Coexpression cluster:C1220
From FANTOM5_SSTAR
Full id: C1220_Mesenchymal_Fibroblast_Renal_Alveolar_Trabecular_Smooth_Hepatic
Phase1 CAGE Peaks
| Hg19::chr16:31483374..31483390,+ | p2@TGFB1I1 |
| Hg19::chr19:4400432..4400570,- | p1@SH3GL1 |
| Hg19::chr8:22423168..22423206,+ | p4@SORBS3 |
| Hg19::chr8:22423219..22423330,+ | p1@SORBS3 |
| Hg19::chr8:22423457..22423476,+ | p9@SORBS3 |
| Hg19::chr8:22423479..22423528,+ | p2@SORBS3 |
| Hg19::chr8:22423529..22423543,+ | p7@SORBS3 |
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:0051496 | positive regulation of stress fiber formation | 0.00953586230242861 |
| GO:0051495 | positive regulation of cytoskeleton organization and biogenesis | 0.00953586230242861 |
| GO:0032233 | positive regulation of actin filament bundle formation | 0.00953586230242861 |
| GO:0017166 | vinculin binding | 0.00953586230242861 |
| GO:0030054 | cell junction | 0.00953586230242861 |
| GO:0008134 | transcription factor binding | 0.00953586230242861 |
| GO:0051492 | regulation of stress fiber formation | 0.00953586230242861 |
| GO:0032231 | regulation of actin filament bundle formation | 0.00953586230242861 |
| GO:0043149 | stress fiber formation | 0.00988875127094105 |
| GO:0043410 | positive regulation of MAPKKK cascade | 0.0101709875930319 |
| GO:0006366 | transcription from RNA polymerase II promoter | 0.0137426466736377 |
| GO:0051130 | positive regulation of cellular component organization and biogenesis | 0.0146666708048605 |
| GO:0043408 | regulation of MAPKKK cascade | 0.0146666708048605 |
| GO:0031901 | early endosome membrane | 0.0154340161621278 |
| GO:0051017 | actin filament bundle formation | 0.016098849256612 |
| GO:0050681 | androgen receptor binding | 0.0174741809876831 |
| GO:0048522 | positive regulation of cellular process | 0.0177970360144775 |
| GO:0022610 | biological adhesion | 0.0177970360144775 |
| GO:0007155 | cell adhesion | 0.0177970360144775 |
| GO:0035258 | steroid hormone receptor binding | 0.0179571336086724 |
| GO:0048518 | positive regulation of biological process | 0.0179571336086724 |
| GO:0030521 | androgen receptor signaling pathway | 0.0179571336086724 |
| GO:0005925 | focal adhesion | 0.0179571336086724 |
| GO:0048523 | negative regulation of cellular process | 0.0179571336086724 |
| GO:0005924 | cell-substrate adherens junction | 0.0179571336086724 |
| GO:0007165 | signal transduction | 0.0179571336086724 |
| GO:0030055 | cell-matrix junction | 0.0179571336086724 |
| GO:0048519 | negative regulation of biological process | 0.0179571336086724 |
| GO:0007015 | actin filament organization | 0.0179571336086724 |
| GO:0016363 | nuclear matrix | 0.0182556209063587 |
| GO:0005769 | early endosome | 0.0182556209063587 |
| GO:0007154 | cell communication | 0.0182556209063587 |
| GO:0030518 | steroid hormone receptor signaling pathway | 0.0182556209063587 |
| GO:0005912 | adherens junction | 0.0182556209063587 |
| GO:0030522 | intracellular receptor-mediated signaling pathway | 0.0182556209063587 |
| GO:0035257 | nuclear hormone receptor binding | 0.0182556209063587 |
| GO:0051493 | regulation of cytoskeleton organization and biogenesis | 0.0182556209063587 |
