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Coexpression cluster:C3720: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279294494542274!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436815661130766!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.017971858106138!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066379447490902!RXRA#6256;2:13.3830780927555:0.00719643442946573:0.0298284881287047
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279294494542274!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436815661130766!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.017971858106138!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066379447490902!RXRA#6256;2:13.3830780927555:0.00719643442946573:0.0298284881287047
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}}
}}

Revision as of 16:18, 26 November 2012


Full id: C3720_Neural_duodenum_parietal_dura_Small_Astrocyte_temporal



Phase1 CAGE Peaks

Hg19::chr18:42260840..42260860,+p2@SETBP1
Hg19::chr18:42260861..42260882,+p5@SETBP1
Hg19::chr18:42260920..42260951,+p4@SETBP1


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 lineage9.56e-0924
pro-B cell9.56e-0924
B cell1.42e-0814
Uber Anatomy
Ontology termp-valuen
adult organism1.37e-31114
central nervous system6.05e-2081
nervous system7.23e-2089
ectoderm-derived structure2.66e-18171
ectoderm2.66e-18171
presumptive ectoderm2.66e-18171
neural tube2.83e-1756
neural rod2.83e-1756
future spinal cord2.83e-1756
neural keel2.83e-1756
ecto-epithelium1.88e-16104
brain2.62e-1668
future brain2.62e-1668
regional part of nervous system3.32e-1653
regional part of brain3.32e-1653
neural plate8.30e-1582
presumptive neural plate8.30e-1582
organ system subdivision2.05e-13223
neurectoderm4.12e-1386
regional part of forebrain8.04e-1341
forebrain8.04e-1341
anterior neural tube8.04e-1341
future forebrain8.04e-1341
telencephalon4.15e-1234
brain grey matter7.08e-1234
gray matter7.08e-1234
cerebral cortex7.54e-1225
pallium7.54e-1225
cerebral hemisphere1.45e-1132
regional part of telencephalon2.39e-1132
structure with developmental contribution from neural crest6.84e-11132
neocortex3.58e-1020
pre-chordal neural plate4.60e-1061
regional part of cerebral cortex1.14e-0922


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
CTCF#1066435.360256373075030.0064925092527670.0279294494542274
GATA2#2624312.7449317335540.0004829527704283790.00436815661130766
HNF4G#3174219.16894835096450.003543986611284220.017971858106138
RAD21#5885310.35503389545630.0009004912073565420.0066379447490902
RXRA#6256213.38307809275550.007196434429465730.0298284881287047



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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