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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0393665576067778,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.12696629621811,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.031142358737545,0,0.0649646394148393,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0290468398958313,0,0,0,0,0,0,0.251625724314337,0,0,0,0.079970395058755,0,0,0,0.0473601724108001,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0604163273998613,0,0,0,0,0,0.089495363820231,0,0.0831131354048965,0.841921225584259,0.0320973123923737,0,0,0,0,0,0,0,0,0.0362809334158863,0,0.0827755457245375,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C1326_mesenchymal_CD14_Fibroblast_Smooth_Preadipocyte_Endothelial_Renal|gostat_on_coexpression_clusters=GO:0004232!interstitial collagenase activity!0.00412079823606691!4312$GO:0005615!extracellular space!0.00412079823606691!4312;85480$GO:0008133!collagenase activity!0.00412079823606691!4312$GO:0044421!extracellular region part!0.00432581913920992!4312;85480$GO:0030574!collagen catabolic process!0.00432581913920992!4312$GO:0044256!protein digestion!0.00432581913920992!4312$GO:0044254!multicellular organismal protein catabolic process!0.00432581913920992!4312$GO:0044266!multicellular organismal macromolecule catabolic process!0.00432581913920992!4312$GO:0044259!multicellular organismal macromolecule metabolic process!0.00432581913920992!4312$GO:0044268!multicellular organismal protein metabolic process!0.00432581913920992!4312$GO:0032963!collagen metabolic process!0.00432581913920992!4312$GO:0044243!multicellular organismal catabolic process!0.00432581913920992!4312$GO:0044236!multicellular organismal metabolic 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|full_id=C1326_mesenchymal_CD14_Fibroblast_Smooth_Preadipocyte_Endothelial_Renal
|gostat_on_coexpression_clusters=GO:0004232!interstitial collagenase activity!0.00412079823606691!4312$GO:0005615!extracellular space!0.00412079823606691!4312;85480$GO:0008133!collagenase activity!0.00412079823606691!4312$GO:0044421!extracellular region part!0.00432581913920992!4312;85480$GO:0030574!collagen catabolic process!0.00432581913920992!4312$GO:0044256!protein digestion!0.00432581913920992!4312$GO:0044254!multicellular organismal protein catabolic process!0.00432581913920992!4312$GO:0044266!multicellular organismal macromolecule catabolic process!0.00432581913920992!4312$GO:0044259!multicellular organismal macromolecule metabolic process!0.00432581913920992!4312$GO:0044268!multicellular organismal protein metabolic process!0.00432581913920992!4312$GO:0032963!collagen metabolic process!0.00432581913920992!4312$GO:0044243!multicellular organismal catabolic process!0.00432581913920992!4312$GO:0044236!multicellular organismal metabolic process!0.00437322683744746!4312$GO:0007586!digestion!0.0167553098487676!4312$GO:0004222!metalloendopeptidase activity!0.0325440067988259!4312$GO:0005125!cytokine activity!0.047689218626343!85480
|id=C1326
|ontology_enrichment_celltype=CL:0000359!3.20e-13!32;CL:0000680!1.42e-11!57;CL:0000056!1.42e-11!57;CL:0000355!1.42e-11!57;CL:0000055!8.37e-11!180;CL:0000192!1.06e-10!42;CL:0000514!1.06e-10!42;CL:0000048!1.78e-10!430;CL:0000187!1.85e-10!54;CL:0000183!5.51e-10!59;CL:0000723!5.83e-10!436;CL:0000393!1.27e-09!60;CL:0000211!1.27e-09!60;CL:0000034!2.65e-09!444;CL:0002494!4.65e-08!16;CL:0002371!8.11e-08!591;CL:0000569!1.90e-07!4;CL:0000011!1.90e-07!4;CL:0000144!9.40e-07!625
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001637!1.99e-23!42;UBERON:0003509!1.99e-23!42;UBERON:0004572!1.99e-23!42;UBERON:0001981!3.56e-18!60;UBERON:0007500!3.56e-18!60;UBERON:0004537!3.56e-18!60;UBERON:0006965!3.56e-18!60;UBERON:0004573!1.07e-17!33;UBERON:0004571!1.07e-17!33;UBERON:0004872!2.84e-17!84;UBERON:0000055!2.18e-15!69;UBERON:0002049!4.82e-14!79;UBERON:0007798!4.82e-14!79;UBERON:0003914!2.28e-13!118;UBERON:0004535!1.47e-12!110;UBERON:0004290!3.11e-12!70;UBERON:0001009!6.80e-12!113;UBERON:0000914!3.29e-11!83;UBERON:0002329!3.29e-11!83;UBERON:0003077!3.29e-11!83;UBERON:0003059!3.29e-11!83;UBERON:0007282!3.29e-11!83;UBERON:0009618!3.29e-11!83;UBERON:0007285!3.29e-11!83;UBERON:0003081!3.73e-11!216;UBERON:0001134!2.74e-10!61;UBERON:0002036!2.74e-10!61;UBERON:0003082!2.74e-10!61;UBERON:0000486!9.14e-10!82;UBERON:0002385!1.03e-09!63;UBERON:0001015!1.03e-09!63;UBERON:0000383!1.03e-09!63;UBERON:0002204!1.45e-09!167;UBERON:0000947!2.16e-09!21;UBERON:0010191!2.16e-09!21;UBERON:0000490!1.66e-08!138;UBERON:0000926!1.53e-07!448;UBERON:0004120!1.53e-07!448;UBERON:0006603!1.53e-07!448
}}

