Affymetrix human exon 1.0 st array

Expression profiles for the 3 genes, GSE89116, GSE109169, and GSE1390383, were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/), a public functional genomics data repository that supports MIAME-compliant data submissions. In the database, tools are provided to help users query and download experimental and curated gene expression profiles. GSE89116 was sequenced on the GPL6947 platform(Illumina HumanHT-12 V3.0 expression BeadChip) from 9 breast cancer and 24 normal breast tissues, GSE109169 was generated on the GPL5175 platform, (HuEx-1_0-st) Affymetrix Human Exon 1.0 ST Array [transcript (gene) version] from 25 breast cancer and 25 normal breast tissues, and GSE139038 was sequenced on the GPL27630 platform [Print_1437 (Block_Column_Row IDs)] from 41 breast cancer and 18 normal breast tissues.^{13 (link)}

Transcripts characterized by alternative splicing events at their 3′ end were detected by R scripting using Bioconductor 2.12 packages GenomicRanges, TxDb.Hsapiens.UCSC.hg19.knownGene and HuExExonProbesetLocation (www.bioconductor.org). Transcripts were extracted from TxDb.Hsapiens.UCSC.hg19.knownGene (80922 transcripts). After removal of transcripts lacking a link to Entrez Gene Identifier (20 (link)), 71 350 transcripts (26 5661 exons), associated to 22 932 EG, were left for further analysis. Subsequently, we selected all genes associated to the presence of alternative splicing even at the 3′ end (12 839 genes, 58 451 transcripts, 26 608 exons involved in ALE). Affymetrix Human Exon 1.0 ST Array (HuEx-1_0-st) exon-level probe sets chromosomal locations were extracted from HuExExonProbesetLocation (21 ). Only exon-level probesets associated to the Affymetrix core annotation were considered (284805 exon-level probesets). These exon-level probesets mapped on 12839 genes (59 986 UCSC transcripts, 230 112 exons). Out of the 230 112 exons 22 983 were associated to ALE. Alternatively spliced exon-level probesets were retrieved by Lenzken et al. (16 (link)). Four hyndred six exon-level probesets mapping on 418 exons were associated to 262 genes (1191 UCSC transcripts, 4844 exons). Within the 418 exons 89 exons (78 UCSC genes) were involved in ALE.

Expression data of prostate cancer biopsies were obtained as quantile-normalized values from the publication by Brase et al.^{24 (link)} GEO database (NCBI, GEO, GSE29079). For the determination of BRD4 expression levels, we used the core probe set of the Affymetrix human exon 1.0 ST array (Affymetrix, Santa Clara, CA, USA). The BRD4 core probes are located at the very C-terminus of the long BRD4 isoform.