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Table 2 Genes with FDSIs identified

From: Systematic evaluation of isoform function in literature reports of alternative splicing

  Gene Number of FDSIs Number of Ensembl Transcripts Number of Studies Mappable to Ensembl? PULSE Gene Number of FDSIs Number of Ensembl Transcripts Number of Studies Mappable to Ensembl? PULSE
Human AR 3 9 31 Yes NA BCAR1 3 17 1 No Missed
BDNF 3 19 12 No NA BIRC5 3 11 34 Yes NA
BOK 2 2 1 No Missed CD44 2 39 58 Yes Predicted
CFLAR 2 25 6 Yes Predicted CSPP1 2 7 1 Yes NA
DPF3 2 16 2 Yes NA EIF4G1 2 38 6 No NA
EIF4G2 3 32 3 No NA HBS1L 2 14 1 Yes Predicted
KLF6 2 7 16 No Missed MADD 2 23 2 Yes Predicted
MST1R 2 15 11 Yes Predicted PML 2 22 12 Yes Predicted
PGAM5 2 4 1 Yes Missed PRMT5 2 20 4 Yes Missed
STIM2 2 12 2 No NA SUN1 2 35 2 No NA
TICAM1 2 2 1 No NA TICAM2 2 2 1 No NA
TP63 2 14 27 Yes NA       
Mouse Cacna1b 2 10 2 No Missed Calca 2 7 10 Yes NA
Cdc42 2 2 8 Yes NA Enc1 2 1 3 No NA
Homer1 2 12 7 Yes NA Il1rap 2 7 4 Yes Training
Lpin1 2 8 5 No Missed Lrp8 2 12 13 No Predicted
Mecp2 2 6 9 Yes Missed Myh10 2 10 7 No Predicted
Nf1 2 9 5 Yes Missed Opn4 2 3 2 Yes NA
Oprm1 3 31 20 Yes Predicted Rbfox1 2 2 22 No Predicted
Robo3 2 6 5 Yes Missed Rock2 2 12 4 No Missed
Ryr3 2 12 5 No NA Sirt3 2 10 3 No Missed
Snap25 2 3 12 Yes NA Tp63 2 8 9 Yes NA
  1. Studies have provided positive evidence of functional distinctness for these genes in experiments where individual splice isoforms were eliminated and a phenotypic change was observed. See Additional file 3 for study demonstrating functional distinctness. “Number of FDSIs” indicates the number of splice isoforms where depletion of splice isoforms causes a phenotype. “Number of Ensembl Transcripts” indicates number of transcripts found in Ensembl entry for gene. “Number of studies” indicates the number of studies associated with the gene retrieved with the term “alternative splicing” on PubMed. The highest number of FDSIs found in a single gene is three. “Mappable to Ensembl” indicates genes where we successfully linked all FDSIs back to Ensembl. “PULSE” indicates whether the gene was used at all by Hao and colleagues in their computational predictions. “Training” in this column means that the gene was used as part of PULSE’s training set. “Predicted” means that PULSE predicted that the gene has multiple functional splice isoforms. “Missed” means that PULSE failed to predict that the gene has multiple functional splice isoforms. “NA” means that the gene was not an input for PULSE