Annotation clustera | Enrichment scoreb | Biological termsc |
---|---|---|
1 | 2.56 | Membrane fraction (12), cell fraction (14), insoluble fraction (12) |
2 | 1.04 | Endoplasmic reticulum part (6), endoplasmic reticulum membrane (5), endoplasmic reticulum (10), nuclear envelope-endoplasmic reticulum network (5), microsome (4), vesicular fraction (4), organelle membrane (9), endomembrane system (6) |
3 | 0.88 | Blood vessel morphogenesis (4), blood vessel development (4), vasculature development (4) |
4 | 0.86 | Cellular macromolecule catabolic process (9), proteolysis (11), macromolecule catabolic process (9), proteolysis involved in cellular protein catabolic process (7), cellular protein catabolic process (7), protein catabolic process (7), ubiquitin- protein ligase activity (3), small conjugating protein ligase activity (3), ligase activity, forming carbon-nitrogen bonds (3), ubiquitin-dependent protein catabolic process (3), modification-dependent macromolecule catabolic process (6), acid- amino acid ligase activity (3), modification-dependent protein catabolic process (6) |
5 | 0.80 | Intracellular organelle lumen (14), organelle lumen (14), nuclear lumen (10), membrane-enclosed lumen (14), nucleoplasm (8) |
6 | 0.72 | Proteolysis (11), metalloendopeptidase activity (3), endopeptidase activity (5), negative regulation of apoptosis (5), negative regulation of programmed cell death(5), negative regulation of cell death (5), metallopeptidase activity (3), peptidase activity, acting on L-amino acid peptides (5), peptidase activity (5), regulation of apoptosis (6), regulation of programmed cell death (6), regulation of cell death (6) |
7 | 0.72 | Phosphatase activity (5), phosphoprotein phosphatase activity (4), phosphate metabolic process (9), dephosphorylation (4), phosphorus metabolic process (9), protein amino acid dephosphorylation (3), protein serine/threonine kinase activity(3), phosphorylation (5), protein amino acid phosphorylation (5), protein kinase activity (3) |
8 | 0.71 | Positive regulation of multicellular organismal process (4), positive regulation of cell proliferation (5), regulation of growth (4) |
9 | 0.65 | Cell cycle (8), mitotic cell cycle (5), cell cycle process (5), cell cycle phase (4) |
10 | 0.65 | Glycosaminoglycan binding (3), polysaccharide binding (3), pattern binding (3), carbohydrate binding (3) |
a Top ten of annotation clusters identified by official gene symbols of up-regulated gene list on D12 of pregnancy compared with those on D12 of the estrous cycle through DAVID.
b Enrichment score represents significance of each cluster annotation and the relatedness of the terms and the genes associated with terms. Enrichment score is calculated by overall EASE scores (the modified Fisher extract p value) of each term member.
c The gene ontology (GO) terms are group of terms having similar biological meaning with respect to biological process, cellular component, and molecular function. GO functional annotation term (FAT) was used for the analysis because GO term cannot universally define the specificity of a given term. The number in parenthesis indicate the number of differentially expressed genes contribute to the clustered term.
