Table 2

Top gene sets by average rank

#

Set

Cat.

Sign

MSigDB

Description

Enriched GO BP Terms (adj. p-value)


1

GNF2_MKI67

C4

-1

Neighborhood of MKI67

"phosphoinositide-mediated signaling": 1.95 × 10-10, "spindle organization": 5.86 × 10-6, "establishment of mitotic spindle localization": 1.10 × 10-5, "kinetochore assembly": 5.48 × 10-5, "mitotic chromosome condensation": 1.37 × 10-4, "protein complex localization": 2.55 × 10-3, "regulation of striated muscle development": 2.55 × 10-3, "metaphase plate congression": 2.55 × 10-3

2

GNF2_CCNA2

C4

-1

Neighborhood of CCNA2

"phosphoinositide-mediated signaling": 4.05 × 10-16, "DNA replication": 1.04 × 10-9, "mitotic chromosome condensation": 1.32 × 10-8, "regulation of striated muscle development": 3.76 × 10-3, "metaphase plate congression": 3.76 × 10-3

3

GNF2_TTK

C4

-1

Neighborhood of TTK

"phosphoinositide-mediated signaling": < 2.22 × 10-16, "mitotic chromosome condensation": 4.35 × 10-14, "DNA replication": 1.01 × 10-12, "spindle organization": 1.37 × 10-9, "establishment of mitotic spindle localization": 9.59 × 10-5, "kinetochore assembly": 4.76 × 10-4, "DNA repair": 5.78 × 10-3, "mitosis": 9.44 × 10-3

4

GNF2_HMMR

C4

-1

Neighborhood of HMMR

"phosphoinositide-mediated signaling": < 2:22 × 10-16, "mitotic cell cycle spindle assembly checkpoint": 1.26 × 10-11, "spindle organization": 4.89 × 10-10, "mitotic chromosome condensation": 8.46 × 10-8, "cell proliferation": 6.22 × 10-6, "DNA replication": 1.09 × 10-5, "establishment of mitotic spindle localization": 5.33 × 10-5, "kinetochore assembly": 2.65 × 10-4, "protein complex localization": 8.29 × 10-3, "regulation of striated muscle development": 8.29 × 10-3, "metaphase plate congression": 8.29 × 10-3

5

GNF2_CDC20

C4

-1

Neighborhood of CDC20

"phosphoinositide-mediated signaling": < 2.22_10-16, "spindle organization": 2.20 × 10-12, "mitotic cell cycle spindle assembly checkpoint": 4.07 × 10-11, "mitotic chromosome condensation": 1.52 × 10-9, "cell proliferation": 8.96 × 10-9, "mitosis": 1.83 × 10-8, "establishment of mitotic spindle localization": 8.95 × 10-5, "kinetochore assembly": 4.45 × 10-4, "DNA replication": 7.83 × 10-3

6

GNF2_SMC2L1

C4

-1

Neighborhood of SMC2L1

"mitotic cell cycle spindle assembly checkpoint": 5.15 × 10-13, "mitotic chromosome condensation": 7.16 × 10-9, "phosphoinositide-mediated signaling": 2.14 × 10-6, "establishment of mitotic spindle localization": 1.31 × 10-5, "kinetochore assembly": 6.51 × 10-5, "protein complex localization": 2.90 × 10-3, "DNA strand elongation during DNA replication": 2.90 × 10-3, "regulation of striated muscle development": 2.90 × 10-3, "metaphase plate congression": 2.90 × 10-3, "cell proliferation": 2.94 × 10-3, "nucleotide-excision repair, DNA gap filling": 3.56 × 10-3

7

GNF2_H2AFX

C4

-1

Neighborhood of H2AFX

"cell proliferation": 9.28 × 10-10, "phosphoinositide-mediated signaling": 5.54 × 10-7, "mitosis": 8.48 × 10-5, "mitotic cell cycle spindle assembly checkpoint": 1.33 × 10-4, "protein complex localization": 1.63 × 10-3

8

GNF2_ESPL1

C4

-1

Neighborhood of ESPL1

"phosphoinositide-mediated signaling": 5.38 × 10-11, "kinetochore assembly": 3.12 × 10-5, "mitotic chromosome condensation": 6.75 × 10-5, "spindle organization": 7.76 × 10-4, "protein complex localization": 1.67 × 10-3, "regulation of striated muscle development": 1.67 × 10-3, "metaphase plate congression": 1.67 × 10-3

9

GNF2_RRM2

C4

-1

Neighborhood of RRM2

"phosphoinositide-mediated signaling": 4.52 × 10-15, "mitotic cell cycle spindle assembly checkpoint": 1.17 × 10-9, "spindle organization": 1.20 × 10-7, "DNA replication": 5.42 × 10-6, "cell proliferation": 1.97 × 10-5, "establishment of mitotic spindle localization": 4.09 × 10-5, "kinetochore assembly": 2.03 × 10-4, "protein complex localization": 6.80 × 10-3, "regulation of striated muscle development": 6.80 × 10-3, "metaphase plate congression": 6.80 × 10-3

10

GNF2_PCNA

C4

-1

Neighborhood of PCNA

"phosphoinositide-mediated signaling": < 2.22 × 10-16, "DNA replication": 1.47 × 10-15, "mitotic chromosome condensation": 2.36 × 10-7, "spindle organization": 4.33 × 10 -7, "establishment of mitotic spindle localization": 9.59 × 10-5, "cell proliferation": 4.18 × 10-4, "DNA repair": 4.33 × 10-4, "kinetochore assembly": 4.76 × 10-4, "mitosis": 9.44 × 10-3


Top 10 gene sets by average rank over the five datasets, using the set centroid statistic. GO enrichment p-values are from a Bonferroni-adjusted one-sided Fisher's exact test (30,330 tests). Sign = -1 if expression is negatively associated with long-term survival, and vice versa. The background list for the test includes all Affymetrix HG-U133A probesets that could be mapped to GO BP terms, excluding IEA annotations.

Abraham et al. BMC Bioinformatics 2010 11:277   doi:10.1186/1471-2105-11-277

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