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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C718_epididymis_seminal_uterus_cervix_ductus_peripheral_colon
|full_id=C718_epididymis_seminal_uterus_cervix_ductus_peripheral_colon
|id=C718
|id=C718

Revision as of 18:24, 12 September 2012


Full id: C718_epididymis_seminal_uterus_cervix_ductus_peripheral_colon



Phase1 CAGE Peaks

Hg19::chr10:119301969..119301989,-p3@EMX2OS
Hg19::chr10:119301997..119302022,-p5@EMX2OS
Hg19::chr10:119302025..119302049,-p4@EMX2OS
Hg19::chr10:119302051..119302077,-p8@EMX2OS
Hg19::chr10:119302093..119302108,-p6@EMX2OS
Hg19::chr10:119302150..119302163,+p8@EMX2
Hg19::chr10:119302182..119302196,+p6@EMX2
Hg19::chr10:119302232..119302265,+p1@EMX2
Hg19::chr10:119302268..119302282,+p4@EMX2
Hg19::chr10:119302508..119302559,+p5@EMX2
Hg19::chr10:119307702..119307723,+p10@EMX2


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
skin fibroblast3.02e-0923
fat cell6.26e-0715
Uber Anatomy
Ontology termp-valuen
adult organism1.45e-30115
neural tube1.45e-2957
neural rod1.45e-2957
future spinal cord1.45e-2957
neural keel1.45e-2957
central nervous system1.94e-2982
regional part of brain1.95e-2859
regional part of nervous system4.92e-2894
nervous system4.92e-2894
anterior neural tube6.43e-2842
regional part of forebrain2.31e-2741
forebrain2.31e-2741
future forebrain2.31e-2741
brain2.43e-2669
future brain2.43e-2669
neurectoderm2.14e-2590
neural plate3.64e-2586
presumptive neural plate3.64e-2586
telencephalon2.21e-2434
gray matter4.72e-2434
brain grey matter4.72e-2434
regional part of telencephalon1.02e-2333
cerebral hemisphere2.66e-2332
pre-chordal neural plate7.09e-2361
ectoderm1.41e-20173
presumptive ectoderm1.41e-20173
ectoderm-derived structure4.10e-20169
organism subdivision4.79e-19365
cerebral cortex1.20e-1825
pallium1.20e-1825
regional part of cerebral cortex1.04e-1622
head1.75e-16123
anterior region of body2.24e-16129
craniocervical region2.24e-16129
neocortex3.74e-1520
integument8.07e-1245
integumental system8.07e-1245
skin of body6.17e-1040
multi-cellular organism2.61e-09659
organ part5.20e-09219
cell layer4.44e-08312
organ5.54e-08511
epithelium9.22e-08309
basal ganglion2.42e-079
nuclear complex of neuraxis2.42e-079
aggregate regional part of brain2.42e-079
collection of basal ganglia2.42e-079
cerebral subcortex2.42e-079
nucleus of brain7.45e-079
neural nucleus7.45e-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
CTBP2#14881057.01545485393471.13419318602184e-172.43232037279128e-15
EGR1#1958104.534708268009229.42307184802989e-074.03334508498522e-05
JUND#372795.722906861530841.04100398324849e-064.34364422718693e-05
NANOG#799231026.5861622554662.31327859661626e-143.88418815678466e-12
POLR2A#5430101.952230160507340.00304073181841430.0161318190787042
SP1#6667105.180346707400822.55812246304286e-071.32853183449892e-05
SUZ12#235121045.5598008282391.06787563003087e-162.14889909296327e-14
TCF12#693898.700925829061622.64468895283201e-081.82436373543476e-06
YY1#752894.018230613516792.20696821385449e-050.00048382357952718
ZNF263#10127107.474401488191526.91943485229632e-095.39700415637771e-07



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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