site. You can always switch back to the regular site: http://phenogen.ucdenver.edu/PhenoGen/

v2.14 of PhenoGen 1/10/2015


We've added Weighted Gene Co-expression Network Analysis. Look at what's new for a summary of changes.

v2.13 of PhenoGen 9/27/2014

We've updated PhenoGen. Look at what's new for a summary of changes.

Added multiMiR


Using multiMiR(an R package available here) you can view validated and predicted miRNAs that target specific genes. You can also select a miRNA and view all genes targeted by the miRNA. multiMiR is avaialble as a new tab for a selected gene in the Genome/Transcriptome Data Browser and in Gene Lists after selecting a list. It is currently available only for mouse genes, but will be available in rat soon.

Added Rat Liver Transcriptome

We've added rat liver tracks including, a transcriptome reconstructiong track, splice junction track, and stranded read depth count tracks. Available in the Genome/Transcriptome Browser.

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RNA-Seq Data Summary Graphics

Rat Brain RNA-Seq data summary graphics are now available. Click below to browse the RNA-Seq data summary:

Reconstructed transcripts from this RNA-Seq data are still combined with PhenoGen array data in Genome/Transcriptome Data Browser.