Coexpression cluster:C1671
From FANTOM5_SSTAR
Full id: C1671_Alveolar_Mesenchymal_Renal_Pericytes_Fibroblast_Placental_Smooth
Phase1 CAGE Peaks
Hg19::chr12:49961883..49961933,- | p1@MCRS1 |
Hg19::chr17:80009748..80009808,+ | p1@GPS1 |
Hg19::chr19:52693259..52693335,+ | p1@PPP2R1A |
Hg19::chr8:144911476..144911517,- | p1@PUF60 |
Hg19::chr9:131873659..131873703,+ | p1@PPP2R4 |
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 |
---|---|---|---|---|
0.00011825831370825 | 0.0249525041924409 | 2 | 99 | IL-6 Signaling Pathway (Wikipathways):WP364 |
0.00011825831370825 | 0.0249525041924409 | 2 | 99 | Wnt Signaling Pathway and Pluripotency (Wikipathways):WP399 |
1.54262472139839e-05 | 0.00976481448645182 | 2 | 36 | Glycogen Metabolism (Wikipathways):WP500 |
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:0043086 | negative regulation of catalytic activity | 3.78194462493104e-05 |
GO:0045936 | negative regulation of phosphate metabolic process | 0.000158051900403208 |
GO:0000188 | inactivation of MAPK activity | 0.000206622407020211 |
GO:0043407 | negative regulation of MAP kinase activity | 0.000279449198969006 |
GO:0000159 | protein phosphatase type 2A complex | 0.000401363718236737 |
GO:0008601 | protein phosphatase type 2A regulator activity | 0.000401363718236737 |
GO:0008287 | protein serine/threonine phosphatase complex | 0.000691525695820129 |
GO:0006469 | negative regulation of protein kinase activity | 0.000691525695820129 |
GO:0033673 | negative regulation of kinase activity | 0.000691525695820129 |
GO:0051348 | negative regulation of transferase activity | 0.000691525695820129 |
GO:0051174 | regulation of phosphorus metabolic process | 0.000789676369929298 |
GO:0019220 | regulation of phosphate metabolic process | 0.000789676369929298 |
GO:0019888 | protein phosphatase regulator activity | 0.000893608372889712 |
GO:0050790 | regulation of catalytic activity | 0.000893608372889712 |
GO:0019208 | phosphatase regulator activity | 0.000893608372889712 |
GO:0043405 | regulation of MAP kinase activity | 0.00102509877655625 |
GO:0065009 | regulation of a molecular function | 0.00102509877655625 |
GO:0051248 | negative regulation of protein metabolic process | 0.00115829653005875 |
GO:0046982 | protein heterodimerization activity | 0.00115829653005875 |
GO:0032516 | positive regulation of phosphoprotein phosphatase activity | 0.00149739683319767 |
GO:0035305 | negative regulation of dephosphorylation | 0.00149739683319767 |
GO:0035308 | negative regulation of protein amino acid dephosphorylation | 0.00149739683319767 |
GO:0032515 | negative regulation of phosphoprotein phosphatase activity | 0.00149739683319767 |
GO:0000165 | MAPKKK cascade | 0.00187182064475157 |
GO:0043234 | protein complex | 0.00225849552721242 |
GO:0008160 | protein tyrosine phosphatase activator activity | 0.00237504134788093 |
GO:0035304 | regulation of protein amino acid dephosphorylation | 0.00237504134788093 |
GO:0035306 | positive regulation of dephosphorylation | 0.00237504134788093 |
GO:0035307 | positive regulation of protein amino acid dephosphorylation | 0.00237504134788093 |
GO:0044428 | nuclear part | 0.00256907040405961 |
