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Coexpression cluster:C4644: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007625!1.20e-13!11;UBERON:0001009!9.84e-10!113;UBERON:0000970!1.96e-09!20;UBERON:0004535!5.83e-09!110;UBERON:0002104!8.04e-09!21;UBERON:0000019!2.24e-08!19;UBERON:0000047!2.24e-08!19;UBERON:0004088!2.24e-08!19;UBERON:0003072!2.24e-08!19;UBERON:0003071!2.24e-08!19;UBERON:0004128!2.24e-08!19;UBERON:0007100!2.26e-08!27;UBERON:0000020!9.21e-08!23;UBERON:0000483!1.31e-07!309;UBERON:0003075!1.40e-07!86;UBERON:0007284!1.40e-07!86;UBERON:0002346!1.42e-07!90;UBERON:0002049!1.80e-07!79;UBERON:0007798!1.80e-07!79;UBERON:0000488!2.11e-07!4;UBERON:0000948!2.22e-07!24;UBERON:0005498!2.22e-07!24;UBERON:0004140!2.22e-07!24;UBERON:0009881!2.22e-07!24;UBERON:0004141!2.22e-07!24;UBERON:0003084!2.22e-07!24;UBERON:0007005!2.22e-07!24;UBERON:0004139!2.22e-07!24;UBERON:0004291!2.22e-07!24;UBERON:0000119!2.30e-07!312;UBERON:0001032!2.65e-07!24;UBERON:0004456!2.65e-07!24;UBERON:0001456!2.70e-07!21;UBERON:0001473!5.51e-07!8;UBERON:0004536!5.51e-07!8;UBERON:0006558!5.51e-07!8;UBERON:0000415!7.08e-07!4;UBERON:0007240!7.08e-07!4;UBERON:0005742!7.08e-07!4;UBERON:0005734!7.08e-07!4;UBERON:0004664!7.08e-07!4;UBERON:0004663!7.08e-07!4;UBERON:0002465!7.23e-07!10
|ontology_enrichment_uberon=UBERON:0007625!1.20e-13!11;UBERON:0001009!9.84e-10!113;UBERON:0000970!1.96e-09!20;UBERON:0004535!5.83e-09!110;UBERON:0002104!8.04e-09!21;UBERON:0000019!2.24e-08!19;UBERON:0000047!2.24e-08!19;UBERON:0004088!2.24e-08!19;UBERON:0003072!2.24e-08!19;UBERON:0003071!2.24e-08!19;UBERON:0004128!2.24e-08!19;UBERON:0007100!2.26e-08!27;UBERON:0000020!9.21e-08!23;UBERON:0000483!1.31e-07!309;UBERON:0003075!1.40e-07!86;UBERON:0007284!1.40e-07!86;UBERON:0002346!1.42e-07!90;UBERON:0002049!1.80e-07!79;UBERON:0007798!1.80e-07!79;UBERON:0000488!2.11e-07!4;UBERON:0000948!2.22e-07!24;UBERON:0005498!2.22e-07!24;UBERON:0004140!2.22e-07!24;UBERON:0009881!2.22e-07!24;UBERON:0004141!2.22e-07!24;UBERON:0003084!2.22e-07!24;UBERON:0007005!2.22e-07!24;UBERON:0004139!2.22e-07!24;UBERON:0004291!2.22e-07!24;UBERON:0000119!2.30e-07!312;UBERON:0001032!2.65e-07!24;UBERON:0004456!2.65e-07!24;UBERON:0001456!2.70e-07!21;UBERON:0001473!5.51e-07!8;UBERON:0004536!5.51e-07!8;UBERON:0006558!5.51e-07!8;UBERON:0000415!7.08e-07!4;UBERON:0007240!7.08e-07!4;UBERON:0005742!7.08e-07!4;UBERON:0005734!7.08e-07!4;UBERON:0004664!7.08e-07!4;UBERON:0004663!7.08e-07!4;UBERON:0002465!7.23e-07!10
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168396462608561
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}}
}}

Revision as of 14:16, 5 September 2012


Full id: C4644_melanoma_Ciliary_Astrocyte_adrenal_retina_Neural_Lens



Phase1 CAGE Peaks

Hg19::chr7:111032908..111032929,-p5@IMMP2L
Hg19::chr7:111032939..111032959,-p3@IMMP2L
Hg19::chr7:111032974..111032986,-p9@IMMP2L


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
pigment epithelium of eye1.20e-1311
circulatory system9.84e-10113
eye1.96e-0920
cardiovascular system5.83e-09110
visual system8.04e-0921
camera-type eye2.24e-0819
simple eye2.24e-0819
ocular region2.24e-0819
optic cup2.24e-0819
eye primordium2.24e-0819
optic vesicle2.24e-0819
primary circulatory organ2.26e-0827
sense organ9.21e-0823
epithelium1.31e-07309
neural plate1.40e-0786
presumptive neural plate1.40e-0786
neurectoderm1.42e-0790
vasculature1.80e-0779
vascular system1.80e-0779
atypical epithelium2.11e-074
heart2.22e-0724
primitive heart tube2.22e-0724
primary heart field2.22e-0724
anterior lateral plate mesoderm2.22e-0724
heart tube2.22e-0724
heart primordium2.22e-0724
cardiac mesoderm2.22e-0724
cardiogenic plate2.22e-0724
heart rudiment2.22e-0724
cell layer2.30e-07312
sensory system2.65e-0724
entire sense organ system2.65e-0724
face2.70e-0721
lymphatic vessel5.51e-078
lymph vasculature5.51e-078
lymphatic part of lymphoid system5.51e-078
artery wall7.08e-074
tunica adventitia of artery7.08e-074
adventitia7.08e-074
tunica adventitia of blood vessel7.08e-074
aorta tunica adventitia7.08e-074
aorta wall7.08e-074
lymphoid system7.23e-0710


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
EP300#203336.77394172622320.003216880500103790.0168396462608561



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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