Version 3.7.1 has been released with the following updates.
Tissue Specific/Merged Reconstruction GTFs
Normalized Expression Values for Ensembl/Reconstruction, Gene/Transcript, Strain Means/Individual values
Build a custom view on the fly by selecting a few check boxes simply select sissue and track types.
Views can be named and saved for future use
Version 3.7 has been released with HRDP v5.
Transcriptomes are now based on the full HXB/BXH RI panel in brain and liver and available inbred strains now including the F344/Stm and LE/Stm strains.
Updated WGCNA, expression values, eQTLs, and transcriptomes are available.
Transcript level expression is available for the full panel.
Transcript level eQTLs are now available once you've selected a gene.
Transcript level WGCNA is coming in the next 1-2 months.
CircularRNA data is availble now. This includes predictions from BNLx/SHR in Brain/Heart/Liver using CIRI 2.0 and CircExplorer2. Also Heart left ventricle includes data from more than 12,000 previously described cirRNAs using cirRNA arrays. Full reports are coming soon but the browser includes tracks with annotation and structure all available data.
Version 3.6 has been released with HRDP v4. Transcriptomes are now based on the full HXB/BXH RI panel in brain and liver and available inbred strains except for the F344/Stm and LE/Stm. The FXLE/LEXF parents will be included in HRDP v5.
Updated WGCNA, expression values, eQTLs, and transcriptomes are available. Transcript level WGCNA is coming in the next 1-2 months. Transcript level expression is available again now for the full panel.
Links to Literature searches for gene-gene/gene-keyword relationshipts and gene-Addiction relationships.
Shortcuts to the genome browser to get you to sections of interest more directly.
This is the new home for PhenoGen running in the cloud. As such, a large number of changes have occurred in the background that will help us maintain the site and improve performance. Please excuse some ongoing bugs as we are beta testing the site now. This is not currently the recommended version.
However, we would appreciate any help testing the supported features by simply using this site as you would the previous site.
REST API Survey 2/20/2018
Please help us prioritize effort on a REST API to provide access to data on Phenogen. Take the 1 question survey below.
PhenoGen v3.4.2 3/9/2018
Added read depth count tracks to the genome browser for whole brain and liver for the inbred strains:
ACI, Dark-Agouti, Cop, F344-NCl, F344-NHsd, LEW-Crl, LEW-SsNHsd, SHRSP, SR-JrHsd, SS-JrHsd, and WKY.
PhenoGen v3.4.1 2/16/2018
The Genome/Transcriptome Data Browser can now look up genes by either their gene or transcript PhenoGen ID.
NIDA Genetics Consortium Meeting Poster
NIDA Meeting Poster -
Download the poster from the NIDA meeting with an outline of ways to use our WGCNA Modules and recent examples of our use with phenotype QTLs.
PhenoGen v3.4 12/10/2017
Recombinant Inbred Small RNA - Added expression data for small RNA features across RI Panel in Whole Brain and Liver.
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
Gene List tabs have been reformatted so you can submit submit new analyses and view results and running analyses status from a single page.
GO term summaries are available for Gene Lists.
MuliMiR results are available for Rat both in Gene Lists and the browser(individual genes, WGCNA modules).
Minor Updates 6/8/2015
We've made a couple of minor updates since the last release.
The UCSC Repeat Mask track is now available.
You now have the ability to add tracks without going into the edit view option.
We've also fixed a number of bugs and made general functionality improvements.
Workshop Video/Slides 4/16/2015
Watch the workshop:
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
We now support https to keep your connections more secure. We will eventually redirect all traffic to the secure site,
but for now feel free to try it out here: https://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.
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: