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 0.049
4 Late repression
mitotic cell cycle P 70 169 197 18.46 <0.001
DNA replication and chromosome cycle P 47 89 103 17.69 <0.001
DNA metabolism P 79 258 335 15.82 <0.001
M phase P 37 87 105 13.60 <0.001
nucleus C 244 1804 2790 13.34 <0.001
chromosome C 39 105 152 12.72 <0.001
nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism P 192 1534 1926 10.32 <0.001
response to endogenous stimulus P 32 103 124 10.09 <0.001
viral nucleocapsid C 12 21 25 9.36 <0.001
nucleic acid binding F 179 1581 2068 8.40 <0.001
ATP binding F 102 736 1367 8.33 <0.001
nucleocytoplasmic transport P 18 55 64 7.85 <0.001
cytokinesis P 20 70 85 7.46 <0.001
pore complex C 9 18 21 7.44 <0.001
ribonucleoprotein complex C 37 213 281 6.44 <0.001
nucleotidyltransferase activity F 16 65 82 5.89 <0.001
ligase activity\, forming phosphoric ester bonds F 10 32 45 5.64 <0.001
hydrolase activity\, acting on acid anhydrides\, in phosphorus-containing anhydrides F 32 196 245 5.57 <0.001
RNA localization P 5 10 15 5.55 <0.001
ligase activity\, forming carbon-oxygen bonds F 9 28 39 5.47 <0.001
nucleoside monophosphate biosynthesis P 4 8 10 4.96 0.001
stearoyl-CoA 9-desaturase activity F 3 5 7 4.82 0.001
amino acid metabolism P 18 101 121 4.59 <0.001
microtubule cytoskeleton C 18 101 143 4.59 <0.001
regulation of gene expression\, epigenetic P 8 30 37 4.45 <0.001
intracellular transporter activity F 4 10 13 4.27 0.005
cyclin-dependent protein kinase regulator activity F 5 16 18 3.99 <0.001
deoxyribonucleotide metabolism P 3 7 9 3.88 0.01
oxidoreductase activity\, acting on the CH-NH group of donors\, NAD or NADP as acceptor F 3 7 7 3.88 0.008
amino acid permease activity F 3 7 7 3.88 0.006
microtubule organizing center C 5 17 18 3.80 0.007
nuclease activity F 11 60 81 3.69 0.002
motor activity F 11 64 117 3.44 0.004
RNA helicase activity F 4 14 15 3.32 0.013
chromosome organization and biogenesis (sensu Eukarya) P 13 85 171 3.26 0.005
response to heat P 4 15 29 3.14 0.015
chaperone activity F 14 99 168 3.06 0.01
protein methyltransferase activity F 3 10 14 2.99 0.028
one-carbon compound metabolism P 5 23 29 2.94 0.018
regulation of cell cycle P 24 212 258 2.82 0.013
protein metabolism P 112 1360 1758 2.69 0.005
porin activity F 4 18 20 2.68 0.026
endoplasmic reticulum membrane C 5 26 29 2.61 0.03
unlocalized C 7 43 53 2.58 0.018
glycolysis P 6 35 61 2.53 0.03
carboxy-lyase activity F 3 13 23 2.40 0.048
hydrolase activity\, acting on carbon-nitrogen (but not peptide) bonds\, in cyclic amidines F 3 13 17 2.40 0.042
mitochondrion C 38 420 582 2.10 0.048
5 Sustained Repression
RNA metabolism P 53 163 204 11.03 <0.001
mitochondrion C 93 420 582 10.19 <0.001
structural constituent of ribosome F 44 152 266 9.06 <0.001
biosynthesis P 107 583 737 8.74 <0.001
ribosome biogenesis and assembly P 21 54 69 7.99 <0.001
translation regulator activity F 24 71 89 7.63 <0.001
RNA binding F 55 259 321 7.39 <0.001
ribonucleoprotein complex C 46 213 281 6.88 <0.001
methyltransferase activity F 22 71 101 6.78 <0.001
exosome (RNase complex) C 4 4 5 6.54 <0.001
nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism P 195 1534 1926 6.38 <0.001
response to endogenous stimulus P 26 103 124 6.08 <0.001
DNA metabolism P 48 258 335 5.85 <0.001
