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