Table 2

Top 36 multi-exon genes that have significant alternative exon usage associated with glioblastoma multiforme survival
Gene Symbol Estimate1 SE2 P-value AEU3 Fold change4 Exon Count5 Literature6
Ttn 0.0007 0.0001 4.2E-38 0.9993 340 [28]G
Smg1 0.0017 0.0002 2.0E-24 1.0001 209 [29]AS
Neb 0.0007 0.0001 3.2E-21 0.9973 180 [30,31]C, AS
Pkd1 0.0010 0.0001 2.0E-19 1.0018 163 [32]G, AS
Herc2p2 0.0008 0.0001 2.3E-19 1.0012 163 NA
Syne1 0.0018 0.0002 3.0E-18 0.9984 152 [9]G
Snrpn 0.0018 0.0002 3.8E-18 1.0020 151 [33,34]G, AS
Pde4dip 0.0016 0.0002 1.3E-17 0.9993 146 [35,36]G, AS
Golga8c 0.0031 0.0004 4.2E-17 1.0005 141 NA
Sspo 0.0009 0.0001 1.2E-16 1.0003 137 NA
Ankrd36 0.0026 0.0003 1.3E-16 1.0018 137 NA
Tbc1d3 0.0008 0.0001 2.4E-16 1.0026 135 [37]C
Flj45340 0.0018 0.0002 5.5E-16 1.0007 131 NA
Anapc1 0.0009 0.0001 5.8E-15 0.9990 122 [38,39]C, AS
Syne2 0.0012 0.0002 6.2E-15 1.0017 115 [40]C, AS
Nbpf10 0.0035 0.0005 1.3E-14 0.9992 118 [41]C, AS
Muc19 0.0015 0.0002 1.4E-14 1.0001 118 [42]C, AS
Obscn 0.0006 0.0001 1.5E-14 0.9999 118 [28,43]G, AS
Npipl3 0.0019 0.0003 4.1E-14 1.0014 114 NA
Dst 0.0013 0.0002 9.4E-14 0.9997 111 [44,45]G, AS
Col7a1 0.0011 0.0001 1.4E-13 1.0001 109 [46,47]C, AS
Ubr4 0.0011 0.0001 1.4E-13 0.9994 109 [48,49]C, AS
Hmcn1 0.0006 0.0001 2.0E-13 0.9975 109 [50]C, AS
Ryr2 0.0011 0.0001 2.7E-13 0.9974 107 [51,52]G, AS
Macf1 0.0011 0.0002 3.1E-13 0.9975 106 [53,54]G, AS
Mdn1 0.0006 0.0001 3.5E-13 0.9993 106 NA
Col4a5 0.0008 0.0001 3.5E-13 0.9992 106 [55,56]C, AS
Ryr1 0.0007 0.0001 4.2E-13 0.9998 105 [31,57,58]G, AS
Golga6l5 0.0013 0.0002 5.2E-13 1.0021 104 NA
Ryr3 0.0009 0.0001 1.3E-12 0.9962 102 [59]C, AS
Dnah14 0.0007 0.0001 2.0E-12 0.9990 99 NA
Herc2 0.0006 0.0001 3.1E-12 1.0003 97 [60]AS
Dnah8 0.0005 0.0001 4.7E-12 0.9997 96 NA
Nomo1 0.0007 0.0001 4.9E-12 0.9996 95 NA
Gpr98 0.0016 0.0002 5.9E-12 0.9948 95 [61]C, AS
Golga6a 0.0017 0.0002 7.8E-12 1.0009 93 NA

1Estimate: exon-survival interaction variance indicator of alternative exon usage.

2SE: standard error of the estimate.

3P-value AEU: unadjusted P-value of alternative exon usage or exon-dependent association between expression and glioblastoma multiforme survival.

4Fold change: fold change in average exon expression per additional survival month.

5Exon Count: number of exons in the gene.

6Literature: review of studies that reported associations of the gene with cancers:

G: reported association of gene with glioblastoma multiforme,

C: reported association of gene with cancer other than glioblastoma multiforme,

AS: identification of different variants due to alternative splicing (AS) event,

NA: not available.

Sadeque et al.

Sadeque et al. BMC Medical Genomics 2012 5:59   doi:10.1186/1755-8794-5-59

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