Table 1

GO category enrichment

BP - overrepresented

BP - underrepresented

CC - overrepresented


DNA replication

Cell cycle

RNA splicing

DNA repair

Chromatin modification

Multicellular organismal process

Cell communication

Signal transduction

System development

Ion transport


Nuclear part

Membrane-bound organelle


Ribonucleoprotein complex


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


Extracellular region

MHC protein complex


Secretory granule

Group 1 (16)


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)


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)


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)


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)


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)


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


DNA replication

Cell cycle phase

DNA metabolic process

Biosynthetic process

Generation of precursor metabolites and energy



Replication fork

Microtubule cytoskeleton


Lipid metabolic process

Lipid biosynthetic process

Cofactor metabolic process

Macromolecule metabolic process

Intracellular signaling cascade

M phase of mitotic cell cycle


Membrane fraction


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.

Naxerova et al. Genome Biology 2008 9:R108   doi:10.1186/gb-2008-9-7-r108

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