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Coexpression cluster:C4334: Difference between revisions

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|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.0090010958563248!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000371958625762568!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243670741416977!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392607335306116!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445453414196688!JUNB#3726;2:20.4070884398808:0.00313146219943874:0.0164527005054423!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157271851991032!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309660459572636!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203575263548103!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000302253762739009!SMARCC2#6601;3:94.1553744268976:1.19621075407887e-06:4.86491646983033e-05!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310181761333553
|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.0090010958563248!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000371958625762568!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243670741416977!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392607335306116!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445453414196688!JUNB#3726;2:20.4070884398808:0.00313146219943874:0.0164527005054423!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157271851991032!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309660459572636!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203575263548103!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000302253762739009!SMARCC2#6601;3:94.1553744268976:1.19621075407887e-06:4.86491646983033e-05!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310181761333553
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,1.23863,0.491742,0.63186,0.820209,0.985163,1.11328,0.925331,1.54465,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,1.18324,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 16:41, 26 November 2012


Full id: C4334_Small_Placental_salivary_Pericytes_Urothelial_astrocytoma_Esophageal



Phase1 CAGE Peaks

Hg19::chr3:48632723..48632770,-p1@COL7A1
Hg19::chr3:48632784..48632795,-p2@COL7A1
Hg19::chr3:48633003..48633029,-p3@COL7A1


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
surface structure1.39e-1299
endoderm-derived structure2.46e-11160
endoderm2.46e-11160
presumptive endoderm2.46e-11160
mouth1.27e-0829
stomodeum1.27e-0829
organ1.42e-08503
respiratory system2.23e-0874
mouth mucosa1.42e-0713
head2.03e-0756
subdivision of head2.56e-0749
extraembryonic membrane2.90e-0714
membranous layer2.90e-0714
anterior region of body3.26e-0762
craniocervical region3.26e-0762
oral opening5.17e-0722
organ component layer6.28e-0766
digestive system8.52e-07145
digestive tract8.52e-07145
primitive gut8.52e-07145


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)

{{{tfbs_overrepresentation_jaspar}}}



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
FOS#235338.99795530889440.001372499272417130.0090010958563248
FOSL1#8061339.7135797163731.59554825631833e-050.000371958625762568
FOSL2#2355316.93020060456170.0002060162053171620.00243670741416977
HDAC2#3066313.41562023662630.0004140761399857210.00392607335306116
JUN#3725312.51282919233630.0005103313992726250.00445453414196688
JUNB#3726220.40708843988080.003131462199438740.0164527005054423
JUND#372736.994663941871030.002921845042734990.0157271851991032
NR3C1#2908314.9730233311730.0002978331194675480.00309660459572636
SMARCB1#6598318.25271578115740.000164397760679890.00203575263548103
SMARCC1#6599343.66335931963151.20046018043203e-050.000302253762739009
SMARCC2#6601394.15537442689761.19621075407887e-064.86491646983033e-05
SMC3#9126315.04493284493280.0002935825420371870.00310181761333553



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.