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Coexpression cluster:C517: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.161773938088328,

Latest revision as of 11:24, 17 September 2013


Full id: C517_Mesothelial_Synoviocyte_mesothelioma_Fibroblast_Smooth_Preadipocyte_tenocyte



Phase1 CAGE Peaks

Hg19::chr20:48121333..48121349,-p@chr20:48121333..48121349
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Hg19::chr20:48121824..48121844,-p@chr20:48121824..48121844
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Hg19::chr20:48123976..48123992,-p@chr20:48123976..48123992
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Hg19::chr20:48124063..48124075,-p@chr20:48124063..48124075
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Hg19::chr20:48124130..48124143,-p@chr20:48124130..48124143
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Hg19::chr20:48124348..48124365,-p@chr20:48124348..48124365
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Hg19::chr20:48127605..48127622,-p@chr20:48127605..48127622
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Hg19::chr20:48129753..48129781,-p@chr20:48129753..48129781
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Hg19::chr20:48130918..48130935,-p@chr20:48130918..48130935
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Hg19::chr20:48140671..48140693,-p@chr20:48140671..48140693
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Hg19::chr20:48140767..48140776,-p@chr20:48140767..48140776
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Hg19::chr20:48164416..48164441,-p@chr20:48164416..48164441
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Hg19::chr20:48164465..48164477,-p@chr20:48164465..48164477
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Hg19::chr20:48164479..48164499,-p@chr20:48164479..48164499
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Hg19::chr20:48164533..48164548,-p@chr20:48164533..48164548
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Hg19::chr20:48184612..48184630,-p2@PTGIS
Hg19::chr20:48184638..48184694,-p1@PTGIS
Hg19::chr20:48184831..48184858,-p4@PTGIS


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
primary circulatory organ9.44e-1527
heart6.46e-1424
primitive heart tube6.46e-1424
primary heart field6.46e-1424
anterior lateral plate mesoderm6.46e-1424
heart tube6.46e-1424
heart primordium6.46e-1424
cardiac mesoderm6.46e-1424
cardiogenic plate6.46e-1424
heart rudiment6.46e-1424
splanchnic layer of lateral plate mesoderm9.28e-1483
artery6.31e-1142
arterial blood vessel6.31e-1142
arterial system6.31e-1142
systemic artery3.71e-1033
systemic arterial system3.71e-1033
blood vessel layer5.17e-107
circulatory system9.83e-10112
omentum1.92e-096
peritoneum1.92e-096
abdominal cavity1.92e-096
visceral peritoneum1.92e-096
epithelial tube open at both ends3.08e-0959
blood vessel3.08e-0959
blood vasculature3.08e-0959
vascular cord3.08e-0959
epithelial tube3.56e-09117
cardiovascular system5.19e-09109
body cavity or lining1.32e-0749
cavity lining1.33e-0712
serous membrane1.33e-0712
vessel4.34e-0768
vasculature4.42e-0778
vascular system4.42e-0778
artery wall8.22e-074
tunica adventitia of artery8.22e-074
adventitia8.22e-074
tunica adventitia of blood vessel8.22e-074
aorta tunica adventitia8.22e-074
aorta wall8.22e-074


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)
MA0003.10.00101787
MA0004.10.207008
MA0006.10.101986
MA0007.11.07281
MA0009.11.46157
MA0014.10.0124091
MA0017.10.125342
MA0019.10.322194
MA0024.10.50459
MA0025.10.725013
MA0027.12.18072
MA0028.10.111328
MA0029.12.2336
MA0030.10.511665
MA0031.10.454061
MA0038.10.285594
MA0040.10.527306
MA0041.10.220669
MA0042.10.197306
MA0043.10.60049
MA0046.10.590147
MA0048.10.151328
MA0050.10.197941
MA0051.10.282227
MA0052.10.530811
MA0055.10.757344
MA0056.10
MA0057.12.28107
MA0058.10.141262
MA0059.10.433767
MA0060.10.0444001
MA0061.10.137405
MA0063.10
MA0066.11.42268
MA0067.10.900956
MA0068.10.453462
MA0069.10.586593
MA0070.10.576293
MA0071.10.255111
MA0072.10.572162
MA0073.116.4093
MA0074.10.281628
MA0076.10.151641
MA0077.10.565087
MA0078.10.363755
MA0081.10.140536
MA0083.10.607144
MA0084.11.08294
MA0087.10.569916
MA0088.10.938166
MA0089.10
MA0090.10.485893
MA0091.10.208918
MA0092.10.181853
MA0093.10.338722
MA0095.10
MA0098.10
MA0100.10.296726
MA0101.10.343779
MA0103.10.658605
MA0105.10.0429646
MA0106.10.319
MA0107.10.235899
MA0108.21.1451
MA0109.10
MA0111.10.980329
MA0113.10.332535
MA0114.10.495259
MA0115.10.827474
MA0116.10.0681676
MA0117.10.635078
MA0119.10.407815
MA0122.10.659244
MA0124.10.787807
MA0125.10.708116
MA0130.10
MA0131.10.379172
MA0132.10
MA0133.10
MA0135.10.628343
MA0136.10.291242
MA0139.10.123548
MA0140.11.30145
MA0141.10.139313
MA0142.10.426146
MA0143.10.332682
MA0144.10.0574875
MA0145.12.1351
MA0146.10.511463
MA0147.10.525775
MA0148.10.225411
MA0149.10.245595
MA0062.20.0323736
MA0035.22.00764
MA0039.22.11235
MA0138.20.364793
MA0002.20.357374
MA0137.20.368913
MA0104.20.383074
MA0047.20.309071
MA0112.20.160258
MA0065.20.772018
MA0150.10.157331
MA0151.10
MA0152.10.716282
MA0153.10.692238
MA0154.10.117204
MA0155.10.665536
MA0156.10.116546
MA0157.10.402372
MA0158.10
MA0159.10.527394
MA0160.10.666979
MA0161.10
MA0162.10.12543
MA0163.10.472274
MA0164.10.342871
MA0080.20.338854
MA0018.20.320136
MA0099.20.258426
MA0079.25.99097
MA0102.21.11935
MA0258.10.762782
MA0259.10.547239
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

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.

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