OSGA Webinar #8

Using genetic and non-genetic covariates in QTL studies 10/9/2020 10am PDT/1pm EDT

Free Registration Here
Goals of this webinar (quantitative trait to genetic loci):

Identify covariates and mediators in QTL studies
Adjust for covariates in QTL scans
Review genetic relatedness in segregating populations
Adjust for genetic relatedness using linear mixed models

Dr. Saunak Sen
Professor and Chief of Biostatistics
Department of Preventative Medicine
University of Tennessee Health Science Center

Series Information and Previously Recorded Webinars

OSGA Webinar #7

Introduction to Weighted Gene Co-expression Network Analysis 9/25/2020 10am PDT/1pm EDT

View Here Goals of this webinar (molecular networks):

Introduction and motivation for co-expression network analysis
Basics of weighted gene co-expression network analysis
Step-by-step guide to WGCNA using the wgcna package in R.

Background reading available at: http://bit.ly/osga_wgcna
Presented by:
Dr. Laura Saba
Associate Professor
Department of Pharmaceutical Sciences
University of Colorado Anschutz Medical Campus

Series Information and Previously Recorded Webinars

OSGA Webinar #6

Sex as a Biological Covariate in QTL Studies With Dr. Saunak Sen 9/11/2020

View Here Goals of this webinar (trait variance to QTL):

Review QTL mapping
Understand the role of sex in QTL study design
Use sex as a covariate in QTL analysis
Understand X chromosome segregation in crosses
Make adjustments for X chromosome in QTL analysis

Presented by:
Dr. Saunak Sen
Professor and Chief of Biostatistics
Department of Preventative Medicine
University of Tennessee Health Science Center

Series Information and Previously Recorded Webinars

OSGA Webinar #5

Identifying genes from QTL using RNA expression and the PhenoGen website 8/28/2020 10am PDT/1pm EDT

View Here Goals of this webinar (QTL to gene/molecular networks):

Demonstrate how to use the PhenoGen website to identify transcripts:
Physically located within a QTL
Physically located within a QTL and expressed in brain
With a brain cis eQTL within the QTL
With any brain eQTL within the QTL
Within a co-expression network controlled from the same region as the QTL

Presented by:
Dr. Laura Saba
Associate Professor
Department of Pharmaceutical Sciences
University of Colorado Anschutz Medical Campus

Series Information and Previously Recorded Webinars

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

OSGA Webinar #3

QTL to gene/molecular networks 6/12/2020 10am PDT/1pm EDT

Goals of this webinar (QTL to gene/molecular networks):

Define eQTL
Examine the role of eQTL in the relationship of genes and molecular networks with phenotypic QTL
eQTL for co-expression networks

Presented by:
Dr. Laura Saba
Associate Professor
Department of Pharmaceutical Sciences
University of Colorado Anschutz Medical Campus

Series Information and Previously Recorded Webinars

Webinar Series

Quantitative Genetics Tools

The NIDA Center of Excellence in Omics, Systems Genetics, and the Addictome has put together a webinar series, Quantitative Genetics Tools for Mapping Trait Variation to Mechanisms, Therapeutics, and Interventions. The goal of this series is to transverse the path from trait variance to QTL to gene variant to molecular networks to mechanisms to therapeutic and interventions. The target audience for this series are those new to the field of quantitative genetics, so please pass this information on to your trainees or colleagues.
Webinar #3 - 6/12/2020 10amPDT/1pm EDT - QTL to gene/molecular networks - Register More Information
Previously Recorded Webinars

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