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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