Table 3.
Meta-analysis summary: number of GO terms and names of top 5 GO terms grouped into 10 arbitrary categories describing relevant biological and developmental processes and HD phenotypes. Each arbitrary category contains the indicated number of GO terms, which is also expressed as a percentage of total number of GO terms for particular cell type. Numbers in brackets indicate number of genes from the input list, which were assigned by CPDB for each GO term
| Category | PSC—292 total GO terms, 986 genes | NSC—445 GO terms, 4740 genes | Neurons—191 GO terms, 454 genes |
|---|---|---|---|
| Proliferation, cell cycle, and growth | 13 GO terms; 4.45 % | 21 GO terms; 4.80 % | 10 GO terms; 5.23 % |
| Top 5 terms | Positive regulation of cell proliferation (62), negative regulation of cell proliferation (50), regulation of mitotic cell cycle (32), regulation of epithelial cell proliferation (31), positive regulation of cell cycle (21) | Positive regulation of cell proliferation (276), negative regulation of cell proliferation (224), regulation of cell cycle process (146), negative regulation of cell cycle (139), mitotic cell cycle phase transition (130) | Positive regulation of cell proliferation (34), negative regulation of cell proliferation (27), regulation of cell cycle process (20), negative regulation of cell cycle (19), positive regulation of cell cycle (16) |
| Differentiation | 24 GO terms; 8.22 % | 24 GO terms; 5.39 % | 9 GO terms; 4.71 % |
| Top 5 terms | Cell morphogenesis involved in differentiation (89), positive regulation of cell differentiation (67), negative regulation of cell differentiation (53), epithelial cell differentiation (45), stem cell differentiation (42) | Cell morphogenesis involved in differentiation (378), positive regulation of cell differentiation (297), negative regulation of cell differentiation (221), epithelial cell differentiation (204), stem cell differentiation (151) | Cell morphogenesis involved in differentiation (58), negative regulation of cell differentiation (30), positive regulation of cell differentiation (29), epithelial cell differentiation (27), stem cell differentiation (19) |
| Development | 59 GO terms; 20.21 % | 93 GO terms; 20.90 % | 12 GO terms; 6.28 % |
| Top 5 terms | Regulation of cell development (61), chordate embryonic development (58), regulation of cell morphogenesis (43), striated muscle tissue development (38), regulation of vasculature development (30) | Regulation of cell development (303), chordate embryonic development (243), regulation of cell morphogenesis (193), striated muscle tissue development (138), camera-type eye development (117) | Regulation of cell development (35), chordate embryonic development (25), striated muscle tissue development (16), endochondral bone morphogenesis (12), mesenchymal cell development (12) |
| Neurodevelopment | 13 GO terms; 4.45 % | 30 GO terms; 6.74 % | 12 GO terms; 6.28 % |
| Top 5 terms | Neurogenesis (121), neuron differentiation (109), axon development (58), Regulation of nervous system development (54), axon guidance (44) | Neurogenesis (578), neuron differentiation (504), regulation of nervous system development (282), axon development (264), axon guidance (184) | Neurogenesis (74), neuron differentiation (60), axon development (36), regulation of nervous system development (30), axon guidance (27) |
| Control of gene expression | 18 GO terms; 6.16 % | 16 GO terms; 3.60 % | 4 GO terms; 2.09 % |
| Top 5 terms | Regulation of gene expression (206), transcription, DNA-templated (179), sequence-specific DNA binding (63), regulatory region DNA binding (52), transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding (21) | Regulation of gene expression (1057), transcription, DNA-templated (901), sequence-specific DNA binding (281), regulatory region DNA binding (240), transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding (91) | Structure-specific DNA binding (16), DNA conformation change (12), protein-DNA complex assembly (10), establishment of protein localization to chromosome (2) |
| Signaling pathways | 18 GO terms; 6.16 % | 29 GO terms; 6.52 % | 8 GO terms; 4.19 % |
| Top 5 terms | Cell surface receptor signaling pathway (166), intracellular signal transduction (151), positive regulation of signal transduction (94), regulation of intracellular signal transduction (90), negative regulation of signal transduction (71) | Cell surface receptor signaling pathway (839), intracellular signal transduction (805), regulation of intracellular signal transduction (454), positive regulation of signal transduction (430), negative regulation of signal transduction (325) | Cell surface receptor signaling pathway (90), intracellular signal transduction (82), regulation of intracellular signal transduction (50), positive regulation of signal transduction (42), negative regulation of signal transduction (37) |
| Cytoskeletal organization, cell-cell interactions | 13 GO terms; 4.45 % | 22 GO terms; 4.94 % | 14 GO terms; 7.33 % |
| Top 5 terms | Positive regulation of cell communication (106), negative regulation of cell communication (75), actin cytoskeleton (33), positive regulation of cell adhesion (25), regulation of cell-cell adhesion (24) | Positive regulation of cell communication (506), microtubule cytoskeleton (274), negative regulation of cell communication (355), actin cytoskeleton (182), actin filament organization (117) | Positive regulation of cell communication (52), negative regulation of cell communication (38), actin cytoskeleton (29), positive regulation of cell adhesion (20), actin filament organization (18) |
| Oxidative and other cell stress | 3 GO terms; 1.03 % | 11 GO terms; 2.47 % | 10 GO terms; 5.24 % |
| Top 5 terms | Cellular response to reactive oxygen species (12), stress fiber (8), response to X-ray (5) | Stress-activated MAPK cascade (82), response to UV (43), cellular response to reactive oxygen species (40), cellular response to alcohol (37), stress fiber assembly (32) | Cellular response to reactive oxygen species (11), stress fiber (7), regulation of oxidative stress-induced cell death (6), cellular response to ionizing radiation (6), regulation of response to oxidative stress (6) |
| Apoptosis | 6 GO terms; 2.05 % | 8 GO terms; 1.80 % | 10 GO terms; 5.24 % |
| Top 5 terms | Apoptotic process (112), regulation of programmed cell death (97), negative regulation of cell death (67), positive regulation of cell death (40), neuron apoptotic process (24) | Apoptotic process (570), regulation of programmed cell death (447), negative regulation of cell death (289), apoptotic signaling pathway (198), positive regulation of cell death (197) | Apoptotic process (73), regulation of programmed cell death (66), negative regulation of cell death(48), apoptotic signaling pathway (27), positive regulation of cell death (26) |
| Metabolism | 42 GO terms; 14.38 % | 61 GO terms; 13.71 % | 33 GO terms; 17.28 % |
| Top 5 terms | Regulation of cellular biosynthetic process (203), regulation of nucleobase-containing compound metabolic process (198), regulation of macromolecule biosynthetic process (187), positive regulation of cellular metabolic process (183), RNA biosynthetic process (182) | Regulation of cellular biosynthetic process (1055), regulation of nucleobase-containing compound metabolic process (999), regulation of macromolecule biosynthetic process (996), RNA biosynthetic process (926), regulation of RNA metabolic process (907) | Positive regulation of cellular metabolic process (87), positive regulation of macromolecule metabolic process (76), regulation of protein metabolic process (75), regulation of cellular protein metabolic process (68), negative regulation of cellular metabolic process (65) |