Coexpression cluster:C3282: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
| (3 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
{ | |||
Latest revision as of 12:22, 17 September 2013
Full id: C3282_Mesenchymal_Renal_Endothelial_Hepatic_Fibroblast_Pericytes_Trabecular
Phase1 CAGE Peaks
| Hg19::chr12:48213650..48213695,- | p1@HDAC7 |
| Hg19::chr19:54984354..54984463,- | p1@CDC42EP5 |
| Hg19::chr1:26126670..26126721,+ | p1@SEPN1 |
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:0031269 | pseudopodium formation | 0.00423847294024064 |
| GO:0031268 | pseudopodium organization and biogenesis | 0.00423847294024064 |
| GO:0031274 | positive regulation of pseudopodium formation | 0.00423847294024064 |
| GO:0031272 | regulation of pseudopodium formation | 0.00423847294024064 |
| GO:0017049 | GTP-Rho binding | 0.00423847294024064 |
| GO:0030838 | positive regulation of actin filament polymerization | 0.00423847294024064 |
| GO:0031344 | regulation of cell projection organization and biogenesis | 0.00423847294024064 |
| GO:0031346 | positive regulation of cell projection organization and biogenesis | 0.00423847294024064 |
| GO:0030833 | regulation of actin filament polymerization | 0.0119282334752735 |
| GO:0030041 | actin filament polymerization | 0.0141190928522875 |
| GO:0017048 | Rho GTPase binding | 0.0141190928522875 |
| GO:0022603 | regulation of anatomical structure morphogenesis | 0.0141190928522875 |
| GO:0008360 | regulation of cell shape | 0.0141190928522875 |
| GO:0022604 | regulation of cell morphogenesis | 0.0141190928522875 |
| GO:0008064 | regulation of actin polymerization and/or depolymerization | 0.0141190928522875 |
| GO:0030832 | regulation of actin filament length | 0.0141190928522875 |
| GO:0032535 | regulation of cellular component size | 0.0141190928522875 |
| GO:0032956 | regulation of actin cytoskeleton organization and biogenesis | 0.0141190928522875 |
| GO:0030031 | cell projection biogenesis | 0.0141190928522875 |
| GO:0008430 | selenium binding | 0.0141190928522875 |
| GO:0051493 | regulation of cytoskeleton organization and biogenesis | 0.0143745331790643 |
| GO:0033043 | regulation of organelle organization and biogenesis | 0.0143745331790643 |
| GO:0008154 | actin polymerization and/or depolymerization | 0.0149760890815889 |
| GO:0007254 | JNK cascade | 0.0152923045578563 |
| GO:0031098 | stress-activated protein kinase signaling pathway | 0.0153575003160227 |
| GO:0017016 | Ras GTPase binding | 0.0167190430585973 |
| GO:0031267 | small GTPase binding | 0.017135774408785 |
| GO:0051247 | positive regulation of protein metabolic process | 0.017135774408785 |
| GO:0051020 | GTPase binding | 0.0182047674899782 |
| GO:0051258 | protein polymerization | 0.0182047674899782 |
| GO:0051128 | regulation of cellular component organization and biogenesis | 0.0182047674899782 |
| GO:0000165 | MAPKKK cascade | 0.0264343064197099 |
| GO:0007266 | Rho protein signal transduction | 0.0319306848958582 |
| GO:0032990 | cell part morphogenesis | 0.0319306848958582 |
| GO:0030030 | cell projection organization and biogenesis | 0.0319306848958582 |
| GO:0048858 | cell projection morphogenesis | 0.0319306848958582 |
| GO:0050793 | regulation of developmental process | 0.0359240784781714 |
| GO:0030036 | actin cytoskeleton organization and biogenesis | 0.0366031238167997 |
| GO:0030029 | actin filament-based process | 0.0375344561401569 |
| GO:0019899 | enzyme binding | 0.0429014915697675 |
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 | 3.69e-30 | 121 |
| embryonic cell | 4.75e-22 | 250 |
| contractile cell | 6.92e-18 | 59 |
| endothelial cell | 4.62e-17 | 36 |
| meso-epithelial cell | 5.13e-17 | 45 |
| fibroblast | 5.25e-16 | 76 |
| muscle cell | 6.54e-16 | 55 |