Latest revision as of 11:42, 17 September 2013


Full id: C1326_mesenchymal_CD14_Fibroblast_Smooth_Preadipocyte_Endothelial_Renal



Phase1 CAGE Peaks

Hg19::chr11:102668601..102668604,-p14@MMP1
Hg19::chr13:43938419..43938424,-p@chr13:43938419..43938424
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Hg19::chr13:43938433..43938456,-p@chr13:43938433..43938456
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Hg19::chr5:110407337..110407343,+p9@TSLP
Hg19::chr5:110407408..110407415,+p3@TSLP
Hg19::chr5:99385675..99385684,-p@chr5:99385675..99385684
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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 IDGO nameFDR corrected p-value
GO:0004232interstitial collagenase activity0.00412079823606691
GO:0005615extracellular space0.00412079823606691
GO:0008133collagenase activity0.00412079823606691
GO:0044421extracellular region part0.00432581913920992
GO:0030574collagen catabolic process0.00432581913920992
GO:0044256protein digestion0.00432581913920992
GO:0044254multicellular organismal protein catabolic process0.00432581913920992
GO:0044266multicellular organismal macromolecule catabolic process0.00432581913920992
GO:0044259multicellular organismal macromolecule metabolic process0.00432581913920992
GO:0044268multicellular organismal protein metabolic process0.00432581913920992
GO:0032963collagen metabolic process0.00432581913920992
GO:0044243multicellular organismal catabolic process0.00432581913920992
GO:0044236multicellular organismal metabolic process0.00437322683744746
GO:0007586digestion0.0167553098487676
GO:0004222metalloendopeptidase activity0.0325440067988259
GO:0005125cytokine activity0.047689218626343



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
systemic artery3.41e-1433
systemic arterial system3.41e-1433
splanchnic layer of lateral plate mesoderm4.40e-1283
right ovary1.50e-115
artery4.31e-1142
arterial blood vessel4.31e-1142
arterial system4.31e-1142
female gonad1.04e-0913
heart2.85e-0924
primitive heart tube2.85e-0924
primary heart field2.85e-0924
anterior lateral plate mesoderm2.85e-0924
heart tube2.85e-0924
heart primordium2.85e-0924
cardiac mesoderm2.85e-0924
cardiogenic plate2.85e-0924
heart rudiment2.85e-0924
cardiovascular system5.78e-09109
circulatory system1.07e-08112
epithelial tube2.79e-08117
primary circulatory organ2.90e-0827
carotid artery segment3.82e-082
internal thoracic artery6.58e-082
epithelial tube open at both ends8.43e-0859
blood vessel8.43e-0859
blood vasculature8.43e-0859
vascular cord8.43e-0859
brachiocephalic artery9.19e-082
brachiocephalic vasculature9.19e-082
Disease
Ontology termp-valuen
ovarian cancer4.68e-0914


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)
MA0003.10.00461978
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.11.59836
MA0040.10.955415
MA0041.11.41501
MA0042.11.3446
MA0043.11.03713
MA0046.12.33832
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.808182
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.11.24837
MA0063.10
MA0066.11.59928
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00563817
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.81721
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.12.35015
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.811435
MA0145.10.347815
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.0313803
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.26661
MA0047.21.66123
MA0112.20.101413
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.27.22997e-05
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
GATA2#262436.3724658667770.008058821308742550.0318820879072602



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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