Coexpression cluster:C243: Difference between revisions
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Latest revision as of 11:04, 17 September 2013
Full id: C243_Chondrocyte_trachea_Synoviocyte_mesodermal_renal_Fibroblast_Ewing
Phase1 CAGE Peaks
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 |
---|---|---|---|---|
3.89935446244208e-05 | 0.0246829137472584 | 3 | 106 | Amoebiasis (KEGG):05146 |
0.000120675008846136 | 0.0381936402998021 | 3 | 155 | IL-1 up reg. targets (Netpath):NetPath_13 |
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:0044421 | extracellular region part | 0.000205191071528448 |
GO:0005583 | fibrillar collagen | 0.000978053245048239 |
GO:0005201 | extracellular matrix structural constituent | 0.00119181646855413 |
GO:0005578 | proteinaceous extracellular matrix | 0.00119181646855413 |
GO:0001501 | skeletal development | 0.00359209545847259 |
GO:0030198 | extracellular matrix organization and biogenesis | 0.00608470421680022 |
GO:0005581 | collagen | 0.00719737186271699 |
GO:0005585 | collagen type II | 0.0116419404215236 |
GO:0043062 | extracellular structure organization and biogenesis | 0.0135409792303694 |
GO:0005592 | collagen type XI | 0.0153553945672956 |
GO:0030020 | extracellular matrix structural constituent conferring tensile strength | 0.0153553945672956 |
GO:0005539 | glycosaminoglycan binding | 0.0153553945672956 |
GO:0030247 | polysaccharide binding | 0.0153553945672956 |
GO:0001871 | pattern binding | 0.0153553945672956 |
GO:0005584 | collagen type I | 0.0153553945672956 |
GO:0004700 | atypical protein kinase C activity | 0.0153553945672956 |
GO:0044420 | extracellular matrix part | 0.0153553945672956 |
GO:0050954 | sensory perception of mechanical stimulus | 0.0153553945672956 |
GO:0007605 | sensory perception of sound | 0.0153553945672956 |
GO:0032502 | developmental process | 0.0153553945672956 |
GO:0006817 | phosphate transport | 0.0165717751341296 |
GO:0007181 | transforming growth factor beta receptor complex assembly | 0.0165717751341296 |
GO:0007275 | multicellular organismal development | 0.0165717751341296 |
GO:0030021 | extracellular matrix structural constituent conferring compression resistance | 0.0271333600942556 |
GO:0048731 | system development | 0.0300744875262851 |
GO:0030199 | collagen fibril organization | 0.0300744875262851 |
GO:0044409 | entry into host | 0.0300744875262851 |
GO:0030260 | entry into host cell | 0.0300744875262851 |
GO:0019059 | initiation of viral infection | 0.0300744875262851 |
GO:0052192 | movement in environment of other organism during symbiotic interaction | 0.0300744875262851 |
GO:0046718 | entry of virus into host cell | 0.0300744875262851 |
GO:0052126 | movement in host environment | 0.0300744875262851 |
GO:0051828 | entry into other organism during symbiotic interaction | 0.0300744875262851 |
GO:0051806 | entry into cell of other organism during symbiotic interaction | 0.0300744875262851 |
GO:0015698 | inorganic anion transport | 0.0316658241886977 |
GO:0004017 | adenylate kinase activity | 0.0316658241886977 |
GO:0006032 | chitin catabolic process | 0.0316658241886977 |
GO:0006046 | N-acetylglucosamine catabolic process | 0.0316658241886977 |
GO:0006043 | glucosamine catabolic process | 0.0316658241886977 |
GO:0046348 | amino sugar catabolic process | 0.0316658241886977 |
GO:0004697 | protein kinase C activity | 0.0316658241886977 |
GO:0006030 | chitin metabolic process | 0.0316658241886977 |
GO:0004568 | chitinase activity | 0.0316658241886977 |