| muscle precursor cell | 1.03e-15 | 58 |
| myoblast | 1.03e-15 | 58 |
| multi-potent skeletal muscle stem cell | 1.03e-15 | 58 |
| endothelial cell of vascular tree | 7.79e-15 | 24 |
| non-terminally differentiated cell | 3.67e-14 | 106 |
| lining cell | 5.87e-14 | 58 |
| barrier cell | 5.87e-14 | 58 |
| smooth muscle cell | 9.42e-14 | 43 |
| smooth muscle myoblast | 9.42e-14 | 43 |
| electrically responsive cell | 2.74e-13 | 61 |
| electrically active cell | 2.74e-13 | 61 |
| blood vessel endothelial cell | 4.28e-12 | 18 |
| embryonic blood vessel endothelial progenitor cell | 4.28e-12 | 18 |
| vascular associated smooth muscle cell | 1.40e-11 | 32 |
| somatic cell | 1.47e-07 | 588 |
| endothelial cell of artery | 6.48e-07 | 9 |
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 | 3.22681 |
| MA0004.1 | 0.826076 |
| MA0006.1 | 0.639288 |
| MA0007.1 | 0.804807 |
| MA0009.1 | 1.3275 |
| MA0014.1 | 2.44638 |
| MA0017.1 | 0.686276 |
| MA0019.1 | 0.990656 |
| MA0024.1 | 1.21731 |
| MA0025.1 | 1.46617 |
| MA0027.1 | 2.95767 |
| MA0028.1 | 0.658629 |
| MA0029.1 | 1.23771 |
| MA0030.1 | 1.22561 |
| MA0031.1 | 1.15713 |
| MA0038.1 | 0.94098 |
| MA0040.1 | 1.24388 |
| MA0041.1 | 0.847069 |
| MA0042.1 | 0.810843 |
| MA0043.1 | 1.32783 |
| MA0046.1 | 1.31611 |
| MA0048.1 | 0.341392 |
| MA0050.1 | 0.81185 |
| MA0051.1 | 0.936307 |
| MA0052.1 | 1.24796 |
| MA0055.1 | 1.06172 |
| MA0056.1 | 0 |
| MA0057.1 | 1.59304 |
| MA0058.1 | 0.716037 |
| MA0059.1 | 0.714521 |
| MA0060.1 | 0.492218 |
| MA0061.1 | 0.456531 |
| MA0063.1 | 0 |
| MA0066.1 | 0.941452 |
| MA0067.1 | 1.65513 |
| MA0068.1 | 0.405474 |
| MA0069.1 | 1.31207 |
| MA0070.1 | 1.30033 |
| MA0071.1 | 0.897953 |
| MA0072.1 | 1.29561 |
| MA0073.1 | 3.33427 |
| MA0074.1 | 0.935474 |
| MA0076.1 | 0.734647 |
| MA0077.1 | 1.28751 |
| MA0078.1 | 1.04495 |
| MA0081.1 | 0.714712 |
| MA0083.1 | 1.33535 |
| MA0084.1 | 1.84562 |
| MA0087.1 | 1.29304 |
| MA0088.1 | 0.257905 |
| MA0089.1 | 0 |
| MA0090.1 | 0.751469 |
| MA0091.1 | 0.829044 |
| MA0092.1 | 1.84783 |
| MA0093.1 | 0.642957 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.956299 |
| MA0101.1 | 0.646932 |
| MA0103.1 | 0.628063 |
| MA0105.1 | 0.31555 |
| MA0106.1 | 0.986396 |
| MA0107.1 | 0.556367 |
| MA0108.2 | 1.15387 |
| MA0109.1 | 0 |
| MA0111.1 | 0.767139 |
| MA0113.1 | 1.00436 |
| MA0114.1 | 0.549955 |
| MA0115.1 | 1.57693 |
| MA0116.1 | 0.560723 |
| MA0117.1 | 1.36676 |
| MA0119.1 | 0.695578 |
| MA0122.1 | 1.39371 |
| MA0124.1 | 1.53432 |
| MA0125.1 | 1.44766 |
| MA0130.1 | 0 |
| MA0131.1 | 1.06461 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.35921 |
| MA0136.1 | 0.948776 |
| MA0139.1 | 0.440097 |
| MA0140.1 | 0.894983 |
| MA0141.1 | 0.712476 |
| MA0142.1 | 1.12317 |
| MA0143.1 | 1.00455 |
| MA0144.1 | 0.531867 |
| MA0145.1 | 1.37817 |
| MA0146.1 | 3.00132 |
| MA0147.1 | 0.565108 |
| MA0148.1 | 0.854239 |
| MA0149.1 | 0.884158 |
| MA0062.2 | 0.449458 |
| MA0035.2 | 0.894194 |
| MA0039.2 | 6.2923 |
| MA0138.2 | 1.04628 |
| MA0002.2 | 0.476938 |
| MA0137.2 | 0.666381 |
| MA0104.2 | 0.491226 |
| MA0047.2 | 0.973066 |
| MA0112.2 | 1.34467 |
| MA0065.2 | 1.39232 |
| MA0150.1 | 0.744617 |
| MA0151.1 | 0 |
| MA0152.1 | 0.902317 |
| MA0153.1 | 1.43021 |
| MA0154.1 | 0.312019 |
| MA0155.1 | 0.711948 |
| MA0156.1 | 0.669101 |
| MA0157.1 | 1.09377 |
| MA0158.1 | 0 |
| MA0159.1 | 1.38935 |
| MA0160.1 | 0.871361 |
| MA0161.1 | 0 |
| MA0162.1 | 0.8915 |
| MA0163.1 | 3.19905 |
| MA0164.1 | 1.01792 |
| MA0080.2 | 0.643061 |
| MA0018.2 | 0.987913 |
| MA0099.2 | 0.902716 |
| MA0079.2 | 10.8725 |
| MA0102.2 | 1.88331 |
| MA0258.1 | 0.519674 |
| MA0259.1 | 0.575594 |
| 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
No analysis results for this cluster
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.
