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Coexpression cluster:C1794: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007100!9.42e-53!27;UBERON:0000948!7.26e-45!24;UBERON:0005498!7.26e-45!24;UBERON:0004140!7.26e-45!24;UBERON:0009881!7.26e-45!24;UBERON:0004141!7.26e-45!24;UBERON:0003084!7.26e-45!24;UBERON:0007005!7.26e-45!24;UBERON:0004139!7.26e-45!24;UBERON:0004291!7.26e-45!24;UBERON:0003103!2.81e-27!68;UBERON:0004872!3.16e-22!83;UBERON:0003914!3.48e-22!117;UBERON:0007023!3.03e-21!114;UBERON:0001009!2.53e-18!112;UBERON:0004535!6.83e-15!109;UBERON:0004111!7.40e-14!240;UBERON:0000025!2.33e-13!192;UBERON:0003498!7.59e-13!5;UBERON:0005985!7.59e-13!5;UBERON:0001048!1.86e-12!160;UBERON:0005256!5.23e-10!122;UBERON:0000477!9.11e-10!373;UBERON:0000481!1.97e-09!342;UBERON:0004151!3.90e-09!3;UBERON:0003104!6.91e-09!160;UBERON:0009142!6.91e-09!160;UBERON:0006947!7.97e-09!3;UBERON:0004054!7.97e-09!3;UBERON:0004145!1.27e-08!3;UBERON:0001621!1.45e-08!3;UBERON:0001637!1.49e-08!42;UBERON:0003509!1.49e-08!42;UBERON:0004572!1.49e-08!42;UBERON:0002100!1.71e-08!199;UBERON:0004573!1.73e-08!33;UBERON:0004571!1.73e-08!33;UBERON:0000483!3.53e-08!306;UBERON:0000119!5.46e-08!309;UBERON:0003081!5.70e-08!203;UBERON:0010314!6.00e-08!132;UBERON:0007500!2.89e-07!59;UBERON:0001981!2.89e-07!59;UBERON:0004537!2.89e-07!59;UBERON:0006965!2.89e-07!59;UBERON:0001134!6.20e-07!62;UBERON:0002036!6.20e-07!62;UBERON:0003082!6.20e-07!62;UBERON:0000926!8.14e-07!315;UBERON:0004120!8.14e-07!315;UBERON:0006603!8.14e-07!315;UBERON:0002133!8.30e-07!2;UBERON:0000055!9.54e-07!68
|ontology_enrichment_uberon=UBERON:0007100!9.42e-53!27;UBERON:0000948!7.26e-45!24;UBERON:0005498!7.26e-45!24;UBERON:0004140!7.26e-45!24;UBERON:0009881!7.26e-45!24;UBERON:0004141!7.26e-45!24;UBERON:0003084!7.26e-45!24;UBERON:0007005!7.26e-45!24;UBERON:0004139!7.26e-45!24;UBERON:0004291!7.26e-45!24;UBERON:0003103!2.81e-27!68;UBERON:0004872!3.16e-22!83;UBERON:0003914!3.48e-22!117;UBERON:0007023!3.03e-21!114;UBERON:0001009!2.53e-18!112;UBERON:0004535!6.83e-15!109;UBERON:0004111!7.40e-14!240;UBERON:0000025!2.33e-13!192;UBERON:0003498!7.59e-13!5;UBERON:0005985!7.59e-13!5;UBERON:0001048!1.86e-12!160;UBERON:0005256!5.23e-10!122;UBERON:0000477!9.11e-10!373;UBERON:0000481!1.97e-09!342;UBERON:0004151!3.90e-09!3;UBERON:0003104!6.91e-09!160;UBERON:0009142!6.91e-09!160;UBERON:0006947!7.97e-09!3;UBERON:0004054!7.97e-09!3;UBERON:0004145!1.27e-08!3;UBERON:0001621!1.45e-08!3;UBERON:0001637!1.49e-08!42;UBERON:0003509!1.49e-08!42;UBERON:0004572!1.49e-08!42;UBERON:0002100!1.71e-08!199;UBERON:0004573!1.73e-08!33;UBERON:0004571!1.73e-08!33;UBERON:0000483!3.53e-08!306;UBERON:0000119!5.46e-08!309;UBERON:0003081!5.70e-08!203;UBERON:0010314!6.00e-08!132;UBERON:0007500!2.89e-07!59;UBERON:0001981!2.89e-07!59;UBERON:0004537!2.89e-07!59;UBERON:0006965!2.89e-07!59;UBERON:0001134!6.20e-07!62;UBERON:0002036!6.20e-07!62;UBERON:0003082!6.20e-07!62;UBERON:0000926!8.14e-07!315;UBERON:0004120!8.14e-07!315;UBERON:0006603!8.14e-07!315;UBERON:0002133!8.30e-07!2;UBERON:0000055!9.54e-07!68
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|tfbs_overrepresentation_for_novel_motifs=0.508327,1.20042,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.106358,0.621241,0.778743,2.11893,0.721271,0.453496,0.478935,2.21256,0.395009,0.784337,0.501863,0.500405,0.770467,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,1.88355,0.432883,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,1.33238,0.451846,0.0606304,0.533483,0.734485,0.609718,1.85968,0.458489,0.817229,1.76707,1.67994,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.330474,0.189341,1.23387,0.269111,0.255232,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,1.70662,0.549347,0.437618,1.27602,1.05402,0.494368,0.631235,1.37132,1.05995,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,4.30651,1.44357,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.526389,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,2.39025
}}
}}