| GO:0033043 | regulation of organelle organization and biogenesis | 0.0182556209063587 |
| GO:0051427 | hormone receptor binding | 0.0182556209063587 |
| GO:0005856 | cytoskeleton | 0.0182556209063587 |
| GO:0005200 | structural constituent of cytoskeleton | 0.0247925546529704 |
| GO:0016323 | basolateral plasma membrane | 0.0247925546529704 |
| GO:0044440 | endosomal part | 0.0247925546529704 |
| GO:0010008 | endosome membrane | 0.0247925546529704 |
| GO:0051128 | regulation of cellular component organization and biogenesis | 0.028176292534052 |
| GO:0031589 | cell-substrate adhesion | 0.0283881677841821 |
| GO:0007242 | intracellular signaling cascade | 0.0295528142016561 |
| GO:0005737 | cytoplasm | 0.0320387244708274 |
| GO:0000122 | negative regulation of transcription from RNA polymerase II promoter | 0.032836619654347 |
| GO:0016055 | Wnt receptor signaling pathway | 0.036521136109633 |
| GO:0044459 | plasma membrane part | 0.036521136109633 |
| GO:0000165 | MAPKKK cascade | 0.036521136109633 |
| GO:0009967 | positive regulation of signal transduction | 0.036545466937897 |
| GO:0003713 | transcription coactivator activity | 0.0427683417257407 |
| GO:0005768 | endosome | 0.0427683417257407 |
| GO:0010324 | membrane invagination | 0.0427683417257407 |
| GO:0006897 | endocytosis | 0.0427683417257407 |
| GO:0043231 | intracellular membrane-bound organelle | 0.0427683417257407 |
| GO:0043227 | membrane-bound organelle | 0.0427683417257407 |
| GO:0045892 | negative regulation of transcription, DNA-dependent | 0.0427683417257407 |
| GO:0005515 | protein binding | 0.0439555903333185 |
| GO:0045893 | positive regulation of transcription, DNA-dependent | 0.0451167438222109 |
| GO:0008285 | negative regulation of cell proliferation | 0.0451167438222109 |
| GO:0007417 | central nervous system development | 0.0455739196306436 |
| GO:0043232 | intracellular non-membrane-bound organelle | 0.0455739196306436 |
| GO:0043228 | non-membrane-bound organelle | 0.0455739196306436 |
| GO:0030036 | actin cytoskeleton organization and biogenesis | 0.0465410336754617 |
| GO:0030029 | actin filament-based process | 0.0482515979559621 |
| GO:0016020 | membrane | 0.0492796510940489 |
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 |
|---|---|---|
| mesodermal cell | 2.30e-29 | 121 |
| embryonic cell | 3.30e-27 | 250 |
| contractile cell | 2.79e-20 | 59 |
| muscle precursor cell | 6.89e-19 | 58 |
| myoblast | 6.89e-19 | 58 |
| multi-potent skeletal muscle stem cell | 6.89e-19 | 58 |
| muscle cell | 1.31e-18 | 55 |
| fibroblast | 2.77e-18 | 76 |
| non-terminally differentiated cell | 2.28e-17 | 106 |
| smooth muscle cell | 2.80e-16 | 43 |
| smooth muscle myoblast | 2.80e-16 | 43 |
| electrically responsive cell | 4.49e-16 | 61 |
| electrically active cell | 4.49e-16 | 61 |
| somatic cell | 2.62e-13 | 588 |
| vascular associated smooth muscle cell | 2.42e-12 | 32 |
| meso-epithelial cell | 3.22e-11 | 45 |
| endothelial cell | 3.07e-10 | 36 |
| lining cell | 4.81e-10 | 58 |
| barrier cell | 4.81e-10 | 58 |
| animal cell | 3.97e-09 | 679 |
| eukaryotic cell | 3.97e-09 | 679 |
| blood vessel endothelial cell | 1.36e-08 | 18 |