GO:0008380 | RNA splicing | 0.00322838175416037 |
GO:0051004 | regulation of lipoprotein lipase activity | 0.00322838175416037 |
GO:0005625 | soluble fraction | 0.00328201699106695 |
GO:0045859 | regulation of protein kinase activity | 0.00328201699106695 |
GO:0043549 | regulation of kinase activity | 0.00328201699106695 |
GO:0006470 | protein amino acid dephosphorylation | 0.00328201699106695 |
GO:0051338 | regulation of transferase activity | 0.00328201699106695 |
GO:0051721 | protein phosphatase 2A binding | 0.00335941899159541 |
GO:0050732 | negative regulation of peptidyl-tyrosine phosphorylation | 0.00335941899159541 |
GO:0042518 | negative regulation of tyrosine phosphorylation of Stat3 protein | 0.00335941899159541 |
GO:0042532 | negative regulation of tyrosine phosphorylation of STAT protein | 0.00335941899159541 |
GO:0016311 | dephosphorylation | 0.00371002105991095 |
GO:0046426 | negative regulation of JAK-STAT cascade | 0.00391272925030626 |
GO:0035303 | regulation of dephosphorylation | 0.00391272925030626 |
GO:0032991 | macromolecular complex | 0.00402677508269199 |
GO:0051346 | negative regulation of hydrolase activity | 0.00439531790564664 |
GO:0019907 | cyclin-dependent protein kinase activating kinase holoenzyme complex | 0.00439531790564664 |
GO:0046983 | protein dimerization activity | 0.00537789962602607 |
GO:0033239 | negative regulation of amine metabolic process | 0.00537789962602607 |
GO:0001933 | negative regulation of protein amino acid phosphorylation | 0.00537789962602607 |
GO:0045763 | negative regulation of amino acid metabolic process | 0.00537789962602607 |
GO:0007243 | protein kinase cascade | 0.00537789962602607 |
GO:0031324 | negative regulation of cellular metabolic process | 0.00541627948881933 |
GO:0005515 | protein binding | 0.0055324140350824 |
GO:0008180 | signalosome | 0.0055324140350824 |
GO:0042516 | regulation of tyrosine phosphorylation of Stat3 protein | 0.0055324140350824 |
GO:0042503 | tyrosine phosphorylation of Stat3 protein | 0.0059348073943482 |
GO:0005095 | GTPase inhibitor activity | 0.0059348073943482 |
GO:0051246 | regulation of protein metabolic process | 0.00595602286000441 |
GO:0009892 | negative regulation of metabolic process | 0.00610674870586535 |
GO:0043666 | regulation of phosphoprotein phosphatase activity | 0.00610674870586535 |
GO:0019211 | phosphatase activator activity | 0.00610674870586535 |
GO:0042326 | negative regulation of phosphorylation | 0.00655577712693528 |
GO:0042509 | regulation of tyrosine phosphorylation of STAT protein | 0.00699071010828025 |
GO:0046425 | regulation of JAK-STAT cascade | 0.00794117338964218 |
GO:0006396 | RNA processing | 0.00819423571368854 |
GO:0019903 | protein phosphatase binding | 0.00873031183308974 |
GO:0007260 | tyrosine phosphorylation of STAT protein | 0.00910738425907021 |
GO:0019902 | phosphatase binding | 0.0109673418675596 |
GO:0045937 | positive regulation of phosphate metabolic process | 0.0122826775851395 |
GO:0030111 | regulation of Wnt receptor signaling pathway | 0.0130769167866152 |
GO:0006275 | regulation of DNA replication | 0.0131889294960938 |
