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Table 2 Functional modules for breast cancer (FDR ≤ 0.1)

From: GO-2D: identifying 2-dimensional cellular-localized functional modules in Gene Ontology

Dimension Biological Process Name (# of genes d in BP) Cellular Component Name (# of genes d in CC) # of genes d in 2D module Observed P Value
1Db nucleosome assembly (31)    8.33E-04
  learning and/or memory (7) --- --- 1.58E-03
2Dc nucleosome assembly (31) nucleosome (21) 20 6.19E-05
  nucleosome assembly (31) nucleus (1779) 31 8.33E-04
  learning and/or memory (7) cell part (4794) 5 4.78E-04
  oxygen and reactive oxygen species metabolism (36) extracellular region part (257) 5 4.78E-04
  lipid biosynthesis (108) mitochondrion (376) 10 4.99E-03
  complement activation (14) extracellular region (388) 11 6.68E-03
  transmembrane receptor protein tyrosine kinase signalling pathway (73) cytoplasmic part (1297) 11 6.68E-03
  G-protein coupled receptor protein signalling pathway (172) integral to plasma membrane (459) 61 7.07E-03
  1. 1Db: Functional modules based on biological process (one-dimensional modules).
  2. 2Dc: Cellular-localized functional modules (two-dimensional modules).
  3. # of genes d: the numbers of genes from the gene expression dataset (annotated in the original BP/CC categories or 2-dimensional modules)
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