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Coexpression cluster:C3536: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!7.75e-24!114;UBERON:0011216!2.28e-23!223;UBERON:0002346!3.77e-22!86;UBERON:0003075!3.23e-21!82;UBERON:0007284!3.23e-21!82;UBERON:0000477!1.01e-19!373;UBERON:0001049!1.35e-19!56;UBERON:0005068!1.35e-19!56;UBERON:0006241!1.35e-19!56;UBERON:0007135!1.35e-19!56;UBERON:0000481!5.09e-19!342;UBERON:0000073!5.39e-19!53;UBERON:0002616!5.39e-19!53;UBERON:0003056!2.16e-17!61;UBERON:0001017!2.28e-17!81;UBERON:0001016!6.14e-17!89;UBERON:0002780!8.80e-16!41;UBERON:0001890!8.80e-16!41;UBERON:0003080!8.80e-16!41;UBERON:0006240!8.80e-16!41;UBERON:0010371!2.63e-15!104;UBERON:0000955!5.13e-15!68;UBERON:0006238!5.13e-15!68;UBERON:0001893!1.50e-13!34;UBERON:0003528!3.03e-13!34;UBERON:0002020!3.03e-13!34;UBERON:0000062!4.28e-13!503;UBERON:0010314!7.47e-13!132;UBERON:0002791!9.13e-13!32;UBERON:0004121!9.95e-13!171;UBERON:0000924!9.95e-13!171;UBERON:0006601!9.95e-13!171;UBERON:0001869!1.07e-12!32;UBERON:0000064!1.70e-12!218;UBERON:0000119!4.89e-12!309;UBERON:0000483!1.09e-11!306;UBERON:0000922!1.34e-11!592;UBERON:0000468!1.75e-11!656;UBERON:0005423!1.50e-10!581;UBERON:0000025!2.68e-10!192;UBERON:0000956!1.02e-09!25;UBERON:0000203!1.02e-09!25;UBERON:0004111!1.47e-09!240;UBERON:0002619!4.10e-09!22;UBERON:0000467!7.63e-09!624;UBERON:0000480!1.17e-08!625;UBERON:0004921!1.84e-08!118;UBERON:0000923!2.77e-08!560;UBERON:0010316!2.77e-08!560;UBERON:0005291!2.77e-08!560;UBERON:0006598!2.77e-08!560;UBERON:0010317!2.77e-08!560;UBERON:0002532!2.77e-08!560;UBERON:0001950!3.79e-08!20;UBERON:0002050!4.10e-08!564;UBERON:0001007!9.40e-08!145;UBERON:0001555!9.40e-08!145;UBERON:0007026!9.40e-08!145;UBERON:0000063!2.25e-07!98;UBERON:0001048!7.44e-07!160
|ontology_enrichment_uberon=UBERON:0007023!7.75e-24!114;UBERON:0011216!2.28e-23!223;UBERON:0002346!3.77e-22!86;UBERON:0003075!3.23e-21!82;UBERON:0007284!3.23e-21!82;UBERON:0000477!1.01e-19!373;UBERON:0001049!1.35e-19!56;UBERON:0005068!1.35e-19!56;UBERON:0006241!1.35e-19!56;UBERON:0007135!1.35e-19!56;UBERON:0000481!5.09e-19!342;UBERON:0000073!5.39e-19!53;UBERON:0002616!5.39e-19!53;UBERON:0003056!2.16e-17!61;UBERON:0001017!2.28e-17!81;UBERON:0001016!6.14e-17!89;UBERON:0002780!8.80e-16!41;UBERON:0001890!8.80e-16!41;UBERON:0003080!8.80e-16!41;UBERON:0006240!8.80e-16!41;UBERON:0010371!2.63e-15!104;UBERON:0000955!5.13e-15!68;UBERON:0006238!5.13e-15!68;UBERON:0001893!1.50e-13!34;UBERON:0003528!3.03e-13!34;UBERON:0002020!3.03e-13!34;UBERON:0000062!4.28e-13!503;UBERON:0010314!7.47e-13!132;UBERON:0002791!9.13e-13!32;UBERON:0004121!9.95e-13!171;UBERON:0000924!9.95e-13!171;UBERON:0006601!9.95e-13!171;UBERON:0001869!1.07e-12!32;UBERON:0000064!1.70e-12!218;UBERON:0000119!4.89e-12!309;UBERON:0000483!1.09e-11!306;UBERON:0000922!1.34e-11!592;UBERON:0000468!1.75e-11!656;UBERON:0005423!1.50e-10!581;UBERON:0000025!2.68e-10!192;UBERON:0000956!1.02e-09!25;UBERON:0000203!1.02e-09!25;UBERON:0004111!1.47e-09!240;UBERON:0002619!4.10e-09!22;UBERON:0000467!7.63e-09!624;UBERON:0000480!1.17e-08!625;UBERON:0004921!1.84e-08!118;UBERON:0000923!2.77e-08!560;UBERON:0010316!2.77e-08!560;UBERON:0005291!2.77e-08!560;UBERON:0006598!2.77e-08!560;UBERON:0010317!2.77e-08!560;UBERON:0002532!2.77e-08!560;UBERON:0001950!3.79e-08!20;UBERON:0002050!4.10e-08!564;UBERON:0001007!9.40e-08!145;UBERON:0001555!9.40e-08!145;UBERON:0007026!9.40e-08!145;UBERON:0000063!2.25e-07!98;UBERON:0001048!7.44e-07!160
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}}
}}