GO:0050730 | regulation of peptidyl-tyrosine phosphorylation | 0.0131889294960938 |
GO:0005634 | nucleus | 0.0136970240374491 |
GO:0006464 | protein modification process | 0.0139019635560335 |
GO:0006672 | ceramide metabolic process | 0.0144746637695659 |
GO:0043412 | biopolymer modification | 0.0151993344077791 |
GO:0046519 | sphingoid metabolic process | 0.0154229990596633 |
GO:0007259 | JAK-STAT cascade | 0.0169640923904088 |
GO:0006915 | apoptosis | 0.0175839219603667 |
GO:0012501 | programmed cell death | 0.0175839219603667 |
GO:0018108 | peptidyl-tyrosine phosphorylation | 0.0175839219603667 |
GO:0018212 | peptidyl-tyrosine modification | 0.0175839219603667 |
GO:0065007 | biological regulation | 0.0175839219603667 |
GO:0001932 | regulation of protein amino acid phosphorylation | 0.0175839219603667 |
GO:0000267 | cell fraction | 0.0175839219603667 |
GO:0033238 | regulation of amine metabolic process | 0.0175839219603667 |
GO:0006521 | regulation of amino acid metabolic process | 0.0175839219603667 |
GO:0008219 | cell death | 0.0175839219603667 |
GO:0016265 | death | 0.0175839219603667 |
GO:0051052 | regulation of DNA metabolic process | 0.0184923501563252 |
GO:0048522 | positive regulation of cellular process | 0.0189376544774643 |
GO:0030308 | negative regulation of cell growth | 0.0195671720898842 |
GO:0045792 | negative regulation of cell size | 0.0197231137967106 |
GO:0044424 | intracellular part | 0.0198778405874726 |
GO:0045926 | negative regulation of growth | 0.0218066619643468 |
GO:0010033 | response to organic substance | 0.0218919223482464 |
GO:0048518 | positive regulation of biological process | 0.0218919223482464 |
GO:0042325 | regulation of phosphorylation | 0.0221818958115347 |
GO:0007254 | JNK cascade | 0.0223018899835282 |
GO:0030155 | regulation of cell adhesion | 0.0224194681089413 |
GO:0031098 | stress-activated protein kinase signaling pathway | 0.0226476577150369 |
GO:0006665 | sphingolipid metabolic process | 0.0226476577150369 |
GO:0048523 | negative regulation of cellular process | 0.0235410929670742 |
GO:0051345 | positive regulation of hydrolase activity | 0.0248182608014528 |
GO:0048519 | negative regulation of biological process | 0.0248950097654811 |
GO:0043283 | biopolymer metabolic process | 0.0265148531260851 |
GO:0048468 | cell development | 0.0267244856626852 |
GO:0051247 | positive regulation of protein metabolic process | 0.0267244856626852 |
GO:0031323 | regulation of cellular metabolic process | 0.0275270140054957 |
GO:0044446 | intracellular organelle part | 0.0310106326982573 |
GO:0044422 | organelle part | 0.0310106326982573 |
GO:0019222 | regulation of metabolic process | 0.0311549359038064 |
GO:0009968 | negative regulation of signal transduction | 0.0312291095401296 |
GO:0005622 | intracellular | 0.0330791608794974 |
GO:0018193 | peptidyl-amino acid modification | 0.0356717009529934 |
GO:0043231 | intracellular membrane-bound organelle | 0.0357841435503027 |
GO:0043227 | membrane-bound organelle | 0.0357841435503027 |
GO:0045595 | regulation of cell differentiation | 0.0412638299707287 |
GO:0016055 | Wnt receptor signaling pathway | 0.0412638299707287 |
