Through the rigorous association and alignment, we obtained precise annotations for 18,894 and 15,288 probesets in Affymetrix arrays MOE430A_2 and HG-U133A respectively (see Additional file 1). These annotations discriminate alternative mRNA variants transcribed from a same gene, thus are at transcript level as opposed to the standard gene-level annotation files provided by Affymetrix. It is worth noting that since the transcript data we used were quite redundant, a conceptual transcript variant may be represented by multiple redundant transcript accessions in the transcript database. In our transcriptlevel annotation file, each conceptual transcript is identified with one IPI ID, as we only investigated the probesets associated with protein-coding transcripts.