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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:25, 17 September 2013


Full id: C526_meningioma_bile_cervical_fibrosarcoma_prostate_epidermoid_lung



Phase1 CAGE Peaks

Hg19::chr10:45295885..45295915,-p@chr10:45295885..45295915
-
Hg19::chr12:12094754..12094758,+p@chr12:12094754..12094758
+
Hg19::chr12:1919552..1919568,+p@chr12:1919552..1919568
+
Hg19::chr12:31158830..31158854,-p1@ENST00000544329
Hg19::chr12:31158902..31158914,-p2@ENST00000544329
Hg19::chr12:52680109..52680121,-p@chr12:52680109..52680121
-
Hg19::chr12:52680234..52680245,-p@chr12:52680234..52680245
-
Hg19::chr12:52681676..52681679,-p6@KRT81
Hg19::chr12:52710803..52710809,-p@chr12:52710803..52710809
-
Hg19::chr14:65823553..65823594,+p@chr14:65823553..65823594
+
Hg19::chr14:94582894..94582917,-p@chr14:94582894..94582917
-
Hg19::chr15:67391010..67391046,+p13@SMAD3
Hg19::chr1:94752932..94752936,+p@chr1:94752932..94752936
+
Hg19::chr2:235107734..235107745,-p@chr2:235107734..235107745
-
Hg19::chr6:31304866..31304870,-p@chr6:31304866..31304870
-
Hg19::chr8:41523346..41523361,-p12@ANK1
Hg19::chr9:16063204..16063225,+p@chr9:16063204..16063225
+


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:0045199maintenance of epithelial cell polarity0.00317899507882246
GO:0030507spectrin binding0.00317899507882246
GO:0019049evasion of host defenses by virus0.00317899507882246
GO:0030011maintenance of cell polarity0.00317899507882246
GO:0044413avoidance of host defenses0.00317899507882246
GO:0051834evasion or tolerance of defenses of other organism during symbiotic interaction0.00317899507882246
GO:0044415evasion or tolerance of host defenses0.00317899507882246
GO:0051832avoidance of defenses of other organism during symbiotic interaction0.00317899507882246
GO:0052173response to defenses of other organism during symbiotic interaction0.00317899507882246
GO:0052200response to host defenses0.00317899507882246
GO:0015460transport accessory protein activity0.00317899507882246
GO:0035090maintenance of apical/basal cell polarity0.00317899507882246
GO:0032906transforming growth factor-beta2 production0.0050860926711619
GO:0007183SMAD protein complex assembly0.0050860926711619
GO:0032909regulation of transforming growth factor-beta2 production0.0050860926711619
GO:0000902cell morphogenesis0.00726499113787996
GO:0032989cellular structure morphogenesis0.00726499113787996
GO:0045197establishment and/or maintenance of epithelial cell polarity0.00726499113787996
GO:0008093cytoskeletal adaptor activity0.00726499113787996
GO:0042993positive regulation of transcription factor import into nucleus0.00726499113787996
GO:0042307positive regulation of protein import into nucleus0.00726499113787996
GO:0035088establishment and/or maintenance of apical/basal cell polarity0.00780138013070573
GO:0046824positive regulation of nucleocytoplasmic transport0.00829107778830017
GO:0051222positive regulation of protein transport0.00839032370778676
GO:0019048virus-host interaction0.00839032370778676
GO:0045930negative regulation of progression through mitotic cell cycle0.00953389737998454
GO:0046332SMAD binding0.0112984359739393
GO:0017015regulation of transforming growth factor beta receptor signaling pathway0.0127084952637695
GO:0042990regulation of transcription factor import into nucleus0.0127084952637695
GO:0042991transcription factor import into nucleus0.0127084952637695
GO:0042306regulation of protein import into nucleus0.0127084952637695
GO:0051701interaction with host0.0127084952637695
GO:0033157regulation of intracellular protein transport0.0127084952637695
GO:0016528sarcoplasm0.0132368466244668
GO:0016529sarcoplasmic reticulum0.0132368466244668
GO:0032386regulation of intracellular transport0.0132368466244668
GO:0051223regulation of protein transport0.014171938827264
GO:0007163establishment and/or maintenance of cell polarity0.014171938827264
GO:0046822regulation of nucleocytoplasmic transport0.014171938827264
GO:0009653anatomical structure morphogenesis0.0141820507980852
GO:0044403symbiosis, encompassing mutualism through parasitism0.0141820507980852
GO:0044419interspecies interaction between organisms0.0141820507980852
GO:0007346regulation of progression through mitotic cell cycle0.0141820507980852
GO:0051649establishment of cellular localization0.0150403730467866
GO:0051641cellular localization0.0154574110135078
GO:0051050positive regulation of transport0.0157400659191755
GO:0001817regulation of cytokine production0.0166199002548351
GO:0006919caspase activation0.0182555558036227
GO:0001666response to hypoxia0.0186594158055212
GO:0007179transforming growth factor beta receptor signaling pathway0.0186735604828549
GO:0043280positive regulation of caspase activity0.0186735604828549
GO:0030308negative regulation of cell growth0.0194041235616757
GO:0045792negative regulation of cell size0.0194041235616757
GO:0022415viral reproductive process0.0199152228069367
GO:0005856cytoskeleton0.0199152228069367
GO:0043281regulation of caspase activity0.0200257339597556
GO:0060090molecular adaptor activity0.0200257339597556
GO:0045926negative regulation of growth0.0200257339597556
GO:0043623cellular protein complex assembly0.0222628797508382
GO:0051345positive regulation of hydrolase activity0.0237125612211264
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0237125612211264
GO:0005200structural constituent of cytoskeleton0.0256718954156682
GO:0016323basolateral plasma membrane0.0256718954156682
GO:0008632apoptotic program0.0264568667793752
GO:0006606protein import into nucleus0.0280929071043848
GO:0051170nuclear import0.0282419938406323
GO:0007050cell cycle arrest0.0286695842200121
GO:0043235receptor complex0.0301029315524942
GO:0051049regulation of transport0.0301029315524942
GO:0006887exocytosis0.0301029315524942
GO:0001816cytokine production0.0301029315524942
GO:0048856anatomical structure development0.0301029315524942
GO:0017038protein import0.0317645736622528
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0326147506026285
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0352080511178059
GO:0006913nucleocytoplasmic transport0.0384598581761161
GO:0051169nuclear transport0.0384598581761161
GO:0042803protein homodimerization activity0.0384598581761161
GO:0001558regulation of cell growth0.0389297755708393
GO:0016049cell growth0.0464088845566007
GO:0040008regulation of growth0.0464088845566007
GO:0045892negative regulation of transcription, DNA-dependent0.0464088845566007
GO:0008361regulation of cell size0.0464088845566007
GO:0005667transcription factor complex0.0464088845566007
GO:0006917induction of apoptosis0.0464088845566007
GO:0005515protein binding0.0464088845566007
GO:0012502induction of programmed cell death0.0464088845566007
GO:0006605protein targeting0.0469516159730965
GO:0045893positive regulation of transcription, DNA-dependent0.0473725810133215
GO:0045786negative regulation of progression through cell cycle0.0473725810133215
GO:0005882intermediate filament0.0478500585324665
GO:0045111intermediate filament cytoskeleton0.0478500585324665
GO:0043232intracellular non-membrane-bound organelle0.0478500585324665
GO:0043228non-membrane-bound organelle0.0478500585324665
GO:0045045secretory pathway0.0478500585324665
GO:0043085positive regulation of catalytic activity0.0498376766578191
GO:0043065positive regulation of apoptosis0.0498376766578191
GO:0043068positive regulation of programmed cell death0.0498376766578191



