Coexpression cluster:C1145
From FANTOM5_SSTAR
Full id: C1145_Hodgkin_chronic_acute_Reticulocytes_lymphoma_diffuse_Hep2
Phase1 CAGE Peaks
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
p.value | FDR | nGenes | nPathway | Name |
---|---|---|---|---|
0.000180580969984339 | 0.0127008615555652 | 2 | 100 | Pyrimidine metabolism (KEGG):00240 |
3.67416886898525e-08 | 1.16287444703383e-05 | 3 | 36 | DNA replication (KEGG):03030 |
2.05925492603147e-05 | 0.00260701673635584 | 2 | 34 | Base excision repair (KEGG):03410 |
8.58329659590162e-05 | 0.00679153343150715 | 2 | 69 | G1 to S cell cycle control (Wikipathways):WP45 |
3.15809823992966e-05 | 0.00285582312267925 | 2 | 42 | DNA Replication (Wikipathways):WP1806 |
0.000206748318674481 | 0.0130871685720946 | 2 | 107 | DNA Repair (Reactome):REACT_216 |
6.67157721853038e-06 | 0.00105577709483243 | 3 | 200 | DNA Replication (Reactome):REACT_383 |
2.59719623007301e-05 | 0.00274004202272702 | 3 | 315 | Cell Cycle, Mitotic (Reactome):REACT_152 |
3.75206069989847e-07 | 7.91684807678577e-05 | 3 | 77 | Chromosome Maintenance (Reactome):REACT_22172 |
3.07978931231787e-08 | 1.16287444703383e-05 | 3 | 34 | {PCNA,34} (Static Module):NA |
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
GO ID | GO name | FDR corrected p-value |
---|---|---|
GO:0006260 | DNA replication | 3.23493187209283e-05 |
GO:0006259 | DNA metabolic process | 3.62539169331596e-05 |
GO:0005657 | replication fork | 0.00080180884438166 |
GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.00100012752440769 |
GO:0003887 | DNA-directed DNA polymerase activity | 0.00100012752440769 |
GO:0005634 | nucleus | 0.00100012752440769 |
GO:0044427 | chromosomal part | 0.00131180468070354 |
GO:0005694 | chromosome | 0.00175265536069073 |
GO:0000228 | nuclear chromosome | 0.00235908563354695 |
GO:0043283 | biopolymer metabolic process | 0.00235908563354695 |
GO:0017108 | 5'-flap endonuclease activity | 0.00235908563354695 |
GO:0043626 | PCNA complex | 0.00235908563354695 |
GO:0004170 | dUTP diphosphatase activity | 0.00235908563354695 |
GO:0030337 | DNA polymerase processivity factor activity | 0.00235908563354695 |
GO:0048015 | phosphoinositide-mediated signaling | 0.00264897946591783 |
GO:0043231 | intracellular membrane-bound organelle | 0.00300225166600379 |
GO:0043227 | membrane-bound organelle | 0.00300225166600379 |
GO:0047429 | nucleoside-triphosphate diphosphatase activity | 0.00300225166600379 |
GO:0048256 | flap endonuclease activity | 0.00300225166600379 |
GO:0006287 | base-excision repair, gap-filling | 0.00300225166600379 |
GO:0046974 | histone lysine N-methyltransferase activity (H3-K9 specific) | 0.00300225166600379 |
GO:0008309 | double-stranded DNA specific exodeoxyribonuclease activity | 0.00300225166600379 |
GO:0044428 | nuclear part | 0.00507998581710691 |
GO:0016779 | nucleotidyltransferase activity | 0.00507998581710691 |
GO:0005652 | nuclear lamina | 0.00507998581710691 |
GO:0008409 | 5'-3' exonuclease activity | 0.00507998581710691 |
GO:0032405 | MutLalpha complex binding | 0.00608285954516829 |
GO:0019932 | second-messenger-mediated signaling | 0.00608285954516829 |
GO:0043229 | intracellular organelle | 0.0063152511564931 |
GO:0043226 | organelle | 0.0063152511564931 |
GO:0009650 | UV protection | 0.00639000930182787 |