GO:0006793 | phosphorus metabolic process | 0.0432363809675238 |
GO:0006796 | phosphate metabolic process | 0.0432363809675238 |
GO:0042803 | protein homodimerization activity | 0.0438331172398033 |
GO:0001558 | regulation of cell growth | 0.0445698769321459 |
GO:0006261 | DNA-dependent DNA replication | 0.0450241300018458 |
GO:0048869 | cellular developmental process | 0.0469299736103358 |
GO:0030154 | cell differentiation | 0.0469299736103358 |
GO:0003823 | antigen binding | 0.0471333021701575 |
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>
Ontology term | p-value | n |
---|---|---|
embryonic cell | 1.56e-26 | 250 |
mesodermal cell | 5.52e-21 | 121 |
contractile cell | 8.09e-16 | 59 |
electrically responsive cell | 2.74e-15 | 61 |
electrically active cell | 2.74e-15 | 61 |
non-terminally differentiated cell | 2.89e-15 | 106 |
animal cell | 3.93e-15 | 679 |
eukaryotic cell | 3.93e-15 | 679 |
muscle cell | 1.42e-13 | 55 |
smooth muscle cell | 4.09e-13 | 43 |
smooth muscle myoblast | 4.09e-13 | 43 |
epithelial cell | 4.34e-13 | 253 |
muscle precursor cell | 4.40e-13 | 58 |
myoblast | 4.40e-13 | 58 |
multi-potent skeletal muscle stem cell | 4.40e-13 | 58 |
vascular associated smooth muscle cell | 5.06e-11 | 32 |
somatic cell | 4.51e-09 | 588 |
native cell | 5.97e-09 | 722 |
epithelial cell of nephron | 2.22e-08 | 15 |
lining cell | 2.94e-08 | 58 |
barrier cell | 2.94e-08 | 58 |
kidney cortical cell | 4.64e-07 | 12 |
renal cortical epithelial cell | 4.64e-07 | 12 |
ectodermal cell | 6.92e-07 | 72 |
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 | 2.24383 |
MA0004.1 | 0.626788 |
MA0006.1 | 0.452993 |
MA0007.1 | 0.606704 |
MA0009.1 | 1.11255 |
MA0014.1 | 3.07977 |
MA0017.1 | 0.496101 |
MA0019.1 | 0.784036 |
MA0024.1 | 1.00439 |
MA0025.1 | 1.24931 |
MA0027.1 | 2.73598 |
MA0028.1 | 3.05902 |
MA0029.1 | 1.02437 |
MA0030.1 | 1.01252 |
MA0031.1 | 0.945567 |
MA0038.1 | 0.736268 |
MA0040.1 | 1.03042 |
MA0041.1 | 0.64667 |
MA0042.1 | 0.612397 |
MA0043.1 | 1.11288 |
MA0046.1 | 1.10134 |
MA0048.1 | 0.195817 |
MA0050.1 | 0.613347 |
MA0051.1 | 0.731787 |
MA0052.1 | 1.03442 |
MA0055.1 | 0.288856 |
MA0056.1 | 0 |
MA0057.1 | 0.189508 |
MA0058.1 | 0.523638 |
MA0059.1 | 0.522232 |
MA0060.1 | 1.55172 |
MA0061.1 | 0.791444 |
MA0063.1 | 0 |
MA0066.1 | 0.736721 |
MA0067.1 | 1.43651 |
MA0068.1 | 0.692739 |
MA0069.1 | 1.09737 |
MA0070.1 | 1.08584 |
MA0071.1 | 0.695094 |
MA0072.1 | 1.0812 |
MA0073.1 | 0.0140295 |
MA0074.1 | 0.730989 |
MA0076.1 | 3.37477 |
MA0077.1 | 1.07324 |
MA0078.1 | 0.836493 |
MA0081.1 | 1.2972 |
MA0083.1 | 1.12028 |
MA0084.1 | 1.62584 |
MA0087.1 | 1.07867 |
MA0088.1 | 0.132006 |
MA0089.1 | 0 |
MA0090.1 | 0.556637 |
MA0091.1 | 0.629594 |
MA0092.1 | 0.588959 |
MA0093.1 | 0.456342 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.750974 |
MA0101.1 | 0.459973 |
MA0103.1 | 0.442769 |
MA0105.1 | 0.175503 |
MA0106.1 | 0.779931 |
MA0107.1 | 0.378225 |
MA0108.2 | 0.94238 |
MA0109.1 | 0 |
MA0111.1 | 1.40074 |
MA0113.1 | 0.797251 |
MA0114.1 | 0.372523 |
MA0115.1 | 1.35895 |
MA0116.1 | 0.382106 |
MA0117.1 | 1.1512 |
MA0119.1 | 0.504689 |
MA0122.1 | 1.17777 |
MA0124.1 | 1.31673 |
