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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3574_Mesenchymal_mature_breast_skeletal_medulla_heart_hippocampus
|full_id=C3574_Mesenchymal_mature_breast_skeletal_medulla_heart_hippocampus
|id=C3574
|id=C3574

Revision as of 16:31, 12 September 2012


Full id: C3574_Mesenchymal_mature_breast_skeletal_medulla_heart_hippocampus



Phase1 CAGE Peaks

Hg19::chr16:56666424..56666452,+p6@MT1M
Hg19::chr16:56666456..56666477,+p4@MT1M
Hg19::chr8:48572027..48572044,-p@chr8:48572027..48572044
-


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
fat cell3.49e-1015
Uber Anatomy
Ontology termp-valuen
adult organism4.43e-40115
organism subdivision1.56e-24365
neural tube1.09e-2357
neural rod1.09e-2357
future spinal cord1.09e-2357
neural keel1.09e-2357
neural plate6.36e-2186
presumptive neural plate6.36e-2186
anatomical conduit1.69e-20241
anatomical cluster5.88e-20286
regional part of brain4.36e-1959
neurectoderm1.11e-1890
multi-tissue structure1.66e-18347
tube1.03e-17194
epithelium1.41e-17309
cell layer1.59e-17312
anterior neural tube2.98e-1642
regional part of forebrain1.58e-1541
forebrain1.58e-1541
future forebrain1.58e-1541
brain4.04e-1569
future brain4.04e-1569
head7.01e-15123
anatomical system7.11e-15625
multi-cellular organism7.74e-15659
anatomical group1.09e-14626
anterior region of body1.99e-14129
craniocervical region1.99e-14129
central nervous system4.70e-1482
gray matter1.22e-1334
brain grey matter1.22e-1334
regional part of nervous system3.05e-1394
nervous system3.05e-1394
telencephalon5.20e-1334
pre-chordal neural plate5.79e-1361
regional part of telencephalon1.10e-1233
organ part2.56e-12219
cerebral hemisphere5.27e-1232
tissue2.22e-10787
ectoderm-derived structure3.02e-10169
organ3.84e-10511
germ layer2.05e-09604
embryonic tissue2.05e-09604
presumptive structure2.05e-09604
epiblast (generic)2.05e-09604
ectoderm2.52e-09173
presumptive ectoderm2.52e-09173
regional part of cerebral cortex2.87e-0922
embryonic structure2.88e-09605
developing anatomical structure2.88e-09605
embryo5.76e-09612
posterior neural tube9.09e-0915
chordal neural plate9.09e-0915
cerebral cortex2.36e-0825
pallium2.36e-0825
neocortex4.40e-0820
trunk6.22e-08216
segmental subdivision of nervous system8.87e-0813
adipose tissue1.11e-0714
trunk mesenchyme2.15e-07143
nucleus of brain2.45e-079
neural nucleus2.45e-079
basal ganglion3.24e-079
nuclear complex of neuraxis3.24e-079
aggregate regional part of brain3.24e-079
collection of basal ganglia3.24e-079
cerebral subcortex3.24e-079
segmental subdivision of hindbrain4.30e-0712
hindbrain4.30e-0712
presumptive hindbrain4.30e-0712
brainstem9.12e-078


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
GATA2#2624312.7449317335540.0004829527704283790.00436664396076266
SUZ12#23512233.41052060737530.00117826764536030.00799695182049545



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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