Coexpression cluster:C3132: Difference between revisions
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Latest revision as of 12:19, 17 September 2013
Full id: C3132_Pericytes_Mesenchymal_Skeletal_skeletal_amniotic_Hair_gastric
Phase1 CAGE Peaks
| Hg19::chr11:2158507..2158526,- | p3@IGF2 |
| Hg19::chr17:48277566..48277608,- | p5@COL1A1 |
| Hg19::chr1:168409732..168409736,+ | p@chr1:168409732..168409736 + |
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:0001501 | skeletal development | 0.0030134928219141 |
| GO:0005584 | collagen type I | 0.0062794040249056 |
| GO:0008147 | structural constituent of bone | 0.0062794040249056 |
| GO:0006349 | genetic imprinting | 0.0064749681926325 |
| GO:0018445 | prothoracicotrophic hormone activity | 0.0064749681926325 |
| GO:0005583 | fibrillar collagen | 0.0064749681926325 |
| GO:0005159 | insulin-like growth factor receptor binding | 0.0064749681926325 |
| GO:0051591 | response to cAMP | 0.0064749681926325 |
| GO:0031960 | response to corticosteroid stimulus | 0.00680178652952636 |
| GO:0009612 | response to mechanical stimulus | 0.00784740648934456 |
| GO:0048513 | organ development | 0.00784740648934456 |
| GO:0042542 | response to hydrogen peroxide | 0.00784740648934456 |
| GO:0043434 | response to peptide hormone stimulus | 0.00796790119733836 |
| GO:0000302 | response to reactive oxygen species | 0.00907963454196166 |
| GO:0008286 | insulin receptor signaling pathway | 0.00970930687956354 |
| GO:0005184 | neuropeptide hormone activity | 0.00970930687956354 |
| GO:0048545 | response to steroid hormone stimulus | 0.00988452957792736 |
| GO:0048731 | system development | 0.00988452957792736 |
| GO:0007584 | response to nutrient | 0.00988452957792736 |
| GO:0010035 | response to inorganic substance | 0.00988452957792736 |
| GO:0005581 | collagen | 0.0119441092498285 |
| GO:0048856 | anatomical structure development | 0.0119441092498285 |
| GO:0031667 | response to nutrient levels | 0.0119441092498285 |
| GO:0010033 | response to organic substance | 0.0119441092498285 |
| GO:0040029 | regulation of gene expression, epigenetic | 0.0119441092498285 |
| GO:0009991 | response to extracellular stimulus | 0.0119441092498285 |
| GO:0009725 | response to hormone stimulus | 0.0130795109121471 |
| GO:0007275 | multicellular organismal development | 0.0130795109121471 |
| GO:0031214 | biomineral formation | 0.0137976083286762 |
| GO:0001503 | ossification | 0.0137976083286762 |
| GO:0046849 | bone remodeling | 0.014564672669458 |
| GO:0048771 | tissue remodeling | 0.0154302476562255 |
| GO:0006979 | response to oxidative stress | 0.0166990454661848 |
| GO:0005201 | extracellular matrix structural constituent | 0.0166990454661848 |
| GO:0044420 | extracellular matrix part | 0.0166990454661848 |
| GO:0050954 | sensory perception of mechanical stimulus | 0.0166990454661848 |
| GO:0007605 | sensory perception of sound | 0.0166990454661848 |
| GO:0008544 | epidermis development | 0.0166990454661848 |
| GO:0006817 | phosphate transport | 0.0171539397978626 |
| GO:0007398 | ectoderm development | 0.0171539397978626 |
| GO:0009628 | response to abiotic stimulus | 0.0184838697208335 |
| GO:0032502 | developmental process | 0.0184838697208335 |
| GO:0007169 | transmembrane receptor protein tyrosine kinase signaling pathway | 0.0226393100151102 |
| GO:0032501 | multicellular organismal process | 0.0226393100151102 |
| GO:0005179 | hormone activity | 0.0226393100151102 |
| GO:0008083 | growth factor activity | 0.0258076074285635 |
| GO:0015698 | inorganic anion transport | 0.0259546771181936 |
| GO:0007167 | enzyme linked receptor protein signaling pathway | 0.029184688142699 |
| GO:0009888 | tissue development | 0.029184688142699 |
| GO:0006820 | anion transport | 0.0302808613505519 |
| GO:0005578 | proteinaceous extracellular matrix | 0.038638277528768 |
| GO:0009719 | response to endogenous stimulus | 0.0475404146506583 |
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 |
|---|---|---|
| contractile cell | 5.56e-11 | 59 |
| muscle precursor cell | 7.46e-10 | 58 |
| myoblast | 7.46e-10 | 58 |
| multi-potent skeletal muscle stem cell | 7.46e-10 | 58 |
| fibroblast | 1.08e-09 | 76 |
| muscle cell | 4.13e-09 | 55 |
| non-terminally differentiated cell | 4.50e-08 | 106 |
| stromal cell | 6.59e-08 | 28 |
| electrically responsive cell | 1.15e-07 | 61 |
| electrically active cell | 1.15e-07 | 61 |
| extraembryonic cell | 1.72e-07 | 19 |
| extracellular matrix secreting cell | 5.77e-07 | 15 |
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 | 0.0471418 |
| MA0004.1 | 0.826076 |
| MA0006.1 | 0.639288 |
| MA0007.1 | 0.804807 |
| MA0009.1 | 1.3275 |
| MA0014.1 | 0.377374 |
| 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 | 0.190716 |
| MA0056.1 | 0 |
| MA0057.1 | 0.886807 |
| 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 | 3.923 |
| 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 | 0.785956 |
| MA0093.1 | 0.642957 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.956299 |
| MA0101.1 | 0.646932 |
| MA0103.1 | 0.628063 |
| MA0105.1 | 2.3269 |
| 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 | 0.273764 |
| MA0146.1 | 0.107247 |
| MA0147.1 | 0.565108 |
| MA0148.1 | 0.854239 |
| MA0149.1 | 0.884158 |
| MA0062.2 | 0.449458 |
| MA0035.2 | 0.894194 |
| MA0039.2 | 1.15986 |
| MA0138.2 | 1.04628 |
| MA0002.2 | 0.476938 |
| MA0137.2 | 0.666381 |
| MA0104.2 | 0.491226 |
| MA0047.2 | 0.973066 |
| MA0112.2 | 0.264678 |
| MA0065.2 | 0.277623 |
| MA0150.1 | 0.744617 |
| MA0151.1 | 0 |
| MA0152.1 | 0.902317 |
| MA0153.1 | 1.43021 |
| MA0154.1 | 0.312019 |
| MA0155.1 | 0.256269 |
| MA0156.1 | 0.669101 |
| MA0157.1 | 1.09377 |
| MA0158.1 | 0 |
| MA0159.1 | 0.565904 |
| MA0160.1 | 0.871361 |
| MA0161.1 | 0 |
| MA0162.1 | 0.8915 |
| MA0163.1 | 0.387745 |
| MA0164.1 | 1.01792 |
| MA0080.2 | 0.643061 |
| MA0018.2 | 0.987913 |
| MA0099.2 | 0.902716 |
| MA0079.2 | 3.61229 |
| 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.
