Systematic evaluation of isoform function in literature reports of alternative splicing

BMC Genomics

Table 2 Genes with FDSIs identified

	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

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

ISSN: 1471-2164