Coexpression cluster:C672
From FANTOM5_SSTAR
Full id: C672_CD14_Smooth_Mesenchymal_Placental_Fibroblast_mesenchymal_Alveolar
Phase1 CAGE Peaks
| Hg19::chr6:36646476..36646498,+ | p1@CDKN1A |
| Hg19::chr6:36646510..36646519,+ | p2@CDKN1A |
| Hg19::chr6:36652080..36652094,+ | p1@BC037414 |
| Hg19::chr6:36652270..36652284,+ | p4@BC037414 |
| Hg19::chr6:36652291..36652299,+ | p5@BC037414 |
| Hg19::chr6:36653519..36653558,+ | p@chr6:36653519..36653558 + |
| Hg19::chr6:36653561..36653579,+ | p@chr6:36653561..36653579 + |
| Hg19::chr6:36653603..36653637,+ | p@chr6:36653603..36653637 + |
| Hg19::chr6:36653937..36653958,+ | p@chr6:36653937..36653958 + |
| Hg19::chr6:36653968..36653983,+ | p@chr6:36653968..36653983 + |
| Hg19::chr6:36654158..36654169,+ | p@chr6:36654158..36654169 + |
| Hg19::chr6:36654222..36654237,+ | p@chr6:36654222..36654237 + |
| Hg19::chr6:36654635..36654646,+ | p@chr6:36654635..36654646 + |
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
No results for this coexpression
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:0043071 | positive regulation of non-apoptotic programmed cell death | 0.00326739667961851 |
| GO:0016244 | non-apoptotic programmed cell death | 0.00326739667961851 |
| GO:0030332 | cyclin binding | 0.00326739667961851 |
| GO:0043070 | regulation of non-apoptotic programmed cell death | 0.00326739667961851 |
| GO:0000307 | cyclin-dependent protein kinase holoenzyme complex | 0.00435652890615801 |
| GO:0045736 | negative regulation of cyclin-dependent protein kinase activity | 0.00435652890615801 |
| GO:0030890 | positive regulation of B cell proliferation | 0.00435652890615801 |
| GO:0030888 | regulation of B cell proliferation | 0.00435652890615801 |
| GO:0048146 | positive regulation of fibroblast proliferation | 0.00435652890615801 |
| GO:0048145 | regulation of fibroblast proliferation | 0.00435652890615801 |
| GO:0048144 | fibroblast proliferation | 0.00435652890615801 |
| GO:0042326 | negative regulation of phosphorylation | 0.00435652890615801 |
| GO:0045936 | negative regulation of phosphate metabolic process | 0.00435652890615801 |
| GO:0031668 | cellular response to extracellular stimulus | 0.00435652890615801 |
| GO:0004861 | cyclin-dependent protein kinase inhibitor activity | 0.00435652890615801 |
| GO:0000086 | G2/M transition of mitotic cell cycle | 0.00435652890615801 |
| GO:0050871 | positive regulation of B cell activation | 0.00435652890615801 |
| GO:0042100 | B cell proliferation | 0.00435652890615801 |
| GO:0051716 | cellular response to stimulus | 0.00544566113269752 |
| GO:0050864 | regulation of B cell activation | 0.00544566113269752 |
| GO:0032946 | positive regulation of mononuclear cell proliferation | 0.00594072123567002 |
| GO:0050671 | positive regulation of lymphocyte proliferation | 0.00594072123567002 |
| GO:0009411 | response to UV | 0.00617174928372385 |
| GO:0000082 | G1/S transition of mitotic cell cycle | 0.00617174928372385 |
| GO:0008629 | induction of apoptosis by intracellular signals | 0.00627340162486754 |