| embryonic blood vessel endothelial progenitor cell | 1.36e-08 | 18 |
| endothelial cell of vascular tree | 2.74e-08 | 24 |
| cardiocyte | 5.79e-07 | 16 |
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 | 5.48657 |
| MA0004.1 | 0.502801 |
| MA0006.1 | 0.341337 |
| MA0007.1 | 3.11883 |
| MA0009.1 | 0.973289 |
| MA0014.1 | 4.31657 |
| MA0017.1 | 0.380797 |
| MA0019.1 | 0.652951 |
| MA0024.1 | 0.867125 |
| MA0025.1 | 1.10816 |
| MA0027.1 | 2.59001 |
| MA0028.1 | 2.53091 |
| 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 | 0.766755 |
| MA0050.1 | 0.490116 |
| MA0051.1 | 0.602745 |
| MA0052.1 | 0.896548 |
| MA0055.1 | 0.0407081 |
| MA0056.1 | 0 |
| MA0057.1 | 0.744639 |
| MA0058.1 | 0.406232 |
| MA0059.1 | 1.04442 |
| MA0060.1 | 0.224688 |
| MA0061.1 | 2.43031 |
| MA0063.1 | 0 |
| MA0066.1 | 0.607474 |
| MA0067.1 | 1.29359 |
| MA0068.1 | 0.162298 |
| MA0069.1 | 0.958358 |
| MA0070.1 | 0.947018 |
| MA0071.1 | 0.567661 |
| MA0072.1 | 0.942461 |
| MA0073.1 | 0.672652 |
| 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 | 1.37625 |
| MA0089.1 | 0 |
| MA0090.1 | 0.436918 |
| MA0091.1 | 0.505453 |
| MA0092.1 | 0.467172 |
| MA0093.1 | 0.344385 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.621149 |
| MA0101.1 | 0.347695 |
| MA0103.1 | 0.332048 |
| MA0105.1 | 2.96525 |
| MA0106.1 | 0.648997 |
| 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 | 0.388712 |
| MA0122.1 | 1.03753 |
| MA0124.1 | 1.17486 |
| MA0125.1 | 1.0901 |
| MA0130.1 | 0 |
| MA0131.1 | 0.722072 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.00402 |
| MA0136.1 | 0.614215 |
| MA0139.1 | 1.65047 |
| MA0140.1 | 0.564957 |
| MA0141.1 | 0.403171 |
| MA0142.1 | 0.777365 |
| MA0143.1 | 0.66587 |
| MA0144.1 | 0.254954 |
| MA0145.1 | 0.0807715 |
| MA0146.1 | 4.0644 |
| MA0147.1 | 1.40486 |
| MA0148.1 | 0.528066 |
| MA0149.1 | 0.555119 |
| MA0062.2 | 0.193221 |
| MA0035.2 | 0.564239 |
| MA0039.2 | 1.4671 |
| MA0138.2 | 0.704862 |
| MA0002.2 | 0.213296 |
| MA0137.2 | 0.36398 |
| MA0104.2 | 1.85658 |
| MA0047.2 | 0.636643 |
| MA0112.2 | 0.262665 |
| MA0065.2 | 0.591589 |
| MA0150.1 | 0.430951 |
| MA0151.1 | 0 |
| MA0152.1 | 0.571637 |
| MA0153.1 | 1.07307 |
| MA0154.1 | 0.685508 |
| MA0155.1 | 1.36741 |
| MA0156.1 | 0.36627 |
| MA0157.1 | 0.749547 |
| MA0158.1 | 0 |
| MA0159.1 | 0.281681 |
| MA0160.1 | 0.543522 |
| MA0161.1 | 0 |
| MA0162.1 | 3.0847 |
| MA0163.1 | 8.64005 |
| MA0164.1 | 0.678332 |
| MA0080.2 | 0.344472 |
| MA0018.2 | 0.650405 |
| MA0099.2 | 0.572 |
| MA0079.2 | 6.42888 |
| 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 |
|---|---|---|---|---|
| CCNT2#905 | 5 | 4.52585826925902 | 0.0015515733062647 | 0.009856737502006 |
| E2F1#1869 | 6 | 4.20633361275371 | 0.000413523201700764 | 0.00393799121568579 |
| FOSL1#8061 | 5 | 28.3668426545522 | 2.03338323682158e-07 | 1.09862654873466e-05 |
| POLR2A#5430 | 7 | 2.14745317655807 | 0.00474763644761028 | 0.0223431147689244 |
| ZBTB7A#51341 | 6 | 6.30163654960791 | 3.91424956694869e-05 | 0.000731437306356332 |
| ZNF143#7702 | 6 | 11.5721799019096 | 1.08146108094101e-06 | 4.49986907698796e-05 |
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.