Revision as of 16:11, 26 November 2012


Full id: C3536_hepatocellular_pancreas_Intestinal_skeletal_colon_Hepatocyte_gastric



Phase1 CAGE Peaks

Hg19::chr16:15489603..15489627,+p1@MPV17L
Hg19::chr16:15489629..15489644,+p3@MPV17L
Hg19::chr16:15502477..15502483,+p@chr16:15502477..15502483
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism7.75e-24114
organ system subdivision2.28e-23223
neurectoderm3.77e-2286
neural plate3.23e-2182
presumptive neural plate3.23e-2182
anatomical cluster1.01e-19373
neural tube1.35e-1956
neural rod1.35e-1956
future spinal cord1.35e-1956
neural keel1.35e-1956
multi-tissue structure5.09e-19342
regional part of nervous system5.39e-1953
regional part of brain5.39e-1953
pre-chordal neural plate2.16e-1761
central nervous system2.28e-1781
nervous system6.14e-1789
regional part of forebrain8.80e-1641
forebrain8.80e-1641
anterior neural tube8.80e-1641
future forebrain8.80e-1641
ecto-epithelium2.63e-15104
brain5.13e-1568
future brain5.13e-1568
telencephalon1.50e-1334
brain grey matter3.03e-1334
gray matter3.03e-1334
organ4.28e-13503
structure with developmental contribution from neural crest7.47e-13132
regional part of telencephalon9.13e-1332
ectoderm-derived structure9.95e-13171
ectoderm9.95e-13171
presumptive ectoderm9.95e-13171
cerebral hemisphere1.07e-1232
organ part1.70e-12218
cell layer4.89e-12309
epithelium1.09e-11306
embryo1.34e-11592
multi-cellular organism1.75e-11656
developing anatomical structure1.50e-10581
tube2.68e-10192
cerebral cortex1.02e-0925
pallium1.02e-0925
anatomical conduit1.47e-09240
regional part of cerebral cortex4.10e-0922
anatomical system7.63e-09624
anatomical group1.17e-08625
subdivision of digestive tract1.84e-08118
germ layer2.77e-08560
germ layer / neural crest2.77e-08560
embryonic tissue2.77e-08560
presumptive structure2.77e-08560
germ layer / neural crest derived structure2.77e-08560
epiblast (generic)2.77e-08560
neocortex3.79e-0820
embryonic structure4.10e-08564
digestive system9.40e-08145
digestive tract9.40e-08145
primitive gut9.40e-08145
organ segment2.25e-0798
primordium7.44e-07160


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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