| GO:0004860 | protein kinase inhibitor activity | 0.00630945565719436 |
| GO:0019210 | kinase inhibitor activity | 0.00630945565719436 |
| GO:0050670 | regulation of lymphocyte proliferation | 0.00630945565719436 |
| GO:0032944 | regulation of mononuclear cell proliferation | 0.00630945565719436 |
| GO:0000079 | regulation of cyclin-dependent protein kinase activity | 0.00664370658189097 |
| GO:0051251 | positive regulation of lymphocyte activation | 0.00664370658189097 |
| GO:0032943 | mononuclear cell proliferation | 0.00664370658189097 |
| GO:0030308 | negative regulation of cell growth | 0.00664370658189097 |
| GO:0046651 | lymphocyte proliferation | 0.00664370658189097 |
| GO:0045792 | negative regulation of cell size | 0.00664370658189097 |
| GO:0006469 | negative regulation of protein kinase activity | 0.00664370658189097 |
| GO:0033673 | negative regulation of kinase activity | 0.00664370658189097 |
| GO:0051348 | negative regulation of transferase activity | 0.00664370658189097 |
| GO:0042113 | B cell activation | 0.00664370658189097 |
| GO:0045926 | negative regulation of growth | 0.00664370658189097 |
| GO:0042325 | regulation of phosphorylation | 0.00680043536571006 |
| GO:0009991 | response to extracellular stimulus | 0.00683182942102052 |
| GO:0051174 | regulation of phosphorus metabolic process | 0.00683182942102052 |
| GO:0019220 | regulation of phosphate metabolic process | 0.00683182942102052 |
| GO:0051249 | regulation of lymphocyte activation | 0.00735769326373353 |
| GO:0050865 | regulation of cell activation | 0.0075080604552936 |
| GO:0009416 | response to light stimulus | 0.0075080604552936 |
| GO:0051329 | interphase of mitotic cell cycle | 0.00771468660465481 |
| GO:0043086 | negative regulation of catalytic activity | 0.00773506152726014 |
| GO:0051325 | interphase | 0.00784175203108442 |
| GO:0009314 | response to radiation | 0.00846171960619152 |
| GO:0007050 | cell cycle arrest | 0.00846171960619152 |
| GO:0019887 | protein kinase regulator activity | 0.00863085915370927 |
| GO:0019207 | kinase regulator activity | 0.0098425282694681 |
| GO:0046649 | lymphocyte activation | 0.012277490553718 |
| GO:0001558 | regulation of cell growth | 0.0126028157642428 |
| GO:0009628 | response to abiotic stimulus | 0.0126110047283521 |
| GO:0045321 | leukocyte activation | 0.0135202621225593 |
| GO:0016049 | cell growth | 0.0144990727658071 |
| GO:0040008 | regulation of growth | 0.0144990727658071 |
| GO:0008361 | regulation of cell size | 0.0144990727658071 |
| GO:0001775 | cell activation | 0.0144990727658071 |
| GO:0006917 | induction of apoptosis | 0.0144990727658071 |
| GO:0012502 | induction of programmed cell death | 0.0144990727658071 |
| GO:0045786 | negative regulation of progression through cell cycle | 0.0147111773207944 |
| GO:0008285 | negative regulation of cell proliferation | 0.0147111773207944 |
| GO:0043066 | negative regulation of apoptosis | 0.0147111773207944 |
| GO:0043069 | negative regulation of programmed cell death | 0.0147111773207944 |
| GO:0008284 | positive regulation of cell proliferation | 0.0147111773207944 |
