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Coexpression cluster:C1799: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;5:4.90738921487932:0.000351281809925646:0.0035279854742595!E2F6#1876;4:4.01372458535791:0.00663211823393388:0.0282969113585187!REST#5978;3:5.79001722967681:0.00946878869443394:0.0357007517132847!TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.000199808392253478
|tf_chipseq_enrich=E2F1#1869;5:4.90738921487932:0.000351281809925646:0.0035279854742595!E2F6#1876;4:4.01372458535791:0.00663211823393388:0.0282969113585187!REST#5978;3:5.79001722967681:0.00946878869443394:0.0357007517132847!TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.000199808392253478
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}}
}}

Revision as of 15:07, 26 November 2012


Full id: C1799_occipital_duodenum_temporal_Wilms_brain_pineal_parietal



Phase1 CAGE Peaks

Hg19::chr18:43913919..43913967,+p2@RNF165
Hg19::chr18:43913973..43914005,+p1@RNF165
Hg19::chr18:43914019..43914036,+p4@RNF165
Hg19::chr18:43914051..43914066,+p5@RNF165
Hg19::chr18:43914159..43914222,+p3@RNF165


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
nervous system1.29e-3489
central nervous system4.53e-3481
regional part of nervous system4.51e-3153
regional part of brain4.51e-3153
brain6.03e-3068
future brain6.03e-3068
neural tube7.20e-3056
neural rod7.20e-3056
future spinal cord7.20e-3056
neural keel7.20e-3056
regional part of forebrain2.91e-2741
forebrain2.91e-2741
anterior neural tube2.91e-2741
future forebrain2.91e-2741
adult organism4.98e-27114
organ system subdivision1.65e-26223
telencephalon6.71e-2434
neural plate8.42e-2482
presumptive neural plate8.42e-2482
neurectoderm1.73e-2386
brain grey matter2.13e-2334
gray matter2.13e-2334
cerebral hemisphere2.19e-2332
regional part of telencephalon1.40e-2232
ectoderm-derived structure4.49e-21171
ectoderm4.49e-21171
presumptive ectoderm4.49e-21171
pre-chordal neural plate1.20e-1961
cerebral cortex9.26e-1925
pallium9.26e-1925
ecto-epithelium1.39e-18104
regional part of cerebral cortex1.84e-1822
neocortex6.34e-1720
structure with developmental contribution from neural crest4.15e-13132
anatomical cluster8.69e-11373
organ part2.25e-10218
multi-tissue structure6.14e-08342
embryo2.17e-07592
basal ganglion9.11e-079
nuclear complex of neuraxis9.11e-079
aggregate regional part of brain9.11e-079
collection of basal ganglia9.11e-079
cerebral subcortex9.11e-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
E2F1#186954.907389214879320.0003512818099256460.0035279854742595
E2F6#187644.013724585357910.006632118233933880.0282969113585187
REST#597835.790017229676810.009468788694433940.0357007517132847
TCF7L2#6934510.77017656313736.89693748574565e-060.000199808392253478



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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