Annotation clustera | Enrichment scoreb | Biological termsc |
---|---|---|
1 | 2.04 | Plasma membrane part (22), integral to plasma membrane (11), intrinsic to plasma membrane (11) |
2 | 2.03 | Cell adhesion (11), biological adhesion (11), cell-cell adhesion (4) |
3 | 1.50 | Leukocyte activation (7), cell activation (7), lymphocyte activation (6), T cell activation (4), immune effector process (4), regulation of leukocyte activation (4), regulation of cell activation (4), leukocyte mediated immunity (3), cell surface (5), positive regulation of response to stimulus (4), positive regulation of immune system process (4), immune response (7), external side of plasma membrane (3) |
4 | 1.48 | Immune system development (7), hemopoiesis (6), hemopoietic or lymphoid organ development (6), myeloid cell differentiation (3), protein homodimerization activity (4), nucleoplasm part (3) |
5 | 1.46 | Cell junction (7), adherens junction (4), anchoring junction 4) |
6 | 1.45 | Biopolymer glycosylation (4), glycoprotein biosynthetic process (4), glycoprotein metabolic process (4), glycosylation (4), protein amino acid glycosylation (4) |
7 | 0.98 | Apoptosis (7), programmed cell death (7), cell death (7), death (7), negative regulation of cell proliferation (4) |
8 | 0.83 | DNA metabolic process (8), response to DNA damage stimulus (5), DNA repair (4), cellular response to stress (5), DNA binding (7) |
9 | 0.83 | Induction of apoptosis (5), induction of programmed cell death (5), positive regulation of apoptosis (5), positive regulation of programmed cell death (5), positive regulation of cell death (5), regulation of apoptosis (7), regulation of programmed cell death (7), regulation of cell death (7) |
10 | 0.76 | Response to ionizing radiation (3), response to radiation (3), response to abiotic stimulus (3) |
a Top ten of annotation clusters identified by official gene symbols of up-regulated gene list on D15 of pregnancy compared with those on D15 of the estrous cycle.
b Enrichment score represents significance of each cluster annotation and the relatedness of the terms and the genes associated with terms. Enrichment score is calculated by overall EASE scores (the modified Fisher extract p value) of each term member.
c The gene ontology (GO) terms are group of terms having similar biological meaning with respect to biological process, cellular component, and molecular function. GO functional annotation term (FAT) was used for the analysis because GO term cannot universally define the specificity of a given term. The number in parenthesis indicate the number of differentially expressed genes contribute to the clustered term.
Annotation clustera | Enrichment scoreb | Biological termsc |
---|---|---|
1 | 3.46 | Nuclear speck (7), nuclear body (8), RNA splicing (9) |
2 | 2.21 | Nucleotide binding (30), purine ribonucleotide binding (25), AT P binding (21), ribonucleotide binding (25), purine nucleotide binding (25), adenyl ribonucleotide binding (21), adenyl nucleotide binding (21), purine nucleoside binding (21), nucleoside binding (21) |
3 | 2.12 | Nuclear body (8), nucleoplasm part (12), nucleoplasm (15), membrane-enclosed lumen (24), nuclear lumen (20), intracellular organelle lumen (23), organelle lumen (23), nucleolus (9) |
4 | 1.51 | RNA splicing (9), mrna metabolic process (9), RNA processing (11), mrna processing (8), spliceosome assembly (3), RNA splicing, via transesterification reactions (5), RNA splicing, via transesterification reactions with bulged adenosine as nucleophile (5), nuclear mrna splicing, via spliceosome (5), RNA binding (11), ribonucleoprotein complex assembly (3), ribonucleoprotein complex biogenesis (4), cellular macromolecular complex assembly (5), cellular macromolecular complex subunit organization (5) |
5 | 1.15 | Nuclear body (8), nuclear export (4), nucleocytoplasmic transport (4), nuclear transport (4), mrna transport (3), establishment of RNA localization (3), nucleic acid transport (3), RNA transport (3), RNA localization (3), nucleobase, nucleoside, nucleotide and nucleic acid transport (3), intracellular transport (8) |
6 | 1.06 | Receptor-mediated endocytosis (4), membrane organization (8), membrane invagination (4), endocytosis (4), vesicle-mediated transport (6) |
7 | 0.96 | Helicase activity (6), ATP-dependent helicase activity (3), purine NTP-dependent helicase activity (3), atpase activity, coupled (4), atpase activity (4) |
8 | 0.95 | Enzyme binding (8), protein kinase binding (4), kinase binding(4) |
9 | 0.94 | Macromolecular complex assembly (11), macromolecular complex subunit organization (11), protein complex assembly (8), protein complex biogenesis (8), cellular macromolecular complex assembly (5), cellular macromolecular complex subunit organization (5), protein oligomerization (3) |
10 | 0.75 | Protein serine/threonine kinase activity (7), enzyme linked receptor protein signaling pathway (6), phosphate metabolic process (11), phosphorus metabolic process (11), protein kinase activity (8), protein amino acid phosphorylation (8), phosphorylation (9) |
a Top ten of annotation clusters identified by official gene symbols of up-regulated gene list on D12 of pregnancy compared with those on D12 of the estrous cycle.