| GO:0045859 | regulation of protein kinase activity | 0.0147499621537064 |
| GO:0043549 | regulation of kinase activity | 0.0148490140181724 |
| GO:0051338 | regulation of transferase activity | 0.0149453144419587 |
| GO:0043065 | positive regulation of apoptosis | 0.0151889791593077 |
| GO:0043068 | positive regulation of programmed cell death | 0.0151889791593077 |
| GO:0051239 | regulation of multicellular organismal process | 0.0160901134267436 |
| GO:0000278 | mitotic cell cycle | 0.0186872160974673 |
| GO:0000074 | regulation of progression through cell cycle | 0.0199721390113478 |
| GO:0051726 | regulation of cell cycle | 0.0200512035552657 |
| GO:0022403 | cell cycle phase | 0.0203488502072444 |
| GO:0031324 | negative regulation of cellular metabolic process | 0.0207479689155775 |
| GO:0004857 | enzyme inhibitor activity | 0.0215675073008563 |
| GO:0009892 | negative regulation of metabolic process | 0.0231639829644499 |
| GO:0006974 | response to DNA damage stimulus | 0.0235147584332384 |
| GO:0042127 | regulation of cell proliferation | 0.0242141955481806 |
| GO:0000902 | cell morphogenesis | 0.0242141955481806 |
| GO:0032989 | cellular structure morphogenesis | 0.0242141955481806 |
| GO:0009719 | response to endogenous stimulus | 0.0264896987512366 |
| GO:0005829 | cytosol | 0.0278817849994113 |
| GO:0042981 | regulation of apoptosis | 0.0278817849994113 |
| GO:0043067 | regulation of programmed cell death | 0.0278817849994113 |
| GO:0050790 | regulation of catalytic activity | 0.0289637361343472 |
| GO:0022402 | cell cycle process | 0.0295959844168343 |
| GO:0009605 | response to external stimulus | 0.0296525031999787 |
| GO:0065009 | regulation of a molecular function | 0.0310982010216173 |
| GO:0008283 | cell proliferation | 0.0341643582640812 |
| GO:0007049 | cell cycle | 0.0380742474194434 |
| GO:0006915 | apoptosis | 0.0383196726235531 |
| GO:0012501 | programmed cell death | 0.0383196726235531 |
| GO:0008219 | cell death | 0.0395572824679148 |
| GO:0016265 | death | 0.0395572824679148 |
| GO:0065008 | regulation of biological quality | 0.0407463585928896 |
| GO:0048522 | positive regulation of cellular process | 0.0407463585928896 |
| GO:0009653 | anatomical structure morphogenesis | 0.0442843278130819 |
| GO:0048518 | positive regulation of biological process | 0.0444868624840366 |
| GO:0048523 | negative regulation of cellular process | 0.0471749844409682 |
| GO:0004672 | protein kinase activity | 0.0475930233333111 |
| GO:0048519 | negative regulation of biological process | 0.0481253940848483 |
| GO:0006950 | response to stress | 0.0492933178085657 |
| GO:0048468 | cell development | 0.0496404486371399 |
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><br>
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 | 0.0652591 |
| MA0004.1 | 0.297884 |
| MA0006.1 | 0.169524 |
| MA0007.1 | 0.282081 |
| MA0009.1 | 0.724811 |
| MA0014.1 | 0.54491 |
| MA0017.1 | 0.199401 |
| MA0019.1 | 0.428118 |
| MA0024.1 | 0.6245 |
| MA0025.1 | 0.854131 |
| MA0027.1 | 2.32165 |
