Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A
Zambon AC, Zhang L, Minovitsky S, Kanter JR, Prabhakar S, Salomonis N, Vranizan K, Dubchak I, Conklin BR, Insel PA. Proc Natl Acad Sci U S A. 2005 Jun 14;102(24):8561-6. Epub 2005 Jun 6. [Full Text] [PDF]


Supplemental Table 1: Gene Ontology Analysis of 1st Level HOPACH Clusters

Note: Click on the cluster hyperlinks to view individual HTML output MAPP files

Main Cluster
 Pattern GO Name GO Changed Measured in GO Z Score P Value
1 Early induction
T-helper 1 type immune response P 4 9 10 6.44 <0.001
regulation of metabolism P 8 41 48 5.34 <0.001
G2/M transition of mitotic cell cycle P 3 8 8 5.04 0.001
nucleus C 97 1804 2790 4.10 <0.001
endoplasmic reticulum C 23 293 335 3.77 0.001
regulation of cell cycle P 18 212 258 3.69 <0.001
circadian rhythm P 3 13 23 3.68 0.006
ubiquitin ligase complex C 3 13 15 3.68 0.01
nucleosome assembly P 4 22 36 3.58 0.01
protein transporter activity F 15 178 227 3.33 0.005
Golgi apparatus C 18 230 288 3.31 0.002
transcription P 59 1075 1359 3.22 0.002
phosphoric monoester hydrolase activity F 11 126 165 2.97 0.009
intracellular transport P 23 346 460 2.91 0.008
transcription regulator activity F 41 728 898 2.81 0.004
transition metal ion homeostasis P 3 19 19 2.77 0.03
nucleosome C 3 19 38 2.77 0.037
RAS small monomeric GTPase activity F 3 20 21 2.66 0.038
nucleic acid binding F 77 1581 2068 2.61 0.008
kinase activity F 30 512 675 2.60 0.012
protein binding F 62 1235 1646 2.56 0.014
heart development P 4 33 45 2.54 0.036
cellular_component unknown C 24 393 780 2.53 0.016
endomembrane system C 8 92 101 2.52 0.026
protein amino acid dephosphorylation P 7 77 99 2.49 0.03
ubiquitin-protein ligase activity F 4 35 47 2.40 0.034
hemopoiesis P 5 52 60 2.24 0.048
intracellular signaling cascade P 25 443 567 2.17 0.038
cell differentiation P 12 177 208 2.15 0.048
microtubule associated complex C 5 55 90 2.10 0.044
2 Sustained Induction
protein modification P 67 595 747 4.81 <0.001
phosphotransferase activity\, alcohol group as acceptor F 49 401 512 4.70 <0.001
phosphorus metabolism P 51 441 548 4.37 <0.001
endomembrane system C 16 92 101 4.23 <0.001
cytoplasm C 168 2040 2532 3.50 <0.001
hematopoietin/interferon-class (D200-domain) cytokine receptor activity F 9 49 54 3.35 0.005
small protein conjugating enzyme activity F 5 21 31 3.20 0.017
actin filament-based process P 9 52 62 3.15 0.004
cellular_component unknown C 40 393 780 2.97 0.004
protein binding F 104 1235 1646 2.86 0.006
biological_process unknown P 43 439 804 2.82 0.006
intracellular transport P 35 346 460 2.74 0.008
cell projection organization and biogenesis P 3 12 13 2.59 0.04
morphogenesis of an epithelium P 4 19 22 2.56 0.034
ubiquitin-protein ligase activity F 6 35 47 2.54 0.034
RAS small monomeric GTPase activity F 4 20 21 2.43 0.038
response to biotic stimulus P 41 439 941 2.42 0.022
regulation of cellular process P 19 172 201 2.41 0.022
phosphoric ester hydrolase activity F 18 162 213 2.37 0.025
purine nucleotide binding F 78 933 1171 2.36 0.021
intracellular signaling cascade P 41 443 567 2.36 0.018
3 Late induction
lysosome C 22 73 89 8.12 <0.001
nucleoside kinase activity F 4 8 9 4.94 <0.001
chromatin remodeling P 5 12 20 4.89 0.001
chromatin silencing complex C 3 5 7 4.80 0.001
immune cell homeostasis P 4 9 9 4.57 0.001
antigen processing\, endogenous antigen via MHC class I P 3 6 8 4.28 0.012
MHC class I receptor activity F 3 6 10 4.28 0.012
antigen presentation P 6 20 29 4.21 0.001
membrane lipid metabolism P 10 48 62 3.97 0.001
immune cell chemotaxis P 4 11 14 3.97 0.004
integral to membrane C 196 2360 3419 3.85 <0.001
regulation of endocytosis P 5 17 20 3.78 0.003
immunoglobulin binding F 3 9 9 3.23 0.017
protein amino acid dephosphorylation P 12 77 99 3.18 0.002
lipid kinase activity F 4 16 17 2.96 0.017
regulation of gene expression\, epigenetic P 6 30 37 2.95 0.014
cytoskeletal protein binding F 21 177 206 2.84 0.009
alcohol dehydrogenase activity F 3 11 15 2.76 0.031
GTPase regulator activity F 16 127 161 2.73 0.009
receptor signaling protein activity F 10 68 84 2.69 0.011
intracellular signaling cascade P 43 443 567 2.68 0.012
lymph gland development P 4 18 25 2.67 0.022
hydrolase activity F 103 1238 1642 2.60 0.007
zinc ion binding F 18 154 188 2.55 0.011
negative regulation of transcription\, DNA-dependent P 8 52 60 2.55 0.021
cell death P 26 245 290 2.55 0.008
carbohydrate metabolism P 23 211 272 2.53 0.014
transcriptional repressor activity F 6 36 41 2.43 0.032
inositol/phosphatidylinositol kinase activity F 4 20 23 2.41 0.045
external side of plasma membrane C 5 30 49 2.22 0.048
endosome C 5 31 38 2.13 0.048
integrin-mediated signaling pathway P 6 41 51 2.07