After you get transcription details for a gene identifier, you can:
Parental expression values from Affymetrix exon arrays are derived from normalized expression data from the Affymetrix arrays using RMA and all probe sets available after masking, regardless of annotation level (see Public Data Sets). For the mouse data, the parental strains of the ILSXISS recombinant inbred panel that are used for the remaining analyses are the ILS and ISS strains. For the rat data, the parental strains of the HXB/BXH recombinant inbred panel are the BN-Lx/CubPrin and the SHR/OlaPrin. For the ILS and ISS strains, six animals per strain are included and for the BN-Lx and SHR strains, three to four animals per strain are included, depending on the tissue. The log base 2 difference in means is calculated so that a positive value indicates higher expression in the ILS (or SHR for rat) strain.
Heritability was calculated on the probe set level for all probe sets, regardless of annotation level. See "Heritability Filter" for Affymetrix for details on heritability calculations.
All panel expression values are extracted from the public data set of the RI panel on the Affymetrix exon array that is normalized using RMA and summarized into probe sets (full annotation). See Public Data Sets for more detail.
The Panel Exon Correlation can also be viewed on the Exon Correlation tab for a gene list. See "Viewing Exon-level Correlations" for details.
Expression quantitative trait loci (eQTL) were calculated for transcript clusters associated with Ensembl genes for the mouse RI panel and the rat RI panel and for each tissue separately.P-values were calculated for each transcript cluster and SNP combination using strain means of the recombinant inbred panels and the SNP data sets. Locus-specific p-values were calculated using permutation (10,000 permutations) and converted into negative log base 10 values.
The Circos Plot highlights locations in the genome with p-values below the selected threshold. These locations are connected to the physical location of the selected transcript with a curved line, color-coded to indicate the tissue type.
You can run the Circos Plot again at this time, with additional choices. A subset of chromosomes can be selected to expand the plot in areas of interest. For rats, the tissues can be narrowed to include only one, two, or three selected tissues.
to download the plot as a PDF.
Take a look
