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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2091_Hepatic_spleen_Endothelial_lung_lymph_adipose_acute
|full_id=C2091_Hepatic_spleen_Endothelial_lung_lymph_adipose_acute
|id=C2091
|id=C2091

Revision as of 14:46, 12 September 2012


Full id: C2091_Hepatic_spleen_Endothelial_lung_lymph_adipose_acute



Phase1 CAGE Peaks

Hg19::chr11:10590118..10590129,-p5@LYVE1
Hg19::chr11:10590144..10590159,-p3@LYVE1
Hg19::chr11:10590173..10590191,-p1@LYVE1
Hg19::chr11:10590198..10590230,-p2@LYVE1


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 organism1.07e-58115
neural tube2.75e-2557
neural rod2.75e-2557
future spinal cord2.75e-2557
neural keel2.75e-2557
regional part of brain3.67e-2459
anatomical cluster2.60e-23286
anatomical conduit1.05e-22241
tube4.22e-21194
central nervous system1.32e-2082
brain2.35e-2069
future brain2.35e-2069
anterior neural tube4.24e-2042
regional part of forebrain2.91e-1941
forebrain2.91e-1941
future forebrain2.91e-1941
neural plate5.44e-1886
presumptive neural plate5.44e-1886
neurectoderm6.26e-1790
regional part of nervous system1.19e-1694
nervous system1.19e-1694
gray matter1.63e-1534
brain grey matter1.63e-1534
telencephalon1.66e-1534
regional part of telencephalon5.06e-1533
cerebral hemisphere2.21e-1432
cell layer3.00e-14312
epithelium1.82e-13309
regional part of cerebral cortex3.68e-1222
multi-cellular organism4.52e-12659
pre-chordal neural plate1.05e-1161
anterior region of body3.11e-11129
craniocervical region3.11e-11129
neocortex4.53e-1120
anatomical system6.94e-11625
anatomical group9.13e-11626
cerebral cortex9.34e-1125
pallium9.34e-1125
endothelium9.79e-1118
blood vessel endothelium9.79e-1118
cardiovascular system endothelium9.79e-1118
head3.07e-10123
embryo5.98e-09612
multi-tissue structure7.62e-09347
embryonic structure8.55e-09605
developing anatomical structure8.55e-09605
simple squamous epithelium1.05e-0822
squamous epithelium1.21e-0825
germ layer1.84e-08604
embryonic tissue1.84e-08604
presumptive structure1.84e-08604
epiblast (generic)1.84e-08604
ectoderm-derived structure1.13e-07169
organ1.32e-07511
ectoderm2.30e-07173
presumptive ectoderm2.30e-07173
tissue5.85e-07787


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#235348.99795530889440.0001525147711168630.00194534564981364
GATA2#2624412.7449317335543.78864877853583e-050.000719684775884874
JUN#3725412.51282919233634.07770316866756e-050.000741677536106707
JUND#372746.994663941871030.000417684217818580.00390952877081508
MAFF#23764456.31535648994529.92458849374232e-085.83294371242518e-06
MAFK#7975427.10073313782991.85228494563408e-066.84297090332784e-05
SPI1#668848.204323508522730.000220661881527680.00249008171203343



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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