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Coexpression cluster:C2280: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000055!8.54e-16!68;UBERON:0003914!1.27e-15!117;UBERON:0002049!1.55e-15!78;UBERON:0007798!1.55e-15!78;UBERON:0004872!1.82e-15!83;UBERON:0007500!8.67e-15!59;UBERON:0001981!8.67e-15!59;UBERON:0004537!8.67e-15!59;UBERON:0006965!8.67e-15!59;UBERON:0004111!6.50e-14!240;UBERON:0001009!2.56e-13!112;UBERON:0004535!5.17e-12!109;UBERON:0000477!7.89e-12!373;UBERON:0000025!1.51e-11!192;UBERON:0001637!5.15e-11!42;UBERON:0003509!5.15e-11!42;UBERON:0004572!5.15e-11!42;UBERON:0000119!7.70e-09!309;UBERON:0000483!8.56e-09!306;UBERON:0003103!2.00e-08!68;UBERON:0006914!4.81e-08!25;UBERON:0004573!6.22e-08!33;UBERON:0004571!6.22e-08!33;UBERON:0000490!1.58e-07!148;UBERON:0004638!2.50e-07!18;UBERON:0001986!2.50e-07!18;UBERON:0004852!2.50e-07!18;UBERON:0000487!4.03e-07!22;UBERON:0005256!4.39e-07!122;UBERON:0007100!4.77e-07!27;UBERON:0004876!6.40e-07!11;UBERON:0000481!7.57e-07!342
|ontology_enrichment_uberon=UBERON:0000055!8.54e-16!68;UBERON:0003914!1.27e-15!117;UBERON:0002049!1.55e-15!78;UBERON:0007798!1.55e-15!78;UBERON:0004872!1.82e-15!83;UBERON:0007500!8.67e-15!59;UBERON:0001981!8.67e-15!59;UBERON:0004537!8.67e-15!59;UBERON:0006965!8.67e-15!59;UBERON:0004111!6.50e-14!240;UBERON:0001009!2.56e-13!112;UBERON:0004535!5.17e-12!109;UBERON:0000477!7.89e-12!373;UBERON:0000025!1.51e-11!192;UBERON:0001637!5.15e-11!42;UBERON:0003509!5.15e-11!42;UBERON:0004572!5.15e-11!42;UBERON:0000119!7.70e-09!309;UBERON:0000483!8.56e-09!306;UBERON:0003103!2.00e-08!68;UBERON:0006914!4.81e-08!25;UBERON:0004573!6.22e-08!33;UBERON:0004571!6.22e-08!33;UBERON:0000490!1.58e-07!148;UBERON:0004638!2.50e-07!18;UBERON:0001986!2.50e-07!18;UBERON:0004852!2.50e-07!18;UBERON:0000487!4.03e-07!22;UBERON:0005256!4.39e-07!122;UBERON:0007100!4.77e-07!27;UBERON:0004876!6.40e-07!11;UBERON:0000481!7.57e-07!342
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|tfbs_overrepresentation_for_novel_motifs=0.590005,1.54039,0.581696,0.741427,2.27411,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.169357,0.731221,0.528529,0.632849,2.06579,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,1.23824,0.0842336,3.15145,0.740899,0.463978,1.72725,0.493145,0.66492,0.183156,0.53106,0.0946706,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,1.28263,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,3.02769,0.6318,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,2.04634,1.1057,1.14983,1.05974,0.979006,2.81371,1.04326,0.805616,0.632569,1.28386,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,3.22553,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,3.0147,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,1.47036,0.997702,0.843324,0.423521,0.820225,1.00378
}}
}}

Revision as of 15:24, 26 November 2012


Full id: C2280_gastric_Endothelial_heart_Renal_serous_papillary_Fibroblast



Phase1 CAGE Peaks

Hg19::chr14:105945306..105945352,+p3@CRIP2
Hg19::chr14:105945477..105945495,+p@chr14:105945477..105945495
+
Hg19::chr14:105945518..105945533,+p@chr14:105945518..105945533
+
Hg19::chr14:105945760..105945792,+p@chr14:105945760..105945792
+


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
vessel8.54e-1668
epithelial tube1.27e-15117
vasculature1.55e-1578
vascular system1.55e-1578
splanchnic layer of lateral plate mesoderm1.82e-1583
epithelial tube open at both ends8.67e-1559
blood vessel8.67e-1559
blood vasculature8.67e-1559
vascular cord8.67e-1559
anatomical conduit6.50e-14240
circulatory system2.56e-13112
cardiovascular system5.17e-12109
anatomical cluster7.89e-12373
tube1.51e-11192
artery5.15e-1142
arterial blood vessel5.15e-1142
arterial system5.15e-1142
cell layer7.70e-09309
epithelium8.56e-09306
compound organ2.00e-0868
squamous epithelium4.81e-0825
systemic artery6.22e-0833
systemic arterial system6.22e-0833
unilaminar epithelium1.58e-07148
blood vessel endothelium2.50e-0718
endothelium2.50e-0718
cardiovascular system endothelium2.50e-0718
simple squamous epithelium4.03e-0722
trunk mesenchyme4.39e-07122
primary circulatory organ4.77e-0727
urogenital ridge6.40e-0711
multi-tissue structure7.57e-07342


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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