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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3114_ductus_CD14_Monocytederived_pituitary_seminal_Macrophage_small
|full_id=C3114_ductus_CD14_Monocytederived_pituitary_seminal_Macrophage_small
|id=C3114
|id=C3114

Revision as of 15:59, 12 September 2012


Full id: C3114_ductus_CD14_Monocytederived_pituitary_seminal_Macrophage_small



Phase1 CAGE Peaks

Hg19::chr11:128761220..128761257,+p1@KCNJ5
Hg19::chr11:128761363..128761382,+p2@KCNJ5
Hg19::chr11:128761387..128761409,+p3@KCNJ5


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
respiratory epithelial cell4.33e-0813
Uber Anatomy
Ontology termp-valuen
adult organism4.91e-52115
neural tube6.33e-2857
neural rod6.33e-2857
future spinal cord6.33e-2857
neural keel6.33e-2857
neural plate1.62e-2486
presumptive neural plate1.62e-2486
neurectoderm1.79e-2290
regional part of brain4.72e-2259
anterior neural tube3.09e-2142
brain5.56e-2169
future brain5.56e-2169
central nervous system9.72e-2182
regional part of forebrain1.52e-2041
forebrain1.52e-2041
future forebrain1.52e-2041
regional part of nervous system1.60e-1894
nervous system1.60e-1894
gray matter2.84e-1734
brain grey matter2.84e-1734
telencephalon5.63e-1734
ectoderm-derived structure1.52e-16169
regional part of telencephalon1.54e-1633
anterior region of body6.83e-16129
craniocervical region6.83e-16129
ectoderm1.44e-15173
presumptive ectoderm1.44e-15173
pre-chordal neural plate1.52e-1561
cerebral hemisphere2.23e-1532
organ5.95e-15511
head9.14e-15123
regional part of cerebral cortex1.34e-1322
embryo1.80e-12612
neocortex3.12e-1220
multi-cellular organism8.10e-12659
anatomical system9.36e-12625
anatomical group1.21e-11626
organ part1.79e-11219
cerebral cortex3.42e-1125
pallium3.42e-1125
embryonic structure6.78e-11605
developing anatomical structure6.78e-11605
germ layer1.53e-10604
embryonic tissue1.53e-10604
presumptive structure1.53e-10604
epiblast (generic)1.53e-10604
epithelium2.36e-09309
cell layer5.45e-09312
anatomical conduit8.00e-09241
tube1.80e-08194
nucleus of brain6.40e-089
neural nucleus6.40e-089
posterior neural tube7.77e-0815
chordal neural plate7.77e-0815
anatomical cluster7.84e-08286
brainstem1.56e-078
basal ganglion2.08e-079
nuclear complex of neuraxis2.08e-079
aggregate regional part of brain2.08e-079
collection of basal ganglia2.08e-079
cerebral subcortex2.08e-079
multi-tissue structure8.56e-07347


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
ZZZ3#260093239.4132124352337.25894005043406e-084.37458995918801e-06



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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