Continuing to roll out Bgee release 13 (see first installment), we now provide pre-computed files of differential gene expression. As for present / absent calls, files are organized per species, and come in “simple” and “complete” versions.
A test of differential expression is made when one experiment has several conditions, with replicates for each condition. We separate comparisons of different tissues in the same developmental stage (“anatomy”) from comparisons of the same tissue at different life history stages (“development” – this includes aging). For each gene and condition, a gene can be called “over-expressed”, if it is more expressed than in the average of conditions, “under-expressed”, if it is less expressed than in the average of conditions, or “no diff expression” otherwise. The test is a modified ANOVA.
A same gene in a same condition can be called from several experiments. These may use the same or different platforms (RNA-seq or microarray), and compare the same or different conditions (different combinations of tissue and stage). For a given technique, we resolve conflicts (e.g., the same gene called over- and under-expressed in liver in different experiments) based on a voting system weighted by p-values. Importantly, whenever this is a conflict, the summary call that we provide is noted “low quality”.High quality calls are those with no conflict and p<0.01. We provide summary calls from different experimental types separately in the “complete” file, while we provide one overall summary call per gene-condition combination in the “simple” file. In the latter case, conflicts between different techniques a summarized by an “ambiguity” call.
Overall, we provide 10 299 406 calls for 11 species: C. elegans, chicken, cow, fruitfly, human, macaque, mouse, platypus, rat, xenopus and zebrafish.
In the only species for which we have both abundant RNA-seq and microarray data, mouse, we find that 88% of gene-condition combinations have no conflict between calls from the two techniques. Considering differences in sampling and techniques, this is quite satisfying.
Come and try: http://bgee.org/?page=download