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Coexpression cluster:C1079

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Full id: C1079_synovial_cerebellum_small_Smooth_medulla_spinal_dura



Phase1 CAGE Peaks

Hg19::chr3:146870027..146870031,-p@chr3:146870027..146870031
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Hg19::chr3:146874115..146874120,-p@chr3:146874115..146874120
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Hg19::chr3:147072976..147072980,-p@chr3:147072976..147072980
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Hg19::chr3:147088169..147088187,-p@chr3:147088169..147088187
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Hg19::chr3:147088197..147088208,-p@chr3:147088197..147088208
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Hg19::chr3:147088209..147088251,-p@chr3:147088209..147088251
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Hg19::chr3:147088265..147088276,-p@chr3:147088265..147088276
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Hg19::chr3:147112252..147112256,-p@chr3:147112252..147112256
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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
neural tube1.10e-8956
neural rod1.10e-8956
future spinal cord1.10e-8956
neural keel1.10e-8956
central nervous system2.44e-8081
regional part of nervous system3.37e-8053
regional part of brain3.37e-8053
brain3.39e-7568
future brain3.39e-7568
nervous system8.96e-7589
neural plate1.58e-5882
presumptive neural plate1.58e-5882
neurectoderm2.18e-5586
posterior neural tube6.48e-5315
chordal neural plate6.48e-5315
ecto-epithelium3.23e-44104
regional part of forebrain4.38e-4441
forebrain4.38e-4441
anterior neural tube4.38e-4441
future forebrain4.38e-4441
segmental subdivision of hindbrain8.31e-4312
hindbrain8.31e-4312
presumptive hindbrain8.31e-4312
brain grey matter4.79e-4134
gray matter4.79e-4134
telencephalon7.95e-4134
segmental subdivision of nervous system2.72e-3913
structure with developmental contribution from neural crest6.42e-37132
regional part of telencephalon1.52e-3532
cerebral hemisphere1.89e-3532
ectoderm-derived structure1.80e-34171
ectoderm1.80e-34171
presumptive ectoderm1.80e-34171
regional part of metencephalon1.74e-329
metencephalon1.74e-329
future metencephalon1.74e-329
neocortex2.39e-3220
regional part of cerebral cortex3.18e-2922
cerebral cortex4.01e-2925
pallium4.01e-2925
adult organism6.97e-29114
organ system subdivision3.47e-28223
pre-chordal neural plate8.58e-2861
cerebellum8.16e-236
rhombic lip8.16e-236
brainstem1.11e-216
tube4.91e-21192
cell layer9.51e-16309
anatomical conduit6.55e-15240
gyrus1.49e-136
anatomical cluster1.87e-13373
neural nucleus2.73e-139
nucleus of brain2.73e-139
epithelium4.53e-13306
medulla oblongata5.21e-123
myelencephalon5.21e-123
future myelencephalon5.21e-123
blood-cerebrospinal fluid barrier8.36e-123
temporal lobe9.31e-126
spinal cord9.66e-123
dorsal region element9.66e-123
dorsum9.66e-123
pons2.05e-113
organ part4.29e-11218
parietal lobe5.06e-115
basal ganglion4.54e-099
nuclear complex of neuraxis4.54e-099
aggregate regional part of brain4.54e-099
collection of basal ganglia4.54e-099
cerebral subcortex4.54e-099
multi-tissue structure6.23e-09342
regional part of diencephalon7.76e-094
meninx1.73e-082
membrane organ1.73e-082
meningeal cluster1.73e-082
locus ceruleus2.88e-082
brainstem nucleus2.88e-082
hindbrain nucleus2.88e-082
dorsal plus ventral thalamus3.33e-082
thalamic complex3.33e-082
telencephalic nucleus7.22e-087
middle temporal gyrus1.14e-072
brain vasculature2.57e-075
occipital lobe8.25e-075


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
SUZ12#23512212.52894522776570.01028879170298380.0382225702225989



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.