GO:0005663 | DNA replication factor C complex | 0.00684683280567824 |
GO:0005658 | alpha DNA polymerase:primase complex | 0.00684683280567824 |
GO:0043170 | macromolecule metabolic process | 0.00684683280567824 |
GO:0016895 | exodeoxyribonuclease activity, producing 5'-phosphomonoesters | 0.00686030240274865 |
GO:0000307 | cyclin-dependent protein kinase holoenzyme complex | 0.00686030240274865 |
GO:0032404 | mismatch repair complex binding | 0.00686030240274865 |
GO:0004529 | exodeoxyribonuclease activity | 0.00686030240274865 |
GO:0003677 | DNA binding | 0.00686030240274865 |
GO:0046080 | dUTP metabolic process | 0.0074267459690403 |
GO:0006281 | DNA repair | 0.0088115876286842 |
GO:0009200 | deoxyribonucleoside triphosphate metabolic process | 0.0100477932531831 |
GO:0009211 | pyrimidine deoxyribonucleoside triphosphate metabolic process | 0.0100477932531831 |
GO:0000287 | magnesium ion binding | 0.0100477932531831 |
GO:0006974 | response to DNA damage stimulus | 0.0100477932531831 |
GO:0009120 | deoxyribonucleoside metabolic process | 0.0100477932531831 |
GO:0043601 | nuclear replisome | 0.0100477932531831 |
GO:0030894 | replisome | 0.0100477932531831 |
GO:0046125 | pyrimidine deoxyribonucleoside metabolic process | 0.0100477932531831 |
GO:0044237 | cellular metabolic process | 0.0100477932531831 |
GO:0044238 | primary metabolic process | 0.0101510033057196 |
GO:0016888 | endodeoxyribonuclease activity, producing 5'-phosphomonoesters | 0.0101510033057196 |
GO:0043596 | nuclear replication fork | 0.0105811634345431 |
GO:0044424 | intracellular part | 0.0106570737760598 |
GO:0006213 | pyrimidine nucleoside metabolic process | 0.0113942924920784 |
GO:0006886 | intracellular protein transport | 0.0114259662429928 |
GO:0009719 | response to endogenous stimulus | 0.0114259662429928 |
GO:0009219 | pyrimidine deoxyribonucleotide metabolic process | 0.0118930548377811 |
GO:0016796 | exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters | 0.0118930548377811 |
GO:0004523 | ribonuclease H activity | 0.0118930548377811 |
GO:0000060 | protein import into nucleus, translocation | 0.0118930548377811 |
GO:0018024 | histone-lysine N-methyltransferase activity | 0.0139067156443542 |
GO:0016278 | lysine N-methyltransferase activity | 0.0139067156443542 |
GO:0016279 | protein-lysine N-methyltransferase activity | 0.0139067156443542 |
GO:0006275 | regulation of DNA replication | 0.0141988607925667 |
GO:0000781 | chromosome, telomeric region | 0.0150233136872658 |
GO:0000794 | condensed nuclear chromosome | 0.0150233136872658 |
GO:0009262 | deoxyribonucleotide metabolic process | 0.0150233136872658 |
GO:0004520 | endodeoxyribonuclease activity | 0.0152820594469177 |
GO:0009411 | response to UV | 0.0155333432796311 |
GO:0005515 | protein binding | 0.0157953884552327 |
GO:0042054 | histone methyltransferase activity | 0.0157953884552327 |
GO:0006284 | base-excision repair | 0.0157953884552327 |
GO:0006302 | double-strand break repair | 0.0160259561931682 |
GO:0008283 | cell proliferation | 0.016940445835313 |
GO:0016891 | endoribonuclease activity, producing 5'-phosphomonoesters | 0.0173199076507755 |
GO:0005622 | intracellular | 0.0173199076507755 |
GO:0008276 | protein methyltransferase activity | 0.0198242929997908 |
