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Table 1 Differentially spliced genes in colon cancer detected by the exon microarray and confirmed by PCR.

From: Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

Gene F1 R1 Known AS Event2 Confidence3 Preferential Inclusion of Splice Variants4 FC5
ACTN1 Ex18 Ex20 19a/19b are MEEs Good Ex19a in Tumor, 19b in Normal -1.05
ATP2B4 Ex20 Ex22 Ex21 is CE Good Ex21 in Normal +1.53
VCL Ex18 Ex20 Ex19 is CE Good Ex19 in Normal +1.22
CALD1 Ex5 Ex7 extended Ex5; Ex6 is CE Good extended Ex5 + Ex6 in Normal; Ex6 in Normal +1.36
SLC3A2 Ex1 Ex5 Ex2, 3, 4 are CEs Good Normal skips all exons -1.90
COL6A3 Ex2 Ex5 Ex3 and Ex4 are CEs Good Ex3 or Ex4 in Tumor -1.56
COL6A3 Ex5 Ex7 Ex6 is CE Good Ex6 in Tumor -1.56
CTTN Ex10 Ex14 Ex11 is CE Good Ex11 in Tumor -1.21
FN1 Ex24 Ex26 Ex25 is CE Good Ex 25 in Normal -1.86
TPM1 Ex6 Ex6 Ex7 Ex8 Ex7/Ex8 are usually MEEs Good Ex7 in Tumor; Ex8 in Normal +1.92
GK Ex19 Ex21 Ex20 is CE Mod. Ex20 in Tumor -1.01
MAST2 Ex7 Ex5 Ex9 Ex9 Ex7 alt. start? Mod. Ex7 Alt. Start in Normal +1.26
LGR5 Ex10 Ex11b Ex12 Ex12 extended Ex11; Ex11b is CE Weak extended Ex11 + Ex11b in Tumor -12.1
ZAK Ex11 Ex11b Ex11 Alt. 3' end Weak Alt. 3' end (Ex11b) in Normal -1.07
ZAK Ex16 Ex18 Ex17 appears constitutive Weak different 3' end of gene -1.07
FXYD6 Ex1 Ex4 Ex2 and Ex3 are rare CEs Very Weak Ex2 + Ex3 in Tumor +2.50
  1. 1 Exon locations of the F (forward) and R (reverse) PCR primers. 2 Known Alternative Splicing Event As determined from RefSeq, full length mRNAs and ESTs on the UCSC Genome Browser. 3 Relative confidence in the interpretation. 4 Interpretation of the PCR results in terms of transcript structure. 5 Fold change at the gene level. (-) means that the signal is lower in Tumor. Abbreviations: Ex, exon; CE, cassette exon; MEE, mutually exclusive exon; Alt., alternative.