GO:0001565 | phorbol ester receptor activity | 0.0316658241886977 |
GO:0048856 | anatomical structure development | 0.0373617123603633 |
GO:0006820 | anion transport | 0.0373617123603633 |
GO:0044247 | cellular polysaccharide catabolic process | 0.0405912102693347 |
GO:0000272 | polysaccharide catabolic process | 0.0405912102693347 |
GO:0051701 | interaction with host | 0.0416483223058567 |
GO:0048513 | organ development | 0.0471112555794051 |
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 |
---|---|---|
GAG secreting cell | 1.20e-19 | 9 |
carbohydrate secreting cell | 1.20e-19 | 9 |
collagen secreting cell | 1.21e-15 | 6 |
chondroblast | 1.21e-15 | 6 |
chondrocyte | 1.21e-15 | 6 |
extracellular matrix secreting cell | 2.58e-11 | 15 |
stromal cell | 3.62e-07 | 28 |
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 | 0.104049 |
MA0004.1 | 0.0230278 |
MA0006.1 | 0.0678065 |
MA0007.1 | 0.419216 |
MA0009.1 | 0.231637 |
MA0014.1 | 0.262247 |
MA0017.1 | 0.214918 |
MA0019.1 | 0.231029 |
MA0024.1 | 0.166016 |
MA0025.1 | 0.326531 |
MA0027.1 | 1.69857 |
MA0028.1 | 0.00464806 |
MA0029.1 | 0.177433 |
MA0030.1 | 0.508845 |
MA0031.1 | 0.134441 |
MA0038.1 | 0.414012 |
MA0040.1 | 0.534038 |
MA0041.1 | 0.0269039 |
MA0042.1 | 0.0902904 |
MA0043.1 | 0.231848 |
MA0046.1 | 0.224416 |
MA0048.1 | 0.253558 |
MA0050.1 | 0.433405 |
MA0051.1 | 0.406356 |
MA0052.1 | 0.183297 |
MA0055.1 | 0.456123 |
MA0056.1 | 0 |
MA0057.1 | 2.77018 |
MA0058.1 | 0.00874589 |
MA0059.1 | 0.00861211 |
MA0060.1 | 0.0341282 |
MA0061.1 | 3.67698 |
MA0063.1 | 0 |
MA0066.1 | 0.414788 |
MA0067.1 | 0.473069 |
MA0068.1 | 2.53538 |
MA0069.1 | 0.631819 |
MA0070.1 | 0.214581 |
MA0071.1 | 0.149709 |
MA0072.1 | 0.211675 |
MA0073.1 | 19.8878 |
MA0074.1 | 0.180446 |
MA0076.1 | 0.0105149 |
MA0077.1 | 0.206727 |
MA0078.1 | 0.286718 |
MA0081.1 | 0.124224 |
MA0083.1 | 0.666474 |
MA0084.1 | 0.635217 |
MA0087.1 | 0.2101 |
MA0088.1 | 0.295537 |
MA0089.1 | 0 |
MA0090.1 | 1.14668 |
MA0091.1 | 0.0235515 |
MA0092.1 | 1.30555 |
MA0093.1 | 0.0224819 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.439549 |
MA0101.1 | 1.30631 |
MA0103.1 | 0.262976 |
MA0105.1 | 3.81045 |
MA0106.1 | 0.491621 |
MA0107.1 | 4.27636 |
MA0108.2 | 0.41444 |
MA0109.1 | 0 |
MA0111.1 | 0.0668683 |
MA0113.1 | 0.895397 |
MA0114.1 | 0.795623 |
MA0115.1 | 0.410377 |
MA0116.1 | 1.11423 |
MA0117.1 | 0.257218 |
MA0119.1 | 0.628913 |
MA0122.1 | 0.755856 |
MA0124.1 | 0.377376 |
MA0125.1 | 0.313172 |
MA0130.1 | 0 |
MA0131.1 | 0.308252 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.252217 |
MA0136.1 | 0.0516336 |
MA0139.1 | 0.498759 |
MA0140.1 | 0.616386 |
MA0141.1 | 0.0434582 |
MA0142.1 | 0.376423 |
MA0143.1 | 0.244737 |
MA0144.1 | 2.21595 |
MA0145.1 | 3.22682 |
MA0146.1 | 0.100846 |
MA0147.1 | 0.00128417 |
MA0148.1 | 0.282682 |
MA0149.1 | 0.0347551 |
MA0062.2 | 0.00579851 |
MA0035.2 | 0.962029 |
MA0039.2 | 1.06381 |
MA0138.2 | 0.288154 |
MA0002.2 | 0.877966 |
MA0137.2 | 0.78833 |
MA0104.2 | 0.00280437 |
MA0047.2 | 0.468253 |
MA0112.2 | 1.65985 |
MA0065.2 | 0.807979 |
MA0150.1 | 0.0115619 |
MA0151.1 | 0 |
MA0152.1 | 0.352609 |
MA0153.1 | 0.300753 |
MA0154.1 | 1.84504 |
MA0155.1 | 2.27433 |
MA0156.1 | 0.0876463 |
MA0157.1 | 0.341461 |
MA0158.1 | 0 |
MA0159.1 | 0.637066 |
MA0160.1 | 0.0318984 |
MA0161.1 | 0 |
MA0162.1 | 0.177466 |
MA0163.1 | 5.77335 |
MA0164.1 | 0.258285 |
MA0080.2 | 0.0701428 |
MA0018.2 | 0.0638918 |
MA0099.2 | 0.0391796 |
MA0079.2 | 5.49102 |
MA0102.2 | 0.668584 |
MA0258.1 | 0.466579 |
MA0259.1 | 0.0356699 |
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