GO:0051052 | regulation of DNA metabolic process | 0.0198242929997908 |
GO:0003684 | damaged DNA binding | 0.0198242929997908 |
GO:0008170 | N-methyltransferase activity | 0.0198242929997908 |
GO:0009147 | pyrimidine nucleoside triphosphate metabolic process | 0.0198242929997908 |
GO:0004536 | deoxyribonuclease activity | 0.0198242929997908 |
GO:0015031 | protein transport | 0.0198951299519024 |
GO:0000793 | condensed chromosome | 0.0198951299519024 |
GO:0009116 | nucleoside metabolic process | 0.0198951299519024 |
GO:0016893 | endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters | 0.0207964623323496 |
GO:0046907 | intracellular transport | 0.0212665692053063 |
GO:0045184 | establishment of protein localization | 0.0213738883507893 |
GO:0043232 | intracellular non-membrane-bound organelle | 0.0213738883507893 |
GO:0043228 | non-membrane-bound organelle | 0.0213738883507893 |
GO:0008104 | protein localization | 0.0225955583078951 |
GO:0044454 | nuclear chromosome part | 0.0236785144343018 |
GO:0006220 | pyrimidine nucleotide metabolic process | 0.0241223676371893 |
GO:0033036 | macromolecule localization | 0.0241693364343283 |
GO:0004527 | exonuclease activity | 0.024387293458585 |
GO:0004521 | endoribonuclease activity | 0.024387293458585 |
GO:0003676 | nucleic acid binding | 0.0256838301287325 |
GO:0016740 | transferase activity | 0.0263206029691129 |
GO:0009416 | response to light stimulus | 0.0263206029691129 |
GO:0016043 | cellular component organization and biogenesis | 0.0263206029691129 |
GO:0051649 | establishment of cellular localization | 0.0263206029691129 |
GO:0051641 | cellular localization | 0.0271406759701018 |
GO:0008757 | S-adenosylmethionine-dependent methyltransferase activity | 0.0271406759701018 |
GO:0006606 | protein import into nucleus | 0.029831475488504 |
GO:0051170 | nuclear import | 0.029831475488504 |
GO:0046872 | metal ion binding | 0.029831475488504 |
GO:0004540 | ribonuclease activity | 0.029831475488504 |
GO:0006950 | response to stress | 0.029831475488504 |
GO:0009314 | response to radiation | 0.029831475488504 |
GO:0032403 | protein complex binding | 0.029831475488504 |
GO:0046982 | protein heterodimerization activity | 0.0305734825634199 |
GO:0043167 | ion binding | 0.0305734825634199 |
GO:0003690 | double-stranded DNA binding | 0.0310435675766427 |
GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0328864569882111 |
GO:0003682 | chromatin binding | 0.033308670484058 |
GO:0017038 | protein import | 0.034133394260944 |
GO:0031323 | regulation of cellular metabolic process | 0.0375000074527852 |
GO:0030145 | manganese ion binding | 0.0400260820590306 |
GO:0009141 | nucleoside triphosphate metabolic process | 0.0400260820590306 |
GO:0004519 | endonuclease activity | 0.0406235751363442 |
GO:0044446 | intracellular organelle part | 0.0406235751363442 |
GO:0006913 | nucleocytoplasmic transport | 0.0406235751363442 |
GO:0044422 | organelle part | 0.0406235751363442 |
GO:0051169 | nuclear transport | 0.0406235751363442 |
GO:0019222 | regulation of metabolic process | 0.0406235751363442 |
GO:0043566 | structure-specific DNA binding | 0.0408711770132874 |
GO:0006261 | DNA-dependent DNA replication | 0.0417374929281751 |
GO:0009628 | response to abiotic stimulus | 0.0417374929281751 |
