Table 1.

Validation of AS predictions

PCR validation in cell line panelIllumina validation in MCF7/BT549
RankGeneSpecificityAS typeNo. of PSPCRAffy_callIllu_call
117TJP1cancerCassette exon3AS02
34DST-1cancerAlt start3No AS00
43, 1223*PLEC1cancerAlt start2AS12
146DST-2cancerAlt stop3AS31
107FAM62BCLCassette exon4AS44
58FATCLCassette exon3Weak AS30
135FER1L3CL, LUMCassette exon3AS32
1FLNBCLCassette exon4AS43
6MYO6LUM, BATandem cassette exons6AS31
35SLKCL, cancerCassette exon3AS33
40CLTCCLNovel alt exon2No AS20
170UTRNNVNovel alt exon4No AS40

Abbreviation: NV, not validated.

NOTE: Left columns show the result of assessing AS in a panel of 48 cell lines using RT-PCR. Rank is based on the ordered NSI score data across all probe sets on the HJAY array. Specificity refers to the subgroup in which aberrant splicing (compared with the reference) is most frequent. The ratio of alternative isoforms in the nonmalignant mammary gland cell lines were taken as a reference. The AS type column refers to the type of ASE being tested. Right columns show the result of assessing AS in the cell lines MCF7 (luminal) and BT549 (claudin-low) using Illumina sequencing. The No. of PS column shows the number of probe sets in microarray and sequencing data describing the same ASE validated using RT-PCR. The last three columns summarize RT-PCR, microarray, and sequencing data on AS between two cell lines—MCF7 and BT549. For microarray and Illumina platforms, the number of probe sets exhibiting differential signal between the two cell lines is shown.