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Coexpression cluster:C1984: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003102!8.62e-21!99;UBERON:0002199!2.13e-14!46;UBERON:0002416!2.13e-14!46;UBERON:0002097!9.42e-12!41;UBERON:0004923!1.51e-10!66;UBERON:0000486!1.60e-09!83;UBERON:0000055!6.50e-09!68;UBERON:0007524!9.88e-09!73;UBERON:0002329!1.59e-08!71;UBERON:0003059!1.59e-08!71;UBERON:0007282!1.59e-08!71;UBERON:0004290!1.59e-08!71;UBERON:0009618!1.59e-08!71;UBERON:0003077!1.84e-08!72;UBERON:0007285!1.84e-08!72;UBERON:0002049!2.03e-08!78;UBERON:0007798!2.03e-08!78;UBERON:0000490!4.57e-08!148;UBERON:0007503!2.04e-07!78
|ontology_enrichment_uberon=UBERON:0003102!8.62e-21!99;UBERON:0002199!2.13e-14!46;UBERON:0002416!2.13e-14!46;UBERON:0002097!9.42e-12!41;UBERON:0004923!1.51e-10!66;UBERON:0000486!1.60e-09!83;UBERON:0000055!6.50e-09!68;UBERON:0007524!9.88e-09!73;UBERON:0002329!1.59e-08!71;UBERON:0003059!1.59e-08!71;UBERON:0007282!1.59e-08!71;UBERON:0004290!1.59e-08!71;UBERON:0009618!1.59e-08!71;UBERON:0003077!1.84e-08!72;UBERON:0007285!1.84e-08!72;UBERON:0002049!2.03e-08!78;UBERON:0007798!2.03e-08!78;UBERON:0000490!4.57e-08!148;UBERON:0007503!2.04e-07!78
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,1.57627,0.454983,0.653236,0.733342,1.56012,0.321368,0.106358,0.621241,0.778743,1.37937,0.721271,2.00597,0.478935,0.963929,1.02276,0.784337,0.167776,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.700122,0.642741,0.458349,0.233785,0.598009,1.00172,0.94379,0.27659,0.417272,0.0526856,0.413782,0.654459,1.00769,0.301779,0.415749,0.580638,0.132849,4.03923,0.0606304,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,1.64902,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,1.58259,0.189341,1.23387,0.269111,0.255232,0.240727,0.917983,2.26106,0.543014,1.44891,0.934302,0.755403,1.57121,1.18161,0.0719601,0.166306,1.20877,0.844289,1.79645,1.41984,1.15413,1.01895,0.96134,0.455791,0.381528,0.28626,2.41322,0.849074,1.14173,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.968277,1.22546,1.96265,1.56655,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
}}
}}

Revision as of 15:13, 26 November 2012


Full id: C1984_Olfactory_mesenchymal_basal_leiomyoma_normal_tenocyte_Myoblast



Phase1 CAGE Peaks

Hg19::chr7:116199077..116199114,+p@chr7:116199077..116199114
+
Hg19::chr7:116199144..116199170,+p@chr7:116199144..116199170
+
Hg19::chr7:116199291..116199310,+p@chr7:116199291..116199310
+
Hg19::chr7:116199802..116199867,+p9@CAV1
Hg19::chr7:116200019..116200043,+p13@CAV1


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
fibroblast1.16e-1276
squamous epithelial cell1.05e-1163
mesodermal cell1.72e-11121
embryonic cell2.72e-11250
endothelial cell of vascular tree2.06e-1024
skin fibroblast4.50e-1023
fat cell4.03e-0915
lining cell1.74e-0858
barrier cell1.74e-0858
Uber Anatomy
Ontology termp-valuen
surface structure8.62e-2199
integument2.13e-1446
integumental system2.13e-1446
skin of body9.42e-1241
organ component layer1.51e-1066
multilaminar epithelium1.60e-0983
vessel6.50e-0968
dense mesenchyme tissue9.88e-0973
somite1.59e-0871
presomitic mesoderm1.59e-0871
presumptive segmental plate1.59e-0871
dermomyotome1.59e-0871
trunk paraxial mesoderm1.59e-0871
paraxial mesoderm1.84e-0872
presumptive paraxial mesoderm1.84e-0872
vasculature2.03e-0878
vascular system2.03e-0878
unilaminar epithelium4.57e-08148
epithelial vesicle2.04e-0778


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)

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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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