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Table 1 GO category enrichment

From: Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers

  BP - overrepresented BP - underrepresented CC - overrepresented
eDEV500 DNA replication
Cell cycle
RNA splicing
DNA repair
Chromatin modification 		Multicellular organismal process
Cell communication
Signal transduction
System development
Ion transport 		Intracellular
Nuclear part
Membrane-bound organelle
Spliceosome
Ribonucleoprotein complex
lDEV500 Immune response
Antigen processing and presentation
Cytokine and chemokine mediated signaling pathway
Cell adhesion
Multicellular organismal process 		Biopolymer metabolic process
Biosynthetic process
RNA processing
Cell cycle phase
DNA repair 		Membrane
Extracellular region
MHC protein complex
Lysosome
Secretory granule
Group 1 (16)    
   Up DNA repair (15)
Cell cycle (15)
RNA splicing (13) 		Multicellular organismal process (16)
G-protein coupled receptor protein signaling pathway (16)
Neurological process (16) 		Intracellular (16)
Organelle (15)
Nuclear part (15)
   Down Multicellular organismal process (15)
Organ development (14)
Cell communication (11) 		Primary metabolic process (14)
RNA processing (14)
DNA metabolic process (14) 		Plasma membrane (16)
Extracellular region (13)
Voltage-gated potassium channel complex (8)
Group 2 (6)    
   Up Cell cycle (6)
DNA replication (6)
Response to DNA damage stimulus (6) 		Multicellular organismal development (5)
Anatomical structure development (5)
System development (4) 		Chromosome (6)
Protein complex (5)
Replication fork (5)
   Down Monovalent inorganic cation transport (5)
ATP synthesis coupled proton transport (5)
Oxidative phosphorylation (4) 		DNA recombination (6)
Immune response (5)
Macromolecule metabolic process (5) 		Proton-transporting two-sector ATPase complex (5)
Membrane (5)
Extracellular matrix (3)
Group 3 (13)    
   Up Immune response (10)
Multicellular organismal process (8)
Cell adhesion (6)
Response to wounding (5) 		Cellular metabolic process (10)
Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (9)
RNA metabolic process (8) 		Plasma membrane (10)
Extracellular region (10)
Lysosome (5)
   Down Cellular metabolic process (10)
Protein metabolic process (6)
RNA processing (5) 		Multicellular organismal process (10)
Immune response (10)
Cell activation (8) 		Cytoplasm (10)
Intracellular (8)
Organelle (8)
PEN versus ESEN    
   Up DNA replication
Cell cycle phase
DNA metabolic process 		Biosynthetic process
Generation of precursor metabolites and energy
Translation 		Chromosome
Replication fork
Microtubule cytoskeleton
   Down Lipid metabolic process
Lipid biosynthetic process
Cofactor metabolic process 		Macromolecule metabolic process
Intracellular signaling cascade
M phase of mitotic cell cycle 		Desmosome
Membrane fraction
Microsome
  1. Next to the most significant GO categories for eDEV500, lDEV500 and PEN versus ESEN, the GO categories that are most frequently enriched in the up- and downregulated genes of group 1, 2 and 3 data sets are listed with the number of occurrences in parentheses. BP, biological process; CC, cellular component. For example, DNA repair is enriched in the upregulated genes of 15 out of 16 data sets belonging to group 1.
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