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Coexpression cluster:C1907: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004111!1.29e-16!240;UBERON:0000483!2.69e-15!306;UBERON:0000119!7.09e-15!309;UBERON:0000468!8.76e-15!656;UBERON:0000477!2.79e-14!373;UBERON:0000467!8.63e-14!624;UBERON:0000480!1.61e-13!625;UBERON:0000481!2.02e-11!342;UBERON:0000025!2.42e-11!192;UBERON:0003914!5.67e-11!117;UBERON:0007023!7.30e-11!114;UBERON:0002049!2.24e-10!78;UBERON:0007798!2.24e-10!78;UBERON:0004872!8.93e-10!83;UBERON:0005256!2.24e-09!122;UBERON:0002050!2.53e-09!564;UBERON:0000923!3.40e-09!560;UBERON:0010316!3.40e-09!560;UBERON:0005291!3.40e-09!560;UBERON:0006598!3.40e-09!560;UBERON:0010317!3.40e-09!560;UBERON:0002532!3.40e-09!560;UBERON:0000490!6.47e-09!148;UBERON:0000475!6.59e-09!264;UBERON:0000055!7.07e-09!68;UBERON:0000062!1.01e-08!503;UBERON:0005423!4.31e-08!581;UBERON:0003104!4.62e-08!160;UBERON:0009142!4.62e-08!160;UBERON:0002100!6.91e-08!199;UBERON:0001009!1.17e-07!112;UBERON:0007500!1.77e-07!59;UBERON:0001981!1.77e-07!59;UBERON:0004537!1.77e-07!59;UBERON:0006965!1.77e-07!59;UBERON:0000922!2.57e-07!592;UBERON:0002530!5.15e-07!59;UBERON:0004535!5.59e-07!109
|ontology_enrichment_uberon=UBERON:0004111!1.29e-16!240;UBERON:0000483!2.69e-15!306;UBERON:0000119!7.09e-15!309;UBERON:0000468!8.76e-15!656;UBERON:0000477!2.79e-14!373;UBERON:0000467!8.63e-14!624;UBERON:0000480!1.61e-13!625;UBERON:0000481!2.02e-11!342;UBERON:0000025!2.42e-11!192;UBERON:0003914!5.67e-11!117;UBERON:0007023!7.30e-11!114;UBERON:0002049!2.24e-10!78;UBERON:0007798!2.24e-10!78;UBERON:0004872!8.93e-10!83;UBERON:0005256!2.24e-09!122;UBERON:0002050!2.53e-09!564;UBERON:0000923!3.40e-09!560;UBERON:0010316!3.40e-09!560;UBERON:0005291!3.40e-09!560;UBERON:0006598!3.40e-09!560;UBERON:0010317!3.40e-09!560;UBERON:0002532!3.40e-09!560;UBERON:0000490!6.47e-09!148;UBERON:0000475!6.59e-09!264;UBERON:0000055!7.07e-09!68;UBERON:0000062!1.01e-08!503;UBERON:0005423!4.31e-08!581;UBERON:0003104!4.62e-08!160;UBERON:0009142!4.62e-08!160;UBERON:0002100!6.91e-08!199;UBERON:0001009!1.17e-07!112;UBERON:0007500!1.77e-07!59;UBERON:0001981!1.77e-07!59;UBERON:0004537!1.77e-07!59;UBERON:0006965!1.77e-07!59;UBERON:0000922!2.57e-07!592;UBERON:0002530!5.15e-07!59;UBERON:0004535!5.59e-07!109
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.205703,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.859849,0.345702,0.621241,0.778743,0.274093,0.721271,1.14971,0.478935,0.963929,0.395009,0.287891,0.501863,0.500405,1.83059,0.645033,0.44943,0.549618,0.802434,0.700122,0.642741,0.458349,1.22891,0.598009,1.00172,0.359091,0.27659,1.0713,0.757784,0.413782,1.57519,0.388123,0.301779,0.415749,0.580638,0.132849,2.00042,1.25074,0.533483,0.734485,0.609718,0.124583,1.16046,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.536557,0.166306,2.64291,0.844289,1.79645,1.41984,1.15413,1.01895,1.71087,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,1.11542,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,1.00558,2.47721,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,1.44357,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,1.00998,0.398598,1.15522,0.312599,0.736459,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,1.05945
}}
}}

Revision as of 15:10, 26 November 2012


Full id: C1907_lung_Fibroblast_Renal_breast_Hepatic_Endothelial_heart



Phase1 CAGE Peaks

Hg19::chr2:46524537..46524553,+p1@EPAS1
Hg19::chr2:46609585..46609604,+p@chr2:46609585..46609604
+
Hg19::chr2:46611800..46611855,+p@chr2:46611800..46611855
+
Hg19::chr2:46611868..46611927,+p@chr2:46611868..46611927
+
Hg19::chr2:46612043..46612056,+p@chr2:46612043..46612056
+


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
mesodermal cell3.22e-12121
lining cell8.68e-1158
barrier cell8.68e-1158
endothelial cell2.47e-0936
meso-epithelial cell4.32e-0945
endothelial cell of vascular tree3.37e-0724
Uber Anatomy
Ontology termp-valuen
anatomical conduit1.29e-16240
epithelium2.69e-15306
cell layer7.09e-15309
multi-cellular organism8.76e-15656
anatomical cluster2.79e-14373
anatomical system8.63e-14624
anatomical group1.61e-13625
multi-tissue structure2.02e-11342
tube2.42e-11192
epithelial tube5.67e-11117
adult organism7.30e-11114
vasculature2.24e-1078
vascular system2.24e-1078
splanchnic layer of lateral plate mesoderm8.93e-1083
trunk mesenchyme2.24e-09122
embryonic structure2.53e-09564
germ layer3.40e-09560
germ layer / neural crest3.40e-09560
embryonic tissue3.40e-09560
presumptive structure3.40e-09560
germ layer / neural crest derived structure3.40e-09560
epiblast (generic)3.40e-09560
unilaminar epithelium6.47e-09148
organism subdivision6.59e-09264
vessel7.07e-0968
organ1.01e-08503
developing anatomical structure4.31e-08581
mesenchyme4.62e-08160
entire embryonic mesenchyme4.62e-08160
trunk6.91e-08199
circulatory system1.17e-07112
epithelial tube open at both ends1.77e-0759
blood vessel1.77e-0759
blood vasculature1.77e-0759
vascular cord1.77e-0759
embryo2.57e-07592
gland5.15e-0759
cardiovascular system5.59e-07109


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

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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