View Heritability and Detection Above Background across tissues availble for genes in the region
We have exon array data for 2 recombinant inbred panels and various tissues (ILSXISS Mice(Whole Brain) and HXB/BXH Rats(Whole Brain, Heart, Liver, Brown Adipose). This data is summarized for each region to include the # and avgerage heritability of probesets with a significant heritability and # and average percentage of samples where probesets were detected above background. These are summarized for each gene in each tissue.
View eQTLs for genes in the region
For genes in the region eQTL with the minimum P-value and its location is summarized across tissues. All locations and tissues can be summarized in a circos plot.
View bQTLs overlapping the region
All public bQTLs from MGI and RGD with a defined location that overlaps the current region are displayed in summary table that also links to the associated databases.
View genes controlled from the region
eQTLs are calculated for the recombinant inbred panels at the Gene level(Affy Exon Transcript Clusters having a core annotation)). This is used to return a list of genes that have a core transcript cluster and an eQTL that overlaps the region.
Translate a region of interest from Human/Mouse/Rat to Mouse/Rat to view PhenoGen data.
Try it out
Demos: View the video demo of our Detailed Transcription Information features, with more demos coming soon. View Demo
MEME Updated to v4.9: MEME v4.9 is now available. Old results are still avialable, but new analysis will use 4.9 which will also have better graphics display and will link to the main meme server for further analysis. Available in Gene List Analysis
Human Genotyping Data Available: Affymetrix Genome-Wide Human SNP Array 6.0 data for alcohol dependent subjects receiving outpatient treatment at the Medical University of Vienna (Austria). View in downloads
Detailed Transcription Information:
View Parental Strain Differential Expression
View Parental Strain(Rat) Transcriptome Reconstruction
View Panel Heritability/Detection Above Background accross tissues
View Panel Expression accross tissues
View Exon Correlation Tool
- Identify exons within a gene that are not expressed
- Identify exons within a gene with low heritability
- Use correlation patterns among exons to identify expressed isoforms.
View eQTL information
New Menu Navigation: The new Menu system allows users to easily get between functions that previously required clicking through multiple pages.
Download Resources without Logging in: Resources that used to require a login are now available without logging in.
Exon level analysis tools:Analyze probeset-level data for the public exon arrays.
Exon-exon correlation heatmaps: Perform exon-exon correlation within a gene:
- Select a gene (from a gene list or enter your own). and
- Select an exon dataset (from Rats or Mice).
- Select Brain(Mouse or Rat), Heart(Rat), Liver(Rat), or Brown Adipose tissues(Rat).
- View any Ensembl transcript for the gene, or compare two
transcripts side by side.
Download RNA-sequencing:SAM files from three replicates of polyA+
RNA from whole brain of two rat strains and three replicates of total RNA from whole
brain of the same two rat strains can now be downloaded in the Download Resources tab.
Data storage format:A new system for storing data in the database and HDF5 files speeds up normalization, filtering, and statistics. This is currently implemented
to support analysis on Affymetrix Exon arrays, but future updates will implement the new storage methods for the
remaining array types.