Revision as of 15:06, 26 November 2012


Full id: C1794_heart_Cardiac_seminal_umbilical_ductus_Smooth_left



Phase1 CAGE Peaks

Hg19::chr17:77018850..77018871,+p@chr17:77018850..77018871
+
Hg19::chr17:77018898..77018919,+p@chr17:77018898..77018919
+
Hg19::chr17:77018953..77018966,+p@chr17:77018953..77018966
+
Hg19::chr17:77018991..77019000,+p@chr17:77018991..77019000
+
Hg19::chr17:77019002..77019027,+p@chr17:77019002..77019027
+


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
primary circulatory organ9.42e-5327
heart7.26e-4524
primitive heart tube7.26e-4524
primary heart field7.26e-4524
anterior lateral plate mesoderm7.26e-4524
heart tube7.26e-4524
heart primordium7.26e-4524
cardiac mesoderm7.26e-4524
cardiogenic plate7.26e-4524
heart rudiment7.26e-4524
compound organ2.81e-2768
splanchnic layer of lateral plate mesoderm3.16e-2283
epithelial tube3.48e-22117
adult organism3.03e-21114
circulatory system2.53e-18112
cardiovascular system6.83e-15109
anatomical conduit7.40e-14240
tube2.33e-13192
heart blood vessel7.59e-135
coronary vessel7.59e-135
primordium1.86e-12160
trunk mesenchyme5.23e-10122
anatomical cluster9.11e-10373
multi-tissue structure1.97e-09342
cardiac chamber3.90e-093
mesenchyme6.91e-09160
entire embryonic mesenchyme6.91e-09160
male genital duct7.97e-093
internal male genitalia7.97e-093
outflow tract1.27e-083
coronary artery1.45e-083
artery1.49e-0842
arterial blood vessel1.49e-0842
arterial system1.49e-0842
trunk1.71e-08199
systemic artery1.73e-0833
systemic arterial system1.73e-0833
epithelium3.53e-08306
cell layer5.46e-08309
lateral plate mesoderm5.70e-08203
structure with developmental contribution from neural crest6.00e-08132
epithelial tube open at both ends2.89e-0759
blood vessel2.89e-0759
blood vasculature2.89e-0759
vascular cord2.89e-0759
skeletal muscle tissue6.20e-0762
striated muscle tissue6.20e-0762
myotome6.20e-0762
mesoderm8.14e-07315
mesoderm-derived structure8.14e-07315
presumptive mesoderm8.14e-07315
atrioventricular valve8.30e-072
vessel9.54e-0768
Disease
Ontology termp-valuen
heart disease5.18e-072


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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