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Table 1 Overrepresented DAVID annotation clusters for the obtained SOTA expression clusters

From: Differential transcriptome dynamics during the onset of conceptus elongation and between female and male porcine embryos

Expression cluster Representative enriched functional termsa Enrichment Scoreb
Cluster1 extracellular region part (308, 1.39); extracellular vesicle (226, 1.4); extracellular exosome (224, 1.39) 8.8
response to organic substance (225, 1.46); response to endogenous stimulus (124, 1.47) 7.77
cell motility (134, 1.85); cell migration (123, 1.9) 7.71
cell proliferation (159, 1.57) 7.57
regulation of cell communication (244, 1.48); regulation of signal transduction (225, 1.51) 7.56
circulatory system development (97, 1.88); angiogenesis (50, 2.22) 7.34
regulation of multicellular organismal development (150, 1.6); positive regulation of developmental process (90, 1.52) 7.21
response to cytokine (81, 1.85); cellular response to cytokine stimulus (71, 1.84) 6.22
cell adhesion (142, 1.53); biological adhesion (142, 1.53) 5.11
inflammatory response (64, 1.84); defense response (118, 1.43) 4.85
peptidase regulator activity (32, 2.7); enzyme inhibitor activity (41, 1.95); regulation of proteolysis (62, 1.61) 4.68
membrane region (43, 2.13); membrane raft (34, 2.15) 4.62
multicellular organism metabolic process (23, 3.17) 4.37
regulation of epithelial cell proliferation (35, 2.14); epithelial cell proliferation (37, 1.96) 3.69
actin filament-based process (64, 1.75) 3.61
lipid metabolic process (102, 1.41) 2.76
response to oxygen-containing compound (113, 1.41) 2.12
Cluster2 lipid metabolic process (84, 2.47); lipid biosynthetic process (47, 2.95) 11.91
cardiovascular system development (49, 2.03) 4.39
chemical homeostasis (58, 2.17); homeostatic process (72, 1.71) 3.75
ion transport (68, 1.83); cation transport (45, 1.81); transmembrane transport (56, 1.66) 3.37
membrane depolarization (11, 4.74); regulation of membrane potential (23, 2.5) 3.31
small molecule catabolic process (24, 2.76); carboxylic acid catabolic process (16, 3.23) 3.24
movement of cell or subcellular component (73, 1.59); regulation of cell migration (34, 1.94) 2.87
phospholipid metabolic process (27, 2.69); glycerophospholipid metabolic process (19, 2.68) 2.72
intracellular signal transduction (98, 1.44); regulation of cell communication (107, 1.39) 2.59
positive regulation of multicellular organismal process (59, 1.62) 2.57
response to oxygen-containing compound (59, 1.58) 2.52
phosphorus metabolic process (111, 1.41); phosphate-containing compound metabolic process (110, 1.4) 1.65
Cluster3 vacuole (131, 1.79) 8.09
lipid metabolic process (118, 1.56); lipid biosynthetic process (57, 1.61) 5.41
cell-cell junction (66, 1.7); protein binding involved in cell adhesion (37, 2.09); cadherin binding (35, 1.97); adherens junction (65, 1.55) 4.01
sphingolipid metabolic process (26, 2.95); membrane lipid metabolic process (29, 2.5) 3.93
extracellular organelle (217, 1.27); extracellular vesicle (216, 1.27); extracellular exosome (215, 1.27) 3.44
pigment cell differentiation (11, 5.38); developmental pigmentation (11, 4.12) 3.28
ion transport (123, 1.48); cation transport (88, 1.59); transmembrane transport (112, 1.49) 3.11
biological adhesion (133, 1.37); cell adhesion (132, 1.37) 2.61
cellular homeostasis (79, 1.67); homeostatic process (132, 1.41) 2.6
embryonic organ development (43, 1.81) 2.38
macromolecule localization (205, 1.28) 2.24
actin filament-based process (61, 1.6) 2.07
cellular response to oxygen-containing compound (79, 1.52) 2.03
regulation of kinase activity (71, 1.59); phosphorus metabolic process (217, 1.24) 1.8
regulation of molecular function (205, 1.26) 1.62
regulation of cellular localization (72, 1.52) 1.43
Cluster4 epithelium development (57, 2.03); organ morphogenesis (48, 1.83) 4.55
urogenital system development (27, 3.19) 3.81
blood vessel development (34, 2.23); vasculature development (35, 2.17); cardiovascular system development (47, 1.88); circulatory system development (47, 1.88) 3.73
extracellular exosome (113, 1.42); extracellular vesicle (113, 1.41); extracellular organelle (113, 1.41); extracellular region part (141, 1.28) 3.7
cell surface receptor signaling pathway involved in cell-cell signaling (32, 2.29); Wnt signaling pathway (29, 2.34); cell-cell signaling by wnt (29, 2.33) 3.61
regulation of signal transduction (101, 1.4) 3.4
apoptotic process (76, 1.64); cell death (80, 1.54) 3.4
reproductive system development (36, 3.21) 3.28
actin filament-based process (37, 2.08); actin cytoskeleton organization (32, 2.18) 2.77
regulation of hydrolase activity (61, 1.72); molecular function regulator (62, 1.64); enzyme regulator activity (46, 1.7) 2.68
movement of cell or subcellular component (74, 1.56); regulation of cell motility (37, 1.9) 2.46
regulation of signaling (112, 1.38); regulation of cell communication (110, 1.38) 2.31
regulation of cell proliferation (65, 1.58) 2.26
nervous system development (84, 1.46); negative regulation of cell differentiation (33, 1.95) 1.72
Cluster5 cell death (124, 1.81); apoptotic process (114, 1.86) 10.04
regulation of cell communication (178, 1.68); regulation of signaling (180, 1.67); regulation of signal transduction (164, 1.72) 9.95
cell migration (84, 2.03); locomotion (100, 1.87) 7.37
regulation of multicellular organismal development (106, 1.76); regulation of cell differentiation (97, 1.79); positive regulation of developmental process (70, 1.84) 6.89
cell adhesion (103, 1.73) 6.23
cell development (132, 1.92); nervous system development (128, 1.68) 5.5
cell junction (85, 1.65); focal adhesion (34, 2.33) 4.69
cardiovascular system development (64, 1.93); circulatory system development (64, 1.93) 4.54
MAPK cascade (55, 1.87) 4.48
actin filament-based process (48, 2.04); cytoskeleton organization (67, 1.67) 4.39
transmembrane receptor protein serine/threonine kinase signaling pathway (30, 2.66); response to transforming growth factor beta (20, 2.66); cellular response to transforming growth factor beta stimulus (19, 2.55) 3.72
embryo development (65, 1.95); embryo development ending in birth or egg hatching (39, 1.91); chordate embryonic development (38, 1.88) 3.71
regulation of cytokine production (38, 1.88) 3.19
apoptotic signaling pathway (39, 1.91); regulation of apoptotic signaling pathway (29, 2.18) 2.7
positive regulation of metabolic process (143, 1.34); positive regulation of macromolecule metabolic process (134, 1.34); positive regulation of cellular metabolic process (133, 1.34); regulation of transcription from RNA polymerase II promoter (92, 1.43) 2.63
regulation of protein transport (50, 1.91); regulation of transport (90, 1.43) 2.38
  1. a Values within parentheses indicate the number of genes and fold-enrichment of the functional terms, respectively
  2. b Geometric mean (in –long10 scale) of member’s P-values of the corresponding annotation cluster