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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1971_spleen_Endothelial_heart_lung_adipose_mature_locus
|full_id=C1971_spleen_Endothelial_heart_lung_adipose_mature_locus
|id=C1971
|id=C1971

Revision as of 14:36, 12 September 2012


Full id: C1971_spleen_Endothelial_heart_lung_adipose_mature_locus



Phase1 CAGE Peaks

Hg19::chr6:151004729..151004751,+p7@PLEKHG1
Hg19::chr6:151004757..151004770,+p12@PLEKHG1
Hg19::chr6:151004774..151004794,+p4@PLEKHG1
Hg19::chr6:151004802..151004822,+p3@PLEKHG1
Hg19::chr6:151004835..151004845,+p15@PLEKHG1


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>

Uber Anatomy
Ontology termp-valuen
adult organism6.61e-72115
neural tube1.24e-3857
neural rod1.24e-3857
future spinal cord1.24e-3857
neural keel1.24e-3857
regional part of brain2.98e-3159
anterior neural tube4.38e-3142
regional part of forebrain2.74e-3041
forebrain2.74e-3041
future forebrain2.74e-3041
anatomical conduit1.73e-27241
brain2.18e-2769
future brain2.18e-2769
neural plate1.06e-2686
presumptive neural plate1.06e-2686
central nervous system2.69e-2682
gray matter9.20e-2634
brain grey matter9.20e-2634
tube3.29e-25194
telencephalon3.45e-2534
neurectoderm1.24e-2490
regional part of telencephalon1.96e-2433
cerebral hemisphere1.92e-2332
anatomical cluster3.20e-23286
regional part of nervous system3.33e-2294
nervous system3.33e-2294
regional part of cerebral cortex2.45e-2022
neocortex2.64e-1820
pre-chordal neural plate3.25e-1861
endothelium3.72e-1818
blood vessel endothelium3.72e-1818
cardiovascular system endothelium3.72e-1818
cerebral cortex4.86e-1725
pallium4.86e-1725
anterior region of body2.02e-14129
craniocervical region2.02e-14129
simple squamous epithelium1.15e-1322
head3.56e-13123
epithelium3.69e-13309
cell layer9.56e-13312
anatomical system9.67e-13625
anatomical group1.22e-12626
multi-cellular organism3.06e-12659
squamous epithelium2.81e-1125
ectoderm-derived structure6.64e-11169
nucleus of brain1.76e-109
neural nucleus1.76e-109
basal ganglion2.72e-109
nuclear complex of neuraxis2.72e-109
aggregate regional part of brain2.72e-109
collection of basal ganglia2.72e-109
cerebral subcortex2.72e-109
ectoderm3.13e-10173
presumptive ectoderm3.13e-10173
endothelial tube1.27e-099
arterial system endothelium1.27e-099
endothelium of artery1.27e-099
embryo3.77e-09612
brainstem4.00e-098
organ5.41e-09511
embryonic structure6.27e-09605
developing anatomical structure6.27e-09605
posterior neural tube1.03e-0815
chordal neural plate1.03e-0815
germ layer1.36e-08604
embryonic tissue1.36e-08604
presumptive structure1.36e-08604
epiblast (generic)1.36e-08604
temporal lobe1.46e-087
telencephalic nucleus2.53e-087
vessel2.59e-0869
organ part1.02e-07219
vein2.37e-079
venous blood vessel2.37e-079
venous system2.37e-079
segmental subdivision of nervous system5.88e-0713
gyrus6.12e-076


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
FOS#235358.99795530889441.69470025615156e-050.000389766130923173
GATA2#2624512.7449317335542.9719152914525e-060.000101366381817116
JUN#3725512.51282919233633.25800591331781e-060.000109268747456968
MAX#414956.452555509007128.93743970843928e-050.00130785661441739



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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