GO:0005635 | nuclear envelope | 0.0485919622754928 |
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>
Ontology term | p-value | n |
---|---|---|
animal cell | 6.15e-22 | 679 |
eukaryotic cell | 6.15e-22 | 679 |
epithelial cell | 1.36e-17 | 253 |
native cell | 2.19e-16 | 722 |
embryonic cell | 2.06e-09 | 250 |
migratory neural crest cell | 8.97e-08 | 41 |
Ontology term | p-value | n |
---|---|---|
larynx | 1.62e-07 | 9 |
Ontology term | p-value | n |
---|---|---|
cancer | 1.75e-36 | 235 |
disease of cellular proliferation | 9.23e-36 | 239 |
hematologic cancer | 1.38e-19 | 51 |
immune system cancer | 1.38e-19 | 51 |
organ system cancer | 5.10e-19 | 137 |
leukemia | 2.18e-15 | 39 |
cell type cancer | 4.47e-15 | 143 |
carcinoma | 6.17e-14 | 106 |
myeloid leukemia | 2.58e-11 | 31 |
Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
Motifs | -log10(p-value) |
---|---|
MA0003.1 | 1.35295 |
MA0004.1 | 0.502801 |
MA0006.1 | 1.62096 |
MA0007.1 | 0.483857 |
MA0009.1 | 0.973289 |
MA0014.1 | 0.367415 |
MA0017.1 | 0.380797 |
MA0019.1 | 0.652951 |
MA0024.1 | 3.33297 |
MA0025.1 | 1.10816 |
MA0027.1 | 2.59001 |
MA0028.1 | 0.35747 |
MA0029.1 | 0.886702 |
MA0030.1 | 0.875089 |
MA0031.1 | 0.809638 |
MA0038.1 | 0.60704 |
MA0040.1 | 0.892629 |
MA0041.1 | 0.521615 |
MA0042.1 | 0.48922 |
MA0043.1 | 0.973609 |
MA0046.1 | 0.962263 |
MA0048.1 | 0.120314 |
MA0050.1 | 0.490116 |
MA0051.1 | 0.602745 |
MA0052.1 | 0.896548 |
MA0055.1 | 0.649431 |
MA0056.1 | 0 |
MA0057.1 | 0.744639 |
MA0058.1 | 1.04727 |
MA0059.1 | 0.404929 |
MA0060.1 | 1.86058 |
MA0061.1 | 0.198335 |
MA0063.1 | 0 |
MA0066.1 | 0.607474 |
MA0067.1 | 1.29359 |
MA0068.1 | 2.88764 |
MA0069.1 | 0.958358 |
MA0070.1 | 0.947018 |
MA0071.1 | 0.567661 |
MA0072.1 | 0.942461 |
MA0073.1 | 4.03024 |
MA0074.1 | 0.60198 |
MA0076.1 | 0.422297 |
MA0077.1 | 0.934645 |
MA0078.1 | 0.703614 |
MA0081.1 | 0.405093 |
MA0083.1 | 0.980893 |
MA0084.1 | 1.48179 |
MA0087.1 | 0.939982 |
MA0088.1 | 0.252594 |
MA0089.1 | 0 |
MA0090.1 | 0.436918 |
MA0091.1 | 0.505453 |
MA0092.1 | 0.467172 |
MA0093.1 | 0.9112 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.621149 |
MA0101.1 | 0.918548 |
MA0103.1 | 0.332048 |
MA0105.1 | 0.104569 |
MA0106.1 | 5.14579 |
MA0107.1 | 0.752965 |
MA0108.2 | 0.806528 |
MA0109.1 | 0 |
MA0111.1 | 1.14351 |
MA0113.1 | 0.665691 |
MA0114.1 | 0.269076 |
MA0115.1 | 1.21667 |
MA0116.1 | 0.760835 |
MA0117.1 | 1.01134 |
MA0119.1 | 1.00897 |
MA0122.1 | 1.03753 |
MA0124.1 | 1.17486 |
MA0125.1 | 1.0901 |
MA0130.1 | 0 |
MA0131.1 | 1.71579 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 1.00402 |
MA0136.1 | 0.614215 |
MA0139.1 | 0.547495 |
MA0140.1 | 0.564957 |
MA0141.1 | 0.403171 |
MA0142.1 | 0.777365 |
MA0143.1 | 0.66587 |
MA0144.1 | 0.254954 |
MA0145.1 | 0.276317 |
MA0146.1 | 0.547931 |
MA0147.1 | 1.40486 |
MA0148.1 | 0.528066 |
MA0149.1 | 0.555119 |
MA0062.2 | 0.563664 |
MA0035.2 | 0.564239 |
MA0039.2 | 1.82845 |
MA0138.2 | 0.704862 |
MA0002.2 | 0.213296 |
MA0137.2 | 0.36398 |
MA0104.2 | 1.19136 |
MA0047.2 | 0.636643 |
MA0112.2 | 0.944394 |
MA0065.2 | 0.0828768 |
MA0150.1 | 0.430951 |
MA0151.1 | 0 |
MA0152.1 | 0.571637 |
MA0153.1 | 1.07307 |
MA0154.1 | 0.335384 |
MA0155.1 | 0.250175 |
MA0156.1 | 0.36627 |
MA0157.1 | 0.749547 |
MA0158.1 | 0 |
MA0159.1 | 0.281681 |
