This browser allows the user to search for a gene by the HUGO gene symbol and dynamically returns information about its expression. Gene expression data were generated by Lappalainen et al. for a subset of the 1000 Genomes Project population samples.
The Table tab of the Browser page displays a table containing gene expression information for the selected samples with links to repository samples. This table can be downloaded by the user by clicking the 'Download' button beneath the table. The Expression Histogram tab of the Browser page displays an interactive histogram of the gene expression data across the selected samples. Individual samples can be highlighted on the histogram by typing or selecting their sample ID in the dropdown. The About page contains information about data collection and processing. Please Note: We strongly recommend experimental validation to confirm any gene expression profiles that are critical for your research.
Preprocessed TPM and FPKM data were downloaded directly from EBI Expression Atlas and integrated into the application. Please see the experiment supplementary information for details about FPKM and TPM processing.
For CPM, RPKM, and VST normalized data, raw gene counts and annotation information were
downloaded from Array Express
for the E-GEUV-1 dataset. For more information about the generation of the raw count
data see the E-GEUV Array Express
page for details and links to the associated publications. Raw counts were summed
across biological replicates and then normalized using TMM normalization in
edgeR. CPM and RPKM
normalized values were generated using the cpm() and rpkm() functions in edgeR, respectively.
Gene length information required in the RPKM calculation was downloaded from GENCODE v12.
VST normalized data were calculated on the summed count matrix using the DESeq2 package.
All analysis scripts and source code is available on the Coriell Research GitHub page.