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Table 3 Gene Ontology (GO) analysis of the gene list based on z-score

From: Limited redundancy in genes regulated by Cyclin T2 and Cyclin T1

Ontology List Array z-score
Gene Ontologic analysis of genes down-regulated by Cyclin T2 depletion
Biological process unknown 14 566 3.38
Response to chemical stimulus 8 331 2.45
Negative regulation of metabolism 7 241 2.83
Negative regulation of cellular metabolism 6 204 2.65
Negative regulation of transcription 6 167 3.22
Negative regulation of transcription, DNA-dependent 6 109 4.56
Enzyme linked receptor protein signaling pathway 5 176 2.33
Chromatin modification 4 140 2.09
Negative regulation of transcription from RNA polymerase II promoter 4 66 3.98
Regulation of kinase activity 4 126 2.33
Regulation of transferase activity 4 128 2.3
Regulation of Rho protein signal transduction 3 69 2.68
Regulation of small GTPase mediated signal transduction 3 93 2.05
Calcium mediated signaling 2 22 3.69
chloride transport 2 43 2.31
Energy reserve metabolism 2 34 2.75
Frizzled signaling pathway 2 17 4.32
Neurotransmitter transport 2 40 2.44
Oligosaccharide metabolism 2 13 5.05
Protein amino acid ADP-ribosylation 2 24 3.49
Protein processing 2 46 2.18
Ras protein signal transduction 2 30 3.01
Regulation of cyclin dependent protein kinase activity 2 37 2.59
Response to oxidative stress 2 46 2.18
Response to protein stimulus 2 44 2.26
Response to unfolded protein 2 44 2.26
Striated muscle development 2 39 2.49
Transmembrane receptor ptotein tyrosine phosphatase signaling pathway 2 7 7.12
Gene Ontologic analysis of genes down-regulated by Cyclin T1 depletion
Metabolism 178 6465 -2.45
Cellular metabolism 158 6076 -3.31
nucleobase, nucleoside, nucleotide and nucleic acid metabolism 64 2908 -3.24
intracellular signaling cascade 43 1038 2.05
death 28 555 2.72
cell death 27 551 2.51
apoptosis 26 524 2.53
programmed cell death 26 525 2.52
regulation of apoptosis 17 342 2.04
Regulation of programmed cell death 17 343 2.02
small GTPase mediated signal transduction 15 291 2.06
Cellular morphogenesis 14 247 2.36
Regulation of enzyme activity 13 235 2.18
Protein folding 11 197 2.04
Anion transport 10 160 2.32
Growth 10 174 2.04
Cell growth 9 139 2.32
Endocytosis 9 130 2.54
Regulation of Cyclin dependent protein kinase activity 4 37 2.72
Antigen processing 3 31 2.12
RNA metabolism 3 464 -3.11
RNA processing 3 383 -2.66
post-Golgi vesicle mediated transport 2 17 2.07
Protein export from nucleus 2 8 3.58
Regulation of DNA repair 2 7 3.89
Antigen presentation, endogenous antigen 2 16 2.17
Antigen processing, endogenous antigen via MHC class I 2 17 2.07
Gene Ontologic analysis of genes down-regulated by Cyclin T2 or Cyclin T1 depletion
Regulation of cellular process 25 3058 2.04
Regulation of cellular physiological process 24 2840 2.17
Negative regulation of biological process 11 748 3.33
Negative regulation of cellular process 10 696 3.08
Negative regulation of cellular physiological process 9 631 2.89
Negative regulation of physiological process 9 655 2.77
Positive regulation of biological process 9 627 2.91
Positive regulation of cellular process 9 540 3.42
Apoptosis 8 524 2.93
Cell death 8 551 2.77
Cell proliferation 8 499 3.09
Negative regulation of cell proliferation 6 147 5.63
Regulation of apoptosis 6 342 2.91
Innate immune response 2 63 2.72
Positive regulation of I-κB/NF-κB cascade 2 76 2.37
Myeloid cell differentiation 2 37 3.88
Hemopoietic or lymphoid organ development 2 93 2.01
  1. A GO analysis of the gene sets unique (192 and 531) and shared (100) to Cyclin T2 and Cyclin T1 depletion, respectively, was carried out and grouped based on z-score. Only GO categories that were over represented with at least 2 genes were considered. The "List" value is the number of affected genes from the gene list in the group. The "Array" value shows the total number of genes on the microarray that are in this gene ontology. The "z-score" is the expected number of genes in a GO term, subtracted from the observed number of genes. This value is divided by the standard deviation of the observed number of genes.