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Coexpression cluster:C4334: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003102!1.77e-18!95;UBERON:0000475!9.97e-18!365;UBERON:0000062!2.10e-16!511;UBERON:0000468!6.36e-16!659;UBERON:0000481!7.17e-15!347;UBERON:0000922!1.28e-13!612;UBERON:0000480!3.61e-13!626;UBERON:0000467!4.92e-13!625;UBERON:0004119!1.81e-12!169;UBERON:0000925!1.81e-12!169;UBERON:0006595!1.81e-12!169;UBERON:0002050!2.12e-12!605;UBERON:0005423!2.12e-12!605;UBERON:0000923!3.80e-12!604;UBERON:0005291!3.80e-12!604;UBERON:0006598!3.80e-12!604;UBERON:0002532!3.80e-12!604;UBERON:0000064!9.33e-12!219;UBERON:0000924!9.79e-12!173;UBERON:0006601!9.79e-12!173;UBERON:0004121!1.11e-11!169;UBERON:0001444!1.44e-11!48;UBERON:0000165!1.57e-10!28;UBERON:0000930!1.57e-10!28;UBERON:0003104!3.42e-09!238;UBERON:0009142!3.42e-09!238;UBERON:0002097!4.65e-09!40;UBERON:0002199!4.85e-09!45;UBERON:0002416!4.85e-09!45;UBERON:0000033!5.17e-09!123;UBERON:0000153!1.80e-08!129;UBERON:0007811!1.80e-08!129;UBERON:0001007!2.15e-08!155;UBERON:0001555!2.15e-08!155;UBERON:0007026!2.15e-08!155;UBERON:0000166!4.28e-08!21;UBERON:0001004!9.94e-08!72;UBERON:0000161!1.29e-07!35;UBERON:0000464!5.07e-07!104;UBERON:0001048!6.80e-07!168;UBERON:0005256!7.49e-07!143
|ontology_enrichment_uberon=UBERON:0003102!1.77e-18!95;UBERON:0000475!9.97e-18!365;UBERON:0000062!2.10e-16!511;UBERON:0000468!6.36e-16!659;UBERON:0000481!7.17e-15!347;UBERON:0000922!1.28e-13!612;UBERON:0000480!3.61e-13!626;UBERON:0000467!4.92e-13!625;UBERON:0004119!1.81e-12!169;UBERON:0000925!1.81e-12!169;UBERON:0006595!1.81e-12!169;UBERON:0002050!2.12e-12!605;UBERON:0005423!2.12e-12!605;UBERON:0000923!3.80e-12!604;UBERON:0005291!3.80e-12!604;UBERON:0006598!3.80e-12!604;UBERON:0002532!3.80e-12!604;UBERON:0000064!9.33e-12!219;UBERON:0000924!9.79e-12!173;UBERON:0006601!9.79e-12!173;UBERON:0004121!1.11e-11!169;UBERON:0001444!1.44e-11!48;UBERON:0000165!1.57e-10!28;UBERON:0000930!1.57e-10!28;UBERON:0003104!3.42e-09!238;UBERON:0009142!3.42e-09!238;UBERON:0002097!4.65e-09!40;UBERON:0002199!4.85e-09!45;UBERON:0002416!4.85e-09!45;UBERON:0000033!5.17e-09!123;UBERON:0000153!1.80e-08!129;UBERON:0007811!1.80e-08!129;UBERON:0001007!2.15e-08!155;UBERON:0001555!2.15e-08!155;UBERON:0007026!2.15e-08!155;UBERON:0000166!4.28e-08!21;UBERON:0001004!9.94e-08!72;UBERON:0000161!1.29e-07!35;UBERON:0000464!5.07e-07!104;UBERON:0001048!6.80e-07!168;UBERON:0005256!7.49e-07!143
|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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}}
}}

Revision as of 12:22, 5 September 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>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell2.11e-10180
ectodermal cell4.97e-0971
fibroblast1.22e-0875
endo-epithelial cell4.76e-0843
epithelial cell2.51e-07254
ecto-epithelial cell6.63e-0733
Uber Anatomy
Ontology termp-valuen
surface structure1.77e-1895
organism subdivision9.97e-18365
organ2.10e-16511
multi-cellular organism6.36e-16659
multi-tissue structure7.17e-15347
embryo1.28e-13612
anatomical group3.61e-13626
anatomical system4.92e-13625
endoderm-derived structure1.81e-12169
endoderm1.81e-12169
presumptive endoderm1.81e-12169
embryonic structure2.12e-12605
developing anatomical structure2.12e-12605
germ layer3.80e-12604
embryonic tissue3.80e-12604
presumptive structure3.80e-12604
epiblast (generic)3.80e-12604
organ part9.33e-12219
ectoderm9.79e-12173
presumptive ectoderm9.79e-12173
ectoderm-derived structure1.11e-11169
subdivision of head1.44e-1148
mouth1.57e-1028
stomodeum1.57e-1028
mesenchyme3.42e-09238
entire embryonic mesenchyme3.42e-09238
skin of body4.65e-0940
integument4.85e-0945
integumental system4.85e-0945
head5.17e-09123
anterior region of body1.80e-08129
craniocervical region1.80e-08129
digestive system2.15e-08155
digestive tract2.15e-08155
primitive gut2.15e-08155
oral opening4.28e-0821
respiratory system9.94e-0872
orifice1.29e-0735
anatomical space5.07e-07104
primordium6.80e-07168
trunk mesenchyme7.49e-07143


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.

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