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Coexpression cluster:C903: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000468!7.49e-17!656;UBERON:0000467!1.48e-15!624;UBERON:0000480!2.90e-15!625;UBERON:0000064!6.04e-12!218;UBERON:0000062!1.37e-11!503;UBERON:0003102!2.77e-11!99;UBERON:0000477!9.39e-10!373;UBERON:0000119!2.69e-09!309;UBERON:0000483!4.11e-09!306;UBERON:0004121!6.60e-09!171;UBERON:0000924!6.60e-09!171;UBERON:0006601!6.60e-09!171;UBERON:0000481!1.13e-08!342;UBERON:0000922!1.63e-08!592;UBERON:0005423!2.28e-08!581;UBERON:0002050!1.03e-07!564;UBERON:0005156!3.48e-07!59;UBERON:0000990!3.48e-07!59;UBERON:0000923!3.58e-07!560;UBERON:0010316!3.58e-07!560;UBERON:0005291!3.58e-07!560;UBERON:0006598!3.58e-07!560;UBERON:0010317!3.58e-07!560;UBERON:0002532!3.58e-07!560;UBERON:0003100!5.14e-07!41
|ontology_enrichment_uberon=UBERON:0000468!7.49e-17!656;UBERON:0000467!1.48e-15!624;UBERON:0000480!2.90e-15!625;UBERON:0000064!6.04e-12!218;UBERON:0000062!1.37e-11!503;UBERON:0003102!2.77e-11!99;UBERON:0000477!9.39e-10!373;UBERON:0000119!2.69e-09!309;UBERON:0000483!4.11e-09!306;UBERON:0004121!6.60e-09!171;UBERON:0000924!6.60e-09!171;UBERON:0006601!6.60e-09!171;UBERON:0000481!1.13e-08!342;UBERON:0000922!1.63e-08!592;UBERON:0005423!2.28e-08!581;UBERON:0002050!1.03e-07!564;UBERON:0005156!3.48e-07!59;UBERON:0000990!3.48e-07!59;UBERON:0000923!3.58e-07!560;UBERON:0010316!3.58e-07!560;UBERON:0005291!3.58e-07!560;UBERON:0006598!3.58e-07!560;UBERON:0010317!3.58e-07!560;UBERON:0002532!3.58e-07!560;UBERON:0003100!5.14e-07!41
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|tfbs_overrepresentation_for_novel_motifs=0.312007,0.136365,0.305225,0.440628,0.267236,0.439064,1.27477,0.492582,0.161941,0.0287394,1.05643,1.36367,0.127813,0.500805,0.266007,0.287179,0.728104,0.218596,0.137566,0.0599474,3.15088,0.33045,0.431698,0.262652,0.347482,0.575764,0.112018,0.429643,0.270022,0.10044,0.389837,0.764231,1.06082,0.406122,1.2389,1.72894,0.233607,1.9611,2.53583,0.14756,0.663028,0.374544,0.366128,0.264644,0.0112275,0.333541,0.51292,0.4002,4.90009,0.270138,1.4392,0.524278,0.0739421,1.9587,0.99088,0.503626,0.273964,2.06859,0.329728,0.47124,0.804523,0.5152,0.162346,0.700946,2.2681,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,0.0724994,0.988898,0.124338,0.114787,0.105027,0.684401,0.750836,0.905375,0.436045,0.699894,0.532172,0.166331,0.937974,0.0150019,1.23382,1.61674,0.614883,1.54397,1.17124,0.911274,0.78075,0.196636,0.267904,5.09554,6.82701,0.82268,0.619373,0.290348,1.80452,0.775192,1.91213,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.252953,0.315525,1.90652,0.300169,0.41935,1.12352,0.232218,0.419185,1.78582,3.91707,0.199081,0.980696,0.612519,0.436445,0.543065,4.45941,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,1.79896,1.03718,0.539846,1.18405,6.71788,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,0.641461,1.83907,0.971016,0.193834,1.81595,0.150327,0.912334,0.155464,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,2.36759,0.673453,0.531409,0.183544,0.510589,0.00185481
}}
}}

Revision as of 14:33, 26 November 2012


Full id: C903_amniotic_salivary_Prostate_endometrial_epithelioid_gastric_Keratinocyte



Phase1 CAGE Peaks

Hg19::chr14:105419880..105419923,+p@chr14:105419880..105419923
+
Hg19::chr14:105419885..105419897,-p@chr14:105419885..105419897
-
Hg19::chr14:105419929..105420007,+p@chr14:105419929..105420007
+
Hg19::chr14:105419932..105419953,-p@chr14:105419932..105419953
-
Hg19::chr14:105420030..105420079,+p@chr14:105420030..105420079
+
Hg19::chr14:105420048..105420053,-p@chr14:105420048..105420053
-
Hg19::chr14:105420115..105420119,-p@chr14:105420115..105420119
-
Hg19::chr14:105420158..105420169,-p@chr14:105420158..105420169
-
Hg19::chr14:105420260..105420274,-p3@AHNAK2


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
epithelial cell8.07e-23253
embryonic cell7.93e-13250
squamous epithelial cell1.25e-1263
endo-epithelial cell9.83e-1042
fibroblast2.17e-0876
endodermal cell5.50e-0758
Uber Anatomy
Ontology termp-valuen
multi-cellular organism7.49e-17656
anatomical system1.48e-15624
anatomical group2.90e-15625
organ part6.04e-12218
organ1.37e-11503
surface structure2.77e-1199
anatomical cluster9.39e-10373
cell layer2.69e-09309
epithelium4.11e-09306
ectoderm-derived structure6.60e-09171
ectoderm6.60e-09171
presumptive ectoderm6.60e-09171
multi-tissue structure1.13e-08342
embryo1.63e-08592
developing anatomical structure2.28e-08581
embryonic structure1.03e-07564
reproductive structure3.48e-0759
reproductive system3.48e-0759
germ layer3.58e-07560
germ layer / neural crest3.58e-07560
embryonic tissue3.58e-07560
presumptive structure3.58e-07560
germ layer / neural crest derived structure3.58e-07560
epiblast (generic)3.58e-07560
female organism5.14e-0741


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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