MA0125.1 | 1.23103 |
MA0130.1 | 0 |
MA0131.1 | 1.99092 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 1.14377 |
MA0136.1 | 0.743749 |
MA0139.1 | 0.277033 |
MA0140.1 | 0.692258 |
MA0141.1 | 0.520334 |
MA0142.1 | 0.912455 |
MA0143.1 | 0.797437 |
MA0144.1 | 0.356507 |
MA0145.1 | 0.143698 |
MA0146.1 | 1.35428 |
MA0147.1 | 1.00307 |
MA0148.1 | 0.653474 |
MA0149.1 | 0.681935 |
MA0062.2 | 3.94248 |
MA0035.2 | 0.691506 |
MA0039.2 | 1.92202 |
MA0138.2 | 1.95446 |
MA0002.2 | 0.30855 |
MA0137.2 | 0.47779 |
MA0104.2 | 0.858845 |
MA0047.2 | 0.767096 |
MA0112.2 | 0.136971 |
MA0065.2 | 0.146576 |
MA0150.1 | 0.550239 |
MA0151.1 | 0 |
MA0152.1 | 0.69926 |
MA0153.1 | 1.21379 |
MA0154.1 | 0.172764 |
MA0155.1 | 0.813062 |
MA0156.1 | 1.20729 |
MA0157.1 | 0.883854 |
MA0158.1 | 0 |
MA0159.1 | 0.386729 |
MA0160.1 | 0.669748 |
MA0161.1 | 0 |
MA0162.1 | 1.23503 |
MA0163.1 | 1.05321 |
MA0164.1 | 0.810347 |
MA0080.2 | 0.456437 |
MA0018.2 | 0.781393 |
MA0099.2 | 0.699641 |
MA0079.2 | 1.03616 |
MA0102.2 | 1.66336 |
MA0258.1 | 0.345771 |
MA0259.1 | 1.80881 |
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 |
---|---|---|---|---|
BCL3#602 | 2 | 13.8188411214953 | 0.00790282333228084 | 0.0324358628468159 |
E2F1#1869 | 4 | 3.92591137190346 | 0.00721498454710636 | 0.0298686289485984 |
EGR1#1958 | 4 | 3.99054327584811 | 0.006780098300144 | 0.0287602731964071 |
ELF1#1997 | 5 | 4.25809795880754 | 0.000714241693977684 | 0.00572659974492057 |
ETS1#2113 | 5 | 9.72876092220234 | 1.14685159850452e-05 | 0.00029213666852735 |
GABPB1#2553 | 4 | 5.65414706894574 | 0.00177669650209667 | 0.0109054602399338 |
HEY1#23462 | 5 | 4.04011104310571 | 0.000928885220517799 | 0.00673693357955961 |
IRF1#3659 | 4 | 6.10973100285112 | 0.00131552526476799 | 0.00880718866199388 |
MXI1#4601 | 3 | 5.97694297725558 | 0.00865300488936688 | 0.0329448863563336 |
MYC#4609 | 4 | 4.17782549728752 | 0.00569196903682344 | 0.0256721175607533 |
NFKB1#4790 | 4 | 4.39045073935507 | 0.00470773269252496 | 0.0221963294963936 |
NR2C2#7182 | 2 | 13.0458443620963 | 0.0088363641276826 | 0.0335463843377333 |
NRF1#4899 | 3 | 7.32616766862654 | 0.00483968981711754 | 0.022685353656027 |
POU2F2#5452 | 3 | 5.46367443464551 | 0.0111565009446978 | 0.0410055886737036 |
REST#5978 | 4 | 7.72002297290242 | 0.000528636377365057 | 0.00457189918976724 |
SIN3A#25942 | 5 | 5.40888472681514 | 0.000215952267165727 | 0.00247789923429151 |
SIX5#147912 | 4 | 13.6693722843672 | 5.58844770365977e-05 | 0.000937292259069411 |
SP1#6667 | 4 | 4.55870510251272 | 0.0040757356578168 | 0.0194768133775671 |
SP2#6668 | 2 | 10.4614121975379 | 0.0135319118334714 | 0.0477742999112946 |
TAF1#6872 | 5 | 3.34304628574529 | 0.00239460009087031 | 0.0135198204611528 |
TAF7#6879 | 4 | 9.14645552393913 | 0.000272066287241299 | 0.00290238314332932 |
TCF12#6938 | 3 | 6.38067894131185 | 0.00718516865325884 | 0.029825589387031 |
THAP1#55145 | 2 | 12.5476578411405 | 0.00952843466738653 | 0.0358880662204617 |
YY1#7528 | 4 | 3.92893659988308 | 0.00719386626991762 | 0.0298344200200106 |
ZEB1#6935 | 4 | 13.5107456140351 | 5.85221769500384e-05 | 0.00096693523785557 |
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.