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>

Cell Type
Ontology termp-valuen
meningothelial cell7.48e-301
epithelial cell of gall bladder2.74e-152
Disease
Ontology termp-valuen
central nervous system cancer7.48e-301
meningioma7.48e-301
pleomorphic carcinoma1.33e-291
tubular adenocarcinoma1.78e-152
cell type cancer2.54e-07143
disease of anatomical entity3.04e-0739
carcinoma5.64e-07106


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)
MA0003.10.00504314
MA0004.10.221943
MA0006.10.112549
MA0007.12.4995
MA0009.10.621697
MA0014.10.00547893
MA0017.11.3589
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.11.31824
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.11.2374
MA0042.10.211928
MA0043.10.621991
MA0046.10.611559
MA0048.10.345177
MA0050.10.609862
MA0051.10.299199
MA0052.10.551663
MA0055.10.624776
MA0056.10
MA0057.10.0616251
MA0058.10.153757
MA0059.10.15289
MA0060.10.18988
MA0061.10.155208
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.111262
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.13.72477e-05
MA0074.10.298586
MA0076.10.164578
MA0077.10.586275
MA0078.10.995054
MA0081.10.907903
MA0083.11.52135
MA0084.11.10674
MA0087.10.591148
MA0088.10.320704
MA0089.10
MA0090.10.174619
MA0091.10.223914
MA0092.10.570207
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.843378
MA0101.10.116395
MA0103.11.16516
MA0105.10.0516824
MA0106.13.349
MA0107.10.259598
MA0108.20.471286
MA0109.10
MA0111.10.541878
MA0113.11.6534
MA0114.11.37492
MA0115.10.850405
MA0116.10.0765991
MA0117.10.656858
MA0119.10.438293
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.10.0351037
MA0140.10.74193
MA0141.10.151722
MA0142.10.445733
MA0143.10.350722
MA0144.10.231909
MA0145.10.204689
MA0146.10.307985
MA0147.10.269778
MA0148.10.676348
MA0149.10.261654
MA0062.20.0377014
MA0035.20.268747
MA0039.20.106686
MA0138.20.38342
MA0002.23.84357
MA0137.20.398112
MA0104.20.0505812
MA0047.21.56898
MA0112.20.790396
MA0065.22.35272
MA0150.10.98029
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.10.137179
MA0155.10.0782503
MA0156.10.4018
MA0157.10.421609
MA0158.10
MA0159.10.0787617
MA0160.10.252705
MA0161.10
MA0162.10.0130334
MA0163.10.00623
MA0164.10.948242
MA0080.20.366978
MA0018.20.337929
MA0099.20.754549
MA0079.26.23878e-05
MA0102.21.14323
MA0258.10.82387
MA0259.10.0828875
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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