MA0160.1 | 0.543522 |
MA0161.1 | 0 |
MA0162.1 | 1.55314 |
MA0163.1 | 1.72058 |
MA0164.1 | 0.678332 |
MA0080.2 | 0.344472 |
MA0018.2 | 1.56673 |
MA0099.2 | 0.572 |
MA0079.2 | 1.1389 |
MA0102.2 | 1.51913 |
MA0258.1 | 0.245543 |
MA0259.1 | 0.787775 |
MA0442.1 | 0 |
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
TF | #promoters | Enrichment | p-value | q-value |
---|---|---|---|---|
BRCA1#672 | 3 | 8.65038456138161 | 0.00365929333120223 | 0.0184731697707574 |
CCNT2#905 | 6 | 5.43102992311083 | 9.35028339706757e-05 | 0.00135780623985865 |
E2F1#1869 | 7 | 4.90738921487932 | 1.45832274679793e-05 | 0.000346701045647232 |
E2F4#1874 | 7 | 12.6680603152844 | 1.90745058834676e-08 | 1.36633903975547e-06 |
E2F6#1876 | 7 | 5.01715573169739 | 1.24910426162553e-05 | 0.000308040613884082 |
EGR1#1958 | 6 | 4.27558208126583 | 0.000376213061986645 | 0.0037359813616833 |
ELF1#1997 | 5 | 3.04149854200538 | 0.00971956226937075 | 0.0365604669134094 |
GABPB1#2553 | 4 | 4.03867647781838 | 0.0098011349469615 | 0.0368434198152004 |
GATA1#2623 | 3 | 5.81156063305733 | 0.0111931160082029 | 0.0411256936774213 |
GTF2B#2959 | 3 | 13.6902128289961 | 0.000976196317024572 | 0.0070152733195988 |
HDAC2#3066 | 3 | 5.74955152998268 | 0.0115304170404053 | 0.0421691783199528 |
HEY1#23462 | 7 | 4.04011104310571 | 5.68979821988558e-05 | 0.000949563496782727 |
HMGN3#9324 | 5 | 5.84181980239328 | 0.000462918719129959 | 0.00426300750438354 |
HNF4A#3172 | 3 | 9.91383872698015 | 0.00247865482166154 | 0.0139213891325361 |
IRF1#3659 | 6 | 6.54614036019763 | 3.13027310449255e-05 | 0.000631734478763474 |
MAX#4149 | 5 | 4.60896822071937 | 0.00142433701403361 | 0.0091779573919457 |
MYC#4609 | 5 | 3.73020133686386 | 0.00382194422230669 | 0.0188692461299749 |
NFKB1#4790 | 5 | 3.9200453029956 | 0.00303658142448461 | 0.0161163495981171 |
NFYA#4800 | 4 | 10.528903257046 | 0.000265728718323708 | 0.00284436216183353 |
NFYB#4801 | 4 | 9.57702471630654 | 0.000383006171601648 | 0.00376017875126006 |
NRF1#4899 | 5 | 8.72162817693636 | 6.71450045004423e-05 | 0.00107324106596598 |
POLR2A#5430 | 7 | 2.14745317655807 | 0.00474763644761028 | 0.02232701742399 |
POU2F2#5452 | 4 | 5.20349946156716 | 0.00386671431017981 | 0.0190623448591394 |
PRDM1#639 | 2 | 37.6659873649888 | 0.001177328194587 | 0.00799837242662277 |
RFX5#5993 | 4 | 6.88452047268291 | 0.00135220703152858 | 0.00890267604903318 |
SIN3A#25942 | 7 | 5.40888472681514 | 7.3795239773719e-06 | 0.000211443101419134 |
SMARCB1#6598 | 4 | 10.4301233035185 | 0.000275586383300937 | 0.00293633608300006 |
SP1#6667 | 5 | 4.07027241295778 | 0.00254920612899158 | 0.014108236919387 |
SP2#6668 | 3 | 11.2086559259334 | 0.00174151533091611 | 0.0107165990835227 |
SREBF1#6720 | 3 | 20.1453640459236 | 0.000315801026139468 | 0.00323606194750587 |
SRF#6722 | 3 | 5.91307639807192 | 0.0106686813016745 | 0.0393900521959057 |
TAF1#6872 | 7 | 3.34304628574529 | 0.000214233631962245 | 0.0024646779344024 |
TAF7#6879 | 4 | 6.53318251709938 | 0.0016484941094751 | 0.0103106405736897 |
TBP#6908 | 7 | 3.70677068709639 | 0.000103967209750511 | 0.00145047173645921 |
YY1#7528 | 5 | 3.50797910703847 | 0.00507257067280898 | 0.0236126853493269 |
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
This analysis result is provided for C0 - C305 clusters.