eQTLs for HRDP v5

11/1/21 - Brain/Liver/Kidney eQTLs using the full panel of HRDP animals available 43 strains have now been calculated with GEMMA and are available now.

OSGA Webinar #23

Julia: a fast, friendly, and powerful language for data science

11/12/21 10am PDT/1pm EDT

View Here -- Coming soon
Summary of this webinar:
Julia is a high-level dynamic programming language that is gaining popularity. The Julia language is designed for scientific computing and offers several attractive features for data science applications. In this webinar, we will make a case for why a data scientist might consider taking a serious look at Julia. We will show code examples and point the audience to further resources.

To articulate why Julia is attractive for data scientists
To provide an overview of Julia language syntax and design
To provide additional resources about the Julia language and ecosystem

Gregory Farage, PhD
Post-Doctoral Fellow
Department of Preventive Medicine
University of Tennessee Health Science Center

Saunak Sen, PhD
Professor and Division Chief
Department of Preventive Medicine
University of Tennessee Health Science Center

Series Information and Previously Recorded Webinars

Kidney RNA-Seq

9/7/21 - Kidney transcriptome and HXB/BXH expression values and eQTLs are avaialble in the genome browser. WGCNA results will be available soon.

OSGA Webinar #22

Guide to evaluating the application of machine learning methods in genetics literature

10/22/21 10am PDT/1pm EDT

View Here

Summary of this webinar:

To describe the relationship between artificial intelligence (AI), machine learning (ML), and deep learning (DL).
To describe general scenarios when ML is appropriate.
To understand methods for comparing the performance of different ML algorithms
To layout general criteria to examine when evaluating literature that includes machine learning algorithms

Laura Saba, PhD
Associate Professor
Department of Pharmaceutical Sciences
University of Colorado Anschutz Medical Campus

Series Information and Previously Recorded Webinars

PhenoGen update 3.7.5

12/11/20 update to v3.7.5

Sampled counts from every strain are now available as well as total counts.
You can create a custom view and select total/sampled count and choos the density of the count tracks.
Bug Fixes

PhenoGen update 3.7.4

11/18/20 update to v3.7.4

You can now create gene lists from Genome Browser tables - Filter tables from tracks, eQTLs, WGCNA based on expression/tissue and then use gene list tools on the list.
Implemented a reasonable region restriction of 5Mbp for now. - We are working to create a less detailed view that will be displayed in larger regions.
Bug Fixes

PhenoGen v3.7.3

Version 3.7.3 has been released with the following updates.
- RNA-Seq eQTLs based on HRDP
- Heritability based on HRDP
- TPM summary
- Track Table filtering
- Table export to clipboard, csv, xls, and PDF
- Ensembl and Reconstruction based eQTLs/TPM/Heritability

PhenoGen v3.7.2

Version 3.7.2 has been released with the following updates.
- RNA-Seq eQTLs
  - Gene Track Summaries now include RNA-Seq based eQTL summaries
  - Modules for a region can be selected base on overlap of the module QTL with the region.
  - Genes with an eQTL that overlaps the region are now available based on RNA-Seq and Microarrays
- Custom Views
  - Total Counts for all 45 strains to date are available.
- Read counts for all 45 strains are available to add as browser tracks.
- Bug Fixes

PhenoGen v3.7.1

Version 3.7.1 has been released with the following updates.
- Downloads
  - Tissue Specific/Merged Reconstruction GTFs
  - Normalized Expression Values for Ensembl/Reconstruction, Gene/Transcript, Strain Means/Individual values
- Custom Views
  - 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

PhenoGen v3.7

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.

PhenoGen v3.6

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.
New gene list eQTL image/browser.

Rat Genomics Workshop 8/2-8/3

Look for another workshop spring/summer 2020

Summer of Rat Genomics and Genetics Workshop - Aug 2nd-3rd, 2019 - Colorado - NIDA Center for Omics, Systems Genetics and the Addictome
Come to Colorado in August for a 2-day hands-on workshop on web-based tools for rat genetics/genomics including RGD, GeneNetwork2, PhenoGen, GeneWeaver, and several others. Offered by the NIDA Center for Omics, Systems Genetics, and the Addictiome.
More Info
Registration

Complex Traits Consortium 2019

PDFs of posters for CTC 2019 Meeting:
Circular RNA Array/Predictions
PhenoGen REST API - gene level data

Phenogen in the Cloud

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. Download here.

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:

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

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.

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.

Follow on Facebook/Google+/Twitter

Follow PhenoGen to keep up with new features, demonstrations, and help by providing feedback to direct future updates.

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.

Announcements