Table 1

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

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 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.

Gardina et al. BMC Genomics 2006 7:325   doi:10.1186/1471-2164-7-325

Open Data