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Coexpression cluster:C2867: Difference between revisions

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|tf_chipseq_enrich=SRF#6722;3:10.3478836966259:0.00143989377840126:0.00924284365841729!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.0049979916345306!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279945762229799
|tf_chipseq_enrich=SRF#6722;3:10.3478836966259:0.00143989377840126:0.00924284365841729!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.0049979916345306!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279945762229799
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}}
}}

Revision as of 15:46, 26 November 2012


Full id: C2867_neuroectodermal_CD19_smooth_carcinoid_cerebellum_umbilical_appendix



Phase1 CAGE Peaks

Hg19::chr6:70576369..70576372,+p9@COL19A1
Hg19::chr6:70576438..70576454,+p1@COL19A1
Hg19::chr6:70576457..70576468,+p2@COL19A1
Hg19::chr6:70917090..70917094,+p@chr6:70917090..70917094
+


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
lymphocyte of B lineage5.08e-1724
pro-B cell5.08e-1724
B cell1.09e-1414
circulating cell9.09e-076
Uber Anatomy
Ontology termp-valuen
adult organism3.78e-45114
neural tube9.93e-2656
neural rod9.93e-2656
future spinal cord9.93e-2656
neural keel9.93e-2656
regional part of nervous system3.49e-2553
regional part of brain3.49e-2553
brain grey matter2.47e-2334
gray matter2.47e-2334
cerebral hemisphere1.21e-2232
regional part of forebrain2.98e-2241
forebrain2.98e-2241
anterior neural tube2.98e-2241
future forebrain2.98e-2241
central nervous system3.21e-2281
regional part of telencephalon4.62e-2232
telencephalon5.64e-2234
brain2.81e-2168
future brain2.81e-2168
regional part of cerebral cortex9.92e-2122
nervous system3.68e-2089
neocortex4.87e-1920
neurectoderm1.27e-1786
cerebral cortex2.41e-1725
pallium2.41e-1725
neural plate5.33e-1782
presumptive neural plate5.33e-1782
pre-chordal neural plate7.43e-1361
organ system subdivision9.96e-12223
ecto-epithelium1.98e-11104
ectoderm-derived structure7.07e-11171
ectoderm7.07e-11171
presumptive ectoderm7.07e-11171
blood2.87e-1015
haemolymphatic fluid2.87e-1015
organism substance2.87e-1015
structure with developmental contribution from neural crest3.49e-09132
basal ganglion5.60e-089
nuclear complex of neuraxis5.60e-089
aggregate regional part of brain5.60e-089
collection of basal ganglia5.60e-089
cerebral subcortex5.60e-089
temporal lobe1.76e-076
neural nucleus1.94e-079
nucleus of brain1.94e-079


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
SRF#6722310.34788369662590.001439893778401260.00924284365841729
TRIM28#10155313.94289378394690.0005972858184258420.0049979916345306
ZNF263#1012736.166381227758010.006539814347975980.0279945762229799



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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