| MA0028.1 | 0.181601 |
| MA0029.1 | 0.642879 |
| MA0030.1 | 0.63197 |
| MA0031.1 | 1.39986 |
| MA0038.1 | 0.387473 |
| MA0040.1 | 0.648455 |
| MA0041.1 | 0.313738 |
| MA0042.1 | 0.286538 |
| MA0043.1 | 0.725115 |
| MA0046.1 | 0.714324 |
| MA0048.1 | 1.73714 |
| MA0050.1 | 0.287284 |
| MA0051.1 | 0.383704 |
| MA0052.1 | 1.57036 |
| MA0055.1 | 0.183899 |
| MA0056.1 | 0 |
| MA0057.1 | 0.123867 |
| MA0058.1 | 0.625569 |
| MA0059.1 | 0.623149 |
| MA0060.1 | 0.622587 |
| MA0061.1 | 0.542967 |
| MA0063.1 | 0 |
| MA0066.1 | 2.67555 |
| MA0067.1 | 1.03434 |
| MA0068.1 | 0.0529803 |
| MA0069.1 | 0.710614 |
| MA0070.1 | 0.69985 |
| MA0071.1 | 0.930644 |
| MA0072.1 | 0.695528 |
| MA0073.1 | 0.0028571 |
| MA0074.1 | 0.383033 |
| MA0076.1 | 0.231962 |
| MA0077.1 | 0.688123 |
| MA0078.1 | 0.473657 |
| MA0081.1 | 1.82632 |
| MA0083.1 | 0.732051 |
| MA0084.1 | 1.21913 |
| MA0087.1 | 0.693179 |
| MA0088.1 | 2.01936 |
| MA0089.1 | 0 |
| MA0090.1 | 0.243681 |
| MA0091.1 | 0.812021 |
| MA0092.1 | 0.268302 |
| MA0093.1 | 0.171791 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 1.82424 |
| MA0101.1 | 0.17426 |
| MA0103.1 | 0.489275 |
| MA0105.1 | 0.10818 |
| MA0106.1 | 1.90842 |
| MA0107.1 | 0.121572 |
| MA0108.2 | 0.568002 |
| MA0109.1 | 0 |
| MA0111.1 | 1.30787 |
| MA0113.1 | 0.439505 |
| MA0114.1 | 0.118142 |
| MA0115.1 | 0.959312 |
| MA0116.1 | 0.391626 |
| MA0117.1 | 0.76111 |
| MA0119.1 | 0.205526 |
| MA0122.1 | 0.786181 |
| MA0124.1 | 0.918678 |
| MA0125.1 | 0.83671 |
| MA0130.1 | 0 |
| MA0131.1 | 0.490408 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.754112 |
| MA0136.1 | 1.02008 |
| MA0139.1 | 3.02309 |
| MA0140.1 | 0.350813 |
| MA0141.1 | 0.216821 |
| MA0142.1 | 0.541045 |
| MA0143.1 | 0.439666 |
| MA0144.1 | 1.17643 |
| MA0145.1 | 0.194261 |
| MA0146.1 | 1.14469 |
| MA0147.1 | 0.126316 |
| MA0148.1 | 0.319209 |
| MA0149.1 | 0.342334 |
| MA0062.2 | 0.0702147 |
| MA0035.2 | 0.350194 |
| MA0039.2 | 0.224942 |
| MA0138.2 | 0.474787 |
| MA0002.2 | 0.0821804 |
| MA0137.2 | 0.54754 |
| MA0104.2 | 0.298328 |
| MA0047.2 | 0.413608 |
| MA0112.2 | 6.90365 |
| MA0065.2 | 0.641236 |
| MA0150.1 | 0.238884 |
| MA0151.1 | 0 |
| MA0152.1 | 0.356591 |
| MA0153.1 | 0.820317 |
| MA0154.1 | 1.54414 |
| MA0155.1 | 0.167839 |
| MA0156.1 | 0.18827 |
| MA0157.1 | 0.515488 |
| MA0158.1 | 0 |
| MA0159.1 | 0.795271 |
| MA0160.1 | 0.332385 |
| MA0161.1 | 0 |
| MA0162.1 | 0.350522 |
| MA0163.1 | 2.79674 |
| MA0164.1 | 0.450848 |
| MA0080.2 | 0.985821 |
| MA0018.2 | 0.425847 |
| MA0099.2 | 0.356906 |
| MA0079.2 | 0.022543 |
| MA0102.2 | 1.25596 |
| MA0258.1 | 2.93741 |
| MA0259.1 | 0.132107 |
| 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 |
|---|---|---|---|---|
| JUNB#3726 | 3 | 7.06399215226642 | 0.007792750127433 | 0.0320180585608787 |
| POLR2A#5430 | 13 | 2.14745317655807 | 4.83928878402115e-05 | 0.000841089168437984 |
| POU2F2#5452 | 5 | 3.50235540682405 | 0.00961613860265682 | 0.0361909873701937 |
| ZBTB33#10009 | 3 | 7.30724423768796 | 0.00709817327748382 | 0.0295974016419984 |
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.
