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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4868_neuroectodermal_carcinoid_merkel_locus_pons_renal_B
|full_id=C4868_neuroectodermal_carcinoid_merkel_locus_pons_renal_B
|id=C4868
|id=C4868

Revision as of 18:01, 12 September 2012


Full id: C4868_neuroectodermal_carcinoid_merkel_locus_pons_renal_B



Phase1 CAGE Peaks

Hg19::chrX:20075062..20075077,-p7@MAP7D2
Hg19::chrX:20075081..20075102,-p6@MAP7D2
Hg19::chrX:20075103..20075114,-p20@MAP7D2


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
neural tube3.03e-3857
neural rod3.03e-3857
future spinal cord3.03e-3857
neural keel3.03e-3857
neurectoderm2.99e-3590
neural plate2.25e-3386
presumptive neural plate2.25e-3386
regional part of brain1.04e-3159
central nervous system1.16e-2982
brain7.27e-2969
future brain7.27e-2969
regional part of nervous system1.02e-2594
nervous system1.02e-2594
adult organism8.31e-24115
anterior region of body1.05e-23129
craniocervical region1.05e-23129
posterior neural tube2.14e-2315
chordal neural plate2.14e-2315
head7.08e-23123
gray matter1.14e-2034
brain grey matter1.14e-2034
regional part of forebrain8.12e-2041
forebrain8.12e-2041
future forebrain8.12e-2041
cerebral hemisphere8.52e-2032
pre-chordal neural plate1.07e-1961
ectoderm1.42e-19173
presumptive ectoderm1.42e-19173
neocortex2.88e-1920
anterior neural tube3.34e-1942
telencephalon2.43e-1834
ectoderm-derived structure3.97e-18169
segmental subdivision of hindbrain9.82e-1812
hindbrain9.82e-1812
presumptive hindbrain9.82e-1812
regional part of cerebral cortex3.11e-1722
regional part of telencephalon7.50e-1733
segmental subdivision of nervous system3.57e-1613
cerebral cortex8.91e-1525
pallium8.91e-1525
gyrus1.50e-126
regional part of metencephalon7.69e-129
metencephalon7.69e-129
future metencephalon7.69e-129
brainstem2.17e-108
temporal lobe5.41e-097
organism subdivision1.73e-08365
atypical epithelium4.34e-084
anatomical cluster5.12e-08286
pons5.46e-083
medulla oblongata7.14e-083
myelencephalon7.14e-083
future myelencephalon7.14e-083
tube8.87e-08194
spinal cord1.96e-073
nucleus of brain2.07e-079
neural nucleus2.07e-079
basal ganglion3.88e-079
nuclear complex of neuraxis3.88e-079
aggregate regional part of brain3.88e-079
collection of basal ganglia3.88e-079
cerebral subcortex3.88e-079
middle temporal gyrus7.10e-073


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
EBF1#187938.9064668465690.00141523283560980.00919932172267706



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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