Table 1.
Overrepresented DAVID annotation clusters for the obtained SOTA expression clusters
| 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 |
a Values within parentheses indicate the number of genes and fold-enrichment of the functional terms, respectively
b Geometric mean (in –long10 scale) of member’s P-values of the corresponding annotation cluster