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Coexpression cluster:C603: Difference between revisions

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{{Coexpression_clusters
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|full_id=C603_Monocytederived_Hair_Aortic_Hepatocyte_Adipocyte_leiomyoma_mesenchymal
|id=C603
}}

Latest revision as of 11:26, 17 September 2013


Full id: C603_Monocytederived_Hair_Aortic_Hepatocyte_Adipocyte_leiomyoma_mesenchymal



Phase1 CAGE Peaks

Hg19::chr19:13049939..13049976,+p11@CALR
Hg19::chr19:13050317..13050410,+p2@CALR
Hg19::chr19:13050879..13050931,+p10@CALR
Hg19::chr19:13051052..13051073,+p12@CALR
Hg19::chr19:13051092..13051103,+p17@CALR
Hg19::chr19:13051106..13051123,+p4@CALR
Hg19::chr19:13051128..13051144,+p15@CALR
Hg19::chr19:13051152..13051172,+p8@CALR
Hg19::chr19:13051206..13051244,+p5@CALR
Hg19::chr19:13051346..13051391,+p@chr19:13051346..13051391
+
Hg19::chr19:13051420..13051440,+p@chr19:13051420..13051440
+
Hg19::chr19:13051592..13051609,+p@chr19:13051592..13051609
+
Hg19::chr19:13051628..13051646,+p@chr19:13051628..13051646
+
Hg19::chr19:13054338..13054381,+p7@CALR
Hg19::chr19:13054915..13054933,+p@chr19:13054915..13054933
+


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

No GOStat results

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>

Uber Anatomy
Ontology termp-valuen
trunk mesenchyme8.98e-12122
unilaminar epithelium1.14e-11148
epithelial vesicle1.71e-1178
epithelial tube2.01e-11117
artery3.45e-1042
arterial blood vessel3.45e-1042
arterial system3.45e-1042
multilaminar epithelium3.94e-1083
vasculature4.80e-1078
vascular system4.80e-1078
somite6.50e-1071
presomitic mesoderm6.50e-1071
presumptive segmental plate6.50e-1071
dermomyotome6.50e-1071
trunk paraxial mesoderm6.50e-1071
dense mesenchyme tissue9.08e-1073
mesenchyme1.78e-09160
entire embryonic mesenchyme1.78e-09160
paraxial mesoderm1.94e-0972
presumptive paraxial mesoderm1.94e-0972
splanchnic layer of lateral plate mesoderm4.14e-0983
vessel4.34e-0968
epithelial tube open at both ends6.15e-0959
blood vessel6.15e-0959
blood vasculature6.15e-0959
vascular cord6.15e-0959
skeletal muscle tissue2.60e-0862
striated muscle tissue2.60e-0862
myotome2.60e-0862
mesoderm3.41e-08315
mesoderm-derived structure3.41e-08315
presumptive mesoderm3.41e-08315
systemic artery8.92e-0833
systemic arterial system8.92e-0833
muscle tissue1.39e-0764
musculature1.39e-0764
musculature of body1.39e-0764


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)
MA0003.10.00512623
MA0004.10.256222
MA0006.10.137644
MA0007.10.241375
MA0009.16.65548
MA0014.10.00275422
MA0017.12.911
MA0019.10.990457
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.889224
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.687159
MA0043.10.669676
MA0046.10.659066
MA0048.10.0212749
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.120131
MA0056.10
MA0057.10.0196406
MA0058.10.182945
MA0059.10.182001
MA0060.10.0671843
MA0061.13.39881
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.147451
MA0069.10.655419
MA0070.10.644843
MA0071.12.29218
MA0072.10.640598
MA0073.10.20797
MA0074.10.337035
MA0076.11.07748
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.0411204
MA0089.10
MA0090.10.205547
MA0091.10.258318
MA0092.10.228476
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.11.38853
MA0103.11.91714
MA0105.16.3584
MA0106.16.92701
MA0107.11.59875
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.0920489
MA0115.10.900969
MA0116.10.0971018
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.0481205
MA0140.10.30631
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.284854
MA0145.10.278475
MA0146.10.0580435
MA0147.10.0991954
MA0148.10.276339
MA0149.10.298252
MA0062.20.745766
MA0035.20.824687
MA0039.20.0386601
MA0138.20.425279
MA0002.20.220677
MA0137.20.153033
MA0104.20.0667907
MA0047.20.366327
MA0112.20.00868143
MA0065.20.0514203
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.367546
MA0155.12.06149
MA0156.12.8139
MA0157.10.46471
MA0158.10
MA0159.10.671959
MA0160.10.288813
MA0161.10
MA0162.10.0065085
MA0163.10.0128736
MA0164.10.402162
MA0080.21.98476
MA0018.20.378086
MA0099.20.312108
MA0079.21.25728e-05
MA0102.21.1957
MA0258.10.0785319
MA0259.10.693919
MA0442.10



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#promotersEnrichmentp-valueq-value
SP1#666793.419028826884540.0002830127128465880.00301116184973358



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.

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