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Coexpression cluster:C4526: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000955!1.02e-16!68;UBERON:0006238!1.02e-16!68;UBERON:0001017!3.21e-16!81;UBERON:0010314!4.17e-16!132;UBERON:0002346!1.86e-15!86;UBERON:0001016!2.25e-15!89;UBERON:0003075!3.04e-15!82;UBERON:0007284!3.04e-15!82;UBERON:0000481!1.01e-14!342;UBERON:0001049!1.18e-13!56;UBERON:0005068!1.18e-13!56;UBERON:0006241!1.18e-13!56;UBERON:0007135!1.18e-13!56;UBERON:0007023!2.63e-13!114;UBERON:0000477!4.68e-13!373;UBERON:0000025!1.07e-12!192;UBERON:0000073!1.39e-12!53;UBERON:0002616!1.39e-12!53;UBERON:0001893!8.44e-12!34;UBERON:0003528!1.48e-11!34;UBERON:0002020!1.48e-11!34;UBERON:0001869!4.75e-11!32;UBERON:0002791!8.21e-11!32;UBERON:0002780!1.69e-10!41;UBERON:0001890!1.69e-10!41;UBERON:0003080!1.69e-10!41;UBERON:0006240!1.69e-10!41;UBERON:0004121!2.23e-10!171;UBERON:0000924!2.23e-10!171;UBERON:0006601!2.23e-10!171;UBERON:0010371!3.35e-10!104;UBERON:0003056!5.25e-10!61;UBERON:0000468!7.81e-09!656;UBERON:0000119!9.10e-09!309;UBERON:0004111!1.60e-08!240;UBERON:0000483!2.37e-08!306;UBERON:0002619!2.42e-08!22;UBERON:0000956!4.29e-08!25;UBERON:0000203!4.29e-08!25;UBERON:0011216!6.52e-08!223;UBERON:0001950!1.64e-07!20
|ontology_enrichment_uberon=UBERON:0000955!1.02e-16!68;UBERON:0006238!1.02e-16!68;UBERON:0001017!3.21e-16!81;UBERON:0010314!4.17e-16!132;UBERON:0002346!1.86e-15!86;UBERON:0001016!2.25e-15!89;UBERON:0003075!3.04e-15!82;UBERON:0007284!3.04e-15!82;UBERON:0000481!1.01e-14!342;UBERON:0001049!1.18e-13!56;UBERON:0005068!1.18e-13!56;UBERON:0006241!1.18e-13!56;UBERON:0007135!1.18e-13!56;UBERON:0007023!2.63e-13!114;UBERON:0000477!4.68e-13!373;UBERON:0000025!1.07e-12!192;UBERON:0000073!1.39e-12!53;UBERON:0002616!1.39e-12!53;UBERON:0001893!8.44e-12!34;UBERON:0003528!1.48e-11!34;UBERON:0002020!1.48e-11!34;UBERON:0001869!4.75e-11!32;UBERON:0002791!8.21e-11!32;UBERON:0002780!1.69e-10!41;UBERON:0001890!1.69e-10!41;UBERON:0003080!1.69e-10!41;UBERON:0006240!1.69e-10!41;UBERON:0004121!2.23e-10!171;UBERON:0000924!2.23e-10!171;UBERON:0006601!2.23e-10!171;UBERON:0010371!3.35e-10!104;UBERON:0003056!5.25e-10!61;UBERON:0000468!7.81e-09!656;UBERON:0000119!9.10e-09!309;UBERON:0004111!1.60e-08!240;UBERON:0000483!2.37e-08!306;UBERON:0002619!2.42e-08!22;UBERON:0000956!4.29e-08!25;UBERON:0000203!4.29e-08!25;UBERON:0011216!6.52e-08!223;UBERON:0001950!1.64e-07!20
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}}
}}

Revision as of 16:47, 26 November 2012


Full id: C4526_Lens_Smooth_mesenchymal_Ewing_Chondrocyte_Fibroblast_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr5:83680363..83680372,-p9@EDIL3
Hg19::chr5:83680417..83680428,-p7@EDIL3
Hg19::chr5:83680445..83680454,-p8@EDIL3


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
non-terminally differentiated cell1.47e-09106
fibroblast1.43e-0876
vascular associated smooth muscle cell6.61e-0832
Uber Anatomy
Ontology termp-valuen
brain1.02e-1668
future brain1.02e-1668
central nervous system3.21e-1681
structure with developmental contribution from neural crest4.17e-16132
neurectoderm1.86e-1586
nervous system2.25e-1589
neural plate3.04e-1582
presumptive neural plate3.04e-1582
multi-tissue structure1.01e-14342
neural tube1.18e-1356
neural rod1.18e-1356
future spinal cord1.18e-1356
neural keel1.18e-1356
adult organism2.63e-13114
anatomical cluster4.68e-13373
tube1.07e-12192
regional part of nervous system1.39e-1253
regional part of brain1.39e-1253
telencephalon8.44e-1234
brain grey matter1.48e-1134
gray matter1.48e-1134
cerebral hemisphere4.75e-1132
regional part of telencephalon8.21e-1132
regional part of forebrain1.69e-1041
forebrain1.69e-1041
anterior neural tube1.69e-1041
future forebrain1.69e-1041
ectoderm-derived structure2.23e-10171
ectoderm2.23e-10171
presumptive ectoderm2.23e-10171
ecto-epithelium3.35e-10104
pre-chordal neural plate5.25e-1061
multi-cellular organism7.81e-09656
cell layer9.10e-09309
anatomical conduit1.60e-08240
epithelium2.37e-08306
regional part of cerebral cortex2.42e-0822
cerebral cortex4.29e-0825
pallium4.29e-0825
organ system subdivision6.52e-08223
neocortex1.64e-0720


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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