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Coexpression cluster:C1460

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Full id: C1460_neuroectodermal_amygdala_neuroblastoma_medial_frontal_non_occipital



Phase1 CAGE Peaks

Hg19::chr1:102462374..102462385,-p5@OLFM3
Hg19::chr1:102462460..102462469,-p10@OLFM3
Hg19::chr1:102462475..102462493,-p1@OLFM3
Hg19::chr1:102462503..102462522,-p3@OLFM3
Hg19::chr1:102462565..102462591,-p2@OLFM3
Hg19::chr2:166984486..166984506,-p2@ENST00000507401


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
neural tube1.65e-5757
neural rod1.65e-5757
future spinal cord1.65e-5757
neural keel1.65e-5757
regional part of nervous system8.58e-5794
nervous system8.58e-5794
central nervous system1.42e-5682
regional part of forebrain2.46e-4841
forebrain2.46e-4841
future forebrain2.46e-4841
neurectoderm2.59e-4890
regional part of brain7.00e-4859
anterior neural tube7.85e-4742
brain3.30e-4569
future brain3.30e-4569
neural plate1.21e-4386
presumptive neural plate1.21e-4386
telencephalon2.37e-4334
gray matter2.44e-4334
brain grey matter2.44e-4334
regional part of telencephalon6.12e-4233
cerebral hemisphere1.87e-4132
adult organism1.79e-36115
cerebral cortex6.90e-3325
pallium6.90e-3325
pre-chordal neural plate5.67e-3261
ectoderm9.17e-32173
presumptive ectoderm9.17e-32173
regional part of cerebral cortex1.32e-3022
ectoderm-derived structure2.31e-28169
neocortex3.15e-2820
head5.36e-22123
anterior region of body5.53e-22129
craniocervical region5.53e-22129
tube1.02e-13194
basal ganglion6.16e-129
nuclear complex of neuraxis6.16e-129
aggregate regional part of brain6.16e-129
collection of basal ganglia6.16e-129
cerebral subcortex6.16e-129
nucleus of brain9.81e-129
neural nucleus9.81e-129
posterior neural tube1.01e-1115
chordal neural plate1.01e-1115
temporal lobe1.80e-117
gyrus1.16e-096
telencephalic nucleus2.07e-097
segmental subdivision of hindbrain1.17e-0812
hindbrain1.17e-0812
presumptive hindbrain1.17e-0812
anatomical conduit1.21e-08241
embryo1.98e-08612
brainstem4.92e-088
parietal lobe5.72e-085
occipital lobe6.74e-085
limbic system8.28e-085
segmental subdivision of nervous system8.42e-0813
organ part1.50e-07219
sympathetic nervous system7.03e-075
autonomic nervous system7.03e-075
Disease
Ontology termp-valuen
neuroectodermal tumor2.53e-1010


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
CTCF#1066465.360256373075034.21437267579784e-050.000755354158036126
NANOG#79923524.37064873417722.72082401016006e-071.39911442046828e-05
REST#597858.041690596773356.54774545315482e-050.00106202824566243



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.