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Table 2 Functional classes of genes enriched in the RGP library in comparison to the frequency within the whole set of predicted human genes

From: Suppression subtractive hybridization profiles of radial growth phase and metastatic melanoma cell lines reveal novel potential targets

Functional Class (biological process)

Genes

Relative enrichment significance

establishment of cellular localization

AP1G1, DYNC1I2, COPZ1, NUP160, KIF5B, RANBP5, PAFAH1B1, FLJ10292, C14orf108, RAN, SET, SGNE1, SSR1, SSR2, BAT1, SEC24C

O = 16a; E = 8.04b; R = 1.99c P = 0.0067d

nucleocytoplasmic transport

NUP160, RANBP5, FLJ10292, RAN, SET, BAT1

O = 6; E = 1.61; R = 3.73; P = 0.0054

organelle organization and biogenesis

ARPC3, DCTN6, MYST2, DDX1, DYNC1I2, XRN2, KIFAP3, DAAM1, POT1, H3F3A, HDAC1, HMGB2, KIF5B, STMN1, PAFAH1B1, ATRX, KLHL4, PXMP3, RAN, SET, SMYD3, WASPIP, ACTL6A, H2AFV,

O = 24; E = 10.92; R = 2.2; P = 0.00022

chromosome organization and biogenesis

MYST2, POT1, H3F3A, HDAC1, HMGB2, ATRX, SET, SMYD3, ACTL6A, H2AFV

O = 10; E = 4.05; R = 2.47; P = 0.0076

microtubule-based process

DYNC1I2, XRN2, KIFAP3, KIF5B, STMN1, PAFAH1B1, RAN

O = 7; E = 2.13; R = 3.29; P = 0.0056

nucleobase biosynthesis

PAICS, PPAT

O = 2; E = 0.12; R = 16.67; P = 0.0064

regulation of protein biosynthesis

DDX1, EIF4B, EIF4G2, PUM2, TLR3, EIF4E2

O = 6; E = 1.66; R = 3.61; P = 0.0064

DNA metabolism

POLD3, MYST2, XRN2, POT1, H3F3A, HDAC1, HMGB2, NONO, ORC2L, ATRX, RAD23B, RAN, SET, SMYD3, UBE2A, XRCC5, HAT1, ACTL6A, H2AFV

O = 19; E = 8.44; R = 2.25; P = 0.00078

DNA packaging

MYST2, H3F3A, HDAC1, HMGB2, SET, SMYD3, HAT1, ACTL6A, H2AFV

O = 9; E = 3.42; R = 2.63; P = 0.0074

DNA repair

POLD3, XRN2, HMGB2, NONO, ATRX, RAD23B, UBE2A, XRCC5

O = 8; E = 2.91; R = 2.75; P = 0.0088

response to DNA damage stimulus

POLD3, XRN2, HMGB2, NONO, ZAK, ATRX, RAD23B, UBE2A, XRCC5

O = 9; E = 3.24; R = 2.78; P = 0.0053

RNA metabolism

SYNCRIP, DDX17, SF3A3, DDX1, DCP2, ELAVL1, XRN2, SF3B1, LSM5, HNRPC, HNRPU, NONO, FLJ10292, RARSL, SNRPG, BAT1, TTF2, SIP1, DDX23

O = 19; E = 5.8; R = 3.28; P = 5.44-06

RNA processing

SYNCRIP, DDX17, SF3A3, DDX1, XRN2, SF3B1, LSM5, HNRPC, HNRPU, NONO, FLJ10292, SNRPG, BAT1, TTF2, SIP1, DDX23

O = 16; E = 4.68; R = 3.42; P = 1.84374398023E-05

RNA splicing

SYNCRIP, SF3A3, DDX1, SF3B1, LSM5, HNRPC, NONO, FLJ10292, SNRPG, BAT1, TTF2, SIP1, DDX23

O = 13; E = 2.01; R = 6.47; P = 1.03E-07

RNA localization

NUP160, FLJ10292, RAN, BAT1

O = 4; E = 0.64; R = 6.25; P = 0.0037

macromolecule catabolism

YME1L1, DDX1, DCP2, ELAVL1, XRN2, USP33, ARIH1, MDH1, PSMA4, PSMA5, PSMB4, PSMB6, UBE2A, USP8

O = 14; E = 4.57; R = 3.06 P = 0.00019

  1. a: observed number of genes in the category; b: expected number of genes in the category; c: observed/expected ratio; d: p-value of the enrichment significance