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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4701_Mast_optic_mature_small_substantia_adrenal_serous
|full_id=C4701_Mast_optic_mature_small_substantia_adrenal_serous
|id=C4701
|id=C4701

Revision as of 17:49, 12 September 2012


Full id: C4701_Mast_optic_mature_small_substantia_adrenal_serous



Phase1 CAGE Peaks

Hg19::chr7:79764112..79764209,+p1@GNAI1
Hg19::chr7:79764242..79764256,+p3@GNAI1
Hg19::chr7:79764393..79764437,+p2@GNAI1


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
regional part of nervous system1.81e-2494
nervous system1.81e-2494
central nervous system1.05e-2382
neural tube7.51e-2357
neural rod7.51e-2357
future spinal cord7.51e-2357
neural keel7.51e-2357
ectoderm-derived structure9.36e-23169
head3.48e-22123
ectoderm8.54e-22173
presumptive ectoderm8.54e-22173
regional part of brain3.53e-2159
brain1.62e-2069
future brain1.62e-2069
organism subdivision1.94e-20365
anterior region of body9.94e-20129
craniocervical region9.94e-20129
neural plate4.78e-1986
presumptive neural plate4.78e-1986
anterior neural tube5.04e-1842
neurectoderm1.15e-1790
regional part of forebrain1.52e-1741
forebrain1.52e-1741
future forebrain1.52e-1741
telencephalon3.21e-1734
gray matter3.40e-1734
brain grey matter3.40e-1734
regional part of telencephalon1.38e-1633
multi-cellular organism4.26e-16659
cerebral hemisphere6.64e-1632
pre-chordal neural plate2.99e-1561
anatomical system1.26e-14625
organ2.06e-14511
anatomical group2.88e-14626
organ part3.17e-14219
regional part of cerebral cortex2.06e-1322
adult organism3.07e-13115
multi-tissue structure2.43e-12347
neocortex2.45e-1220
cerebral cortex4.27e-1225
pallium4.27e-1225
anatomical cluster1.49e-10286
epithelium3.34e-10309
cell layer4.47e-10312
embryo2.08e-09612
embryonic structure3.29e-09605
developing anatomical structure3.29e-09605
anatomical conduit3.34e-09241
germ layer5.76e-09604
embryonic tissue5.76e-09604
presumptive structure5.76e-09604
epiblast (generic)5.76e-09604


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285853597184222
CTBP2#1488241.81133355955210.0007543408259914850.00593644800887082
CTCF#1066435.360256373075030.0064925092527670.0281322314172399
E2F1#186934.907389214879320.008460985347239390.0327741580253814
NR3C1#290829.982015554115360.01278474365547170.0460819962945232
SMARCB1#6598212.16847718743830.008675002221921740.0330141951337421
SMC3#9126210.02995522995520.0126656379767470.0457822505331215
TFAP2A#7020211.01242291536330.01054990655215560.0390357007865295
USF1#739136.361499277207960.00388404057290560.0191197828711203



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.