In order to make distinction precisely at the transcript level, we preserved the classical Affymetrix probesets, but distinguished them among their alternatively spliced transcript targets according to the consistent alignments of probes against up-to-date mRNA sequences. Our annotation table clearly divides the Affymetrix probesets into three groups with increased transcript-level specificity (reliability): one-to-null probesets that do not recognize any transcript, one-to-many probesets that hybridize to multiple alternative transcript variants of the intended gene, and one-to-one probesets that hybridize to unique alternative transcript variants of the intended gene. We IPI1  IPI2  Gene1  Gene2  PPI-significant datasets  GGI-significant datasets   IPI00003326  IPI00015161  ARL2  PDE6D  15  7  IPI00003894  IPI00019930  RNF11  UBE2D1  17  1  IPI00007411  IPI00021831  AKAP11  PRKAR1A  15  2  IPI00008529  IPI00008527  RPLP2  RPLP1  25  5  IPI00011118  IPI00026689  RRM2  CDC2  17  16  IPI00013871  IPI00011118  RRM1  RRM2  14  10  IPI00015952  IPI00029012  EIF4G2  EIF3S10  14  3  IPI00016910  IPI00290460  EIF3S8  EIF3S4  16  10  IPI00018350  IPI00184330  MCM5  MCM2  16  15  IPI00021700  IPI00026689  PCNA  CDC2  14  13  IPI00022865  IPI00026689  CCNA2  CDC2  16  15  IPI00026689  IPI00015105  CDC2  CKS2  15  13  IPI00027462  IPI00007047  S100A9  S100A8  23  17  IPI00028266  IPI00026689  CCNB2  CDC2  17  15  IPI00165506  IPI00025616  POLDIP2  POLD2  14  2  IPI00246058  IPI00025277  PDCD6IP  PDCD6  16  1  IPI00290461  IPI00029012  EIF3S1  EIF3S10  15  4  IPI00291006  IPI00018206  MDH2  GOT2  16  11  IPI00294696  IPI00026689  CCNB1  CDC2  17  14  IPI00306708  IPI00026689  PBK  CDC2  16  14  IPI00328118  IPI00026689  SPAG5  CDC2  15  10  IPI00604664  IPI00291006  NDUFS1  MDH2  18  10  IPI00647217  IPI00552920  SKIV2L2  EXOSC8  18  2 A PPI-significant dataset is a dataset where the false discovery rate of the PCC value for the PPI pair is less than 0.1, while a GGI-significant dataset is a dataset where the false discovery rate of the PCC value for the GGI pair is less than 0.1. Only PPI pairs with more than 14 'PPI-significant datasets' datasets are shown. The full table is provided in Additional file 4.