b Enrichment score represents significance of each cluster annotation and the relatedness of the terms and the genes associated with terms. Enrichment score is calculated by overall EASE scores (the modified Fisher extract p value) of each term member.
c The gene ontology (GO) terms are group of terms having similar biological meaning with respect to biological process, cellular component, and molecular function. GO functional annotation term (FAT) was used for the analysis because GO term cannot universally define the specificity of a given term. The number in parenthesis indicate the number of differentially expressed genes contribute to the clustered term.
Annotation clustera | Enrichment scoreb | Biological termsc |
---|---|---|
1 | 1.68 | Adenyl ribonucleotide binding (15), purine ribonucleotide binding (17), purine nucleotide binding (17), ribonucleotide binding (17), nucleoside binding (15), adenyl nucleotide binding (15), purine nucleoside binding (15), ATP binding (14), nucleotide binding (18) |
2 | 1.50 | Cytoskeletal part (11), microtubule cytoskeleton (7), intracellular non-membrane- bounded organelle (18), non-membrane- bounded organelle (18), centrosome (4), cytoskeleton (13), microtubule organizing center (4) |
3 | 1.50 | Cytoskeletal part (11), dynein complex (3), microtubule associated complex (4), microtubule-based movement (4), microtubule cytoskeleton (7), motor activity (3), microtubule motor activity (3), microtubule (4), microtubule-based process (4) |
4 | 1.20 | Cytoskeletal part (11), regulation of actin filament length (3), regulation of cellular component size (5), regulation of actin cytoskeleton organization (3), regulation of actin filament-based process (3), regulation of organelle organization (4), actin cytoskeleton (4), cytoskeletal protein binding (6), regulation of cytoskeleton organization (3), actin binding (4) |
5 | 1.17 | Regulation of neuron differentiation (4), regulation of neurogenesis (4), regulation of nervous system development (4), regulation of cell development (4), neuron differentiation (4) |
6 | 0.92 | Protein amino acid dephosphorylation (4), dephosphorylation (4), phosphorus metabolic process (9), phosphoprotein phosphatase activity (4), phosphate metabolic process (9), protein tyrosine phosphatase activity (3), phosphatase activity (4), protein kinase activity (5), protein serine/threonine kinase activity (4), protein amino acid phosphorylation (5), phosphorylation (5) |
7 | 0.84 | Central nervous system neuron axonogenesis (3), central nervous system neuron development (3), central nervous system neuron differentiation (3), cell projection organization (5), cell motion (5), axonogenesis (3), cell morphogenesis involved in neuron differentiation (3), neuron projection morphogenesis (3), cell projection morphogenesis (3), cell morphogenesis involved in differentiation (3), cell part morphogenesis (3), neuron differentiation (4), neuron projection development (3), cell morphogenesis (3), cellular component morphogenesis (3), neuron development (3) |
8 | 0.82 | Regulation of synaptic transmission (3), regulation of transmission of nerve impulse (3), regulation of neurological system process (3), regulation of system process (4) |
9 | 0.75 | Cell projection organization (5), cytoskeletal protein binding (6), cytoskeleton organization (3) |
10 | 0.71 | Learning or memory (3), neurological system process (10), behavior (5), cognition (4) |
a Top ten of annotation clusters identified by official gene symbols of up-regulated gene list on D15 of pregnancy compared with those on D15 of the estrous cycle.
b Enrichment score represents significance of each cluster annotation and the relatedness of the terms and the genes associated with terms. Enrichment score is calculated by overall EASE scores (the modified Fisher extract p value) of each term member.
c The gene ontology (GO) terms are group of terms having similar biological meaning with respect to biological process, cellular component, and molecular function. GO functional annotation term (FAT) was used for the analysis because GO term cannot universally define the specificity of a given term. The number in parenthesis indicate the number of differentially expressed genes contribute to the clustered term.