Welcome to PhenoGen Informatics

The site for quantitative genetics of the transcriptome.

Click on a function in the list below to view additional information.

What can you do with PhenoGen?

Gene List Analysis

Expression Values
Annotations
Promoter Analysis
Compare/Share
Homologs
WGCNA
Gene Ontology
multiMiR

Microarray Data

Access Public Data
Access Previously Analyzed Data

Genome/Transcriptome Data Browser

Browse a Region
Browse by a Gene
Translate regions from one organism to another

Download Data

Genomic Marker Files
Human Whole Genome SNP Data
Microarray Data
RNA-Seq Data
Strain Specific Genomes

QTL Analysis

Visualize eQTLs - Arrays
Visualize eQTLs - RNA-Seq

Promoter Analysis

Demo/Screen Shots

Feature List

Analyze promoters for all the genes in a gene list. PhenoGen supports the following 3 methods for promoter analysis.

oPOSSUM v2 (Mouse Only)
MEME v4.9 patch 2
upstream sequence extraction to a downloadable .fasta file for your own analysis

View Gene Lists

Acknowledgements

Funding

We would like to thank the National Institue on Alcohol Abuse and Alcoholism (NIAAA) for continued funding to develop and support this site. The Banbury Fund for supporting the development of this site.

Computational Resources

We would like acknowledge the UNLV National Supercomputing Institute (UNLV NSI) for access to supercomputing resources to support analysis of sequencing data.

Recombinant Inbred Panels

We are grateful to the following investigators for providing the recombinant inbred panels found on the site.

HXB/BXH Rat RI Panel was provided by Michal Pravenec (Czech Academy of Sciences) and Morton Printz(UC San Diego).
F344/LE Rat RI Panel was provided by Masahide Asano(National BioResource Project for the Rat in Japan).
ILSXISS Mouse RI Panel was provided by Thomas Johnson(CU Boulder) and John DeFries (CU Boulder).