protein-mitochondrial targeting P 4 5 5 5.71 <0.001
nucleus C 215 1804 2790 5.70 <0.001
nuclease activity F 17 60 81 5.49 <0.001
heterocycle metabolism P 13 41 49 5.31 <0.001
helicase activity F 19 76 122 5.14 <0.001
ligase activity F 28 135 181 5.09 <0.001
neutral amino acid transporter activity F 3 4 8 4.75 0.006
phosphotransferase activity\, phosphate group as acceptor F 7 19 23 4.41 <0.001
nucleotide binding F 117 949 1189 4.38 <0.001
nucleobase\, nucleoside\, nucleotide kinase activity F 8 25 30 4.19 <0.001
mitochondrion organization and biogenesis P 3 5 7 4.11 0.002
DNA N-glycosylase activity F 3 5 8 4.11 0.005
protein-synthesizing GTPase activity F 4 9 11 3.85 0.004
RNA polymerase complex C 4 9 12 3.85 0.003
damaged DNA binding F 6 18 21 3.76 0.002
soluble fraction C 6 18 23 3.76 0.004
nucleotidyltransferase activity F 14 65 82 3.75 0.001
inner membrane C 19 101 137 3.70 <0.001
transferase activity\, transferring pentosyl groups F 5 14 15 3.63 0.004
outer membrane C 8 32 39 3.33 0.004
nucleoside metabolism P 4 11 14 3.30 0.018
antigen presentation\, endogenous antigen P 3 7 9 3.24 0.032
cis-trans isomerase activity F 7 27 33 3.23 0.003
nucleocytoplasmic transport P 11 55 64 3.04 0.009
learning P 3 8 15 2.93 0.04
nucleobase\, nucleoside\, nucleotide and nucleic acid transport P 4 14 19 2.68 0.03
transferase activity\, transferring alkyl or aryl (other than methyl) groups F 8 39 44 2.67 0.013
olfactory receptor activity F 3 9 85 2.66 0.039
coenzyme and prosthetic group metabolism P 15 93 109 2.62 0.016
carbon-oxygen lyase activity F 7 33 44 2.60 0.023
oxidoreductase activity\, acting on NADH or NADPH F 7 33 44 2.60 0.017
primary active transporter activity F 21 149 192 2.43 0.014
DNA replication and chromosome cycle P 14 89 103 2.43 0.023
cell cycle checkpoint P 3 10 13 2.42 0.034
metal ion transporter activity F 7 35 46 2.42 0.028
molecular_function unknown F 46 387 762 2.39 0.021
mitotic cell cycle P 23 169 197 2.37 0.014
eukaryotic 43S preinitiation complex C 4 16 18 2.35 0.042
one-carbon compound metabolism P 5 23 29 2.26 0.049
biological_process unknown P 50 439 804 2.17 0.034
hydrolase activity\, acting on acid anhydrides\, in phosphorus-containing anhydrides F 25 196 245 2.12 0.032
6 Early repression
protein tyrosine/serine/threonine phosphatase activity F 4 21 33 4.44 0.005
lysosome C 7 73 89 3.44 0.008
protein modification P 30 595 747 3.27 <0.001
ubiquitin-protein ligase activity F 4 35 47 3.03 0.013
cellular_component unknown C 21 393 780 2.99 0.005
magnesium ion binding F 7 87 106 2.90 0.009
S-adenosylmethionine-dependent methyltransferase activity F 4 38 49 2.83 0.019
vesicle-mediated transport P 9 132 168 2.73 0.011
secretory pathway P 4 43 69 2.53 0.039
biological_process unknown P 21 439 804 2.45 0.019
intracellular transport P 17 346 460 2.31 0.035
phosphorus metabolism P 20 441 548 2.14 0.043
molecular_function unknown F 18 387 762 2.13 0.045
intracellular signaling cascade P 20 443 567 2.12 0.044
Supplemental Table 1-First level HOPACH clusters were analyzed with the MAPPFinder program to determine the GO terms that represent transcripts from each cluster. Parent child GO Terms representing same groups of genes were excluded (see supplemental on line material for methods)

 
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