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Coexpression cluster:C1654

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Full id: C1654_smallcell_cord_small_B_Neural_gastrointestinal_splenic



Phase1 CAGE Peaks

Hg19::chr12:103351813..103351844,+p4@ASCL1
Hg19::chr12:103352277..103352324,+p2@ASCL1
Hg19::chr12:103352326..103352351,+p3@ASCL1
Hg19::chr12:103352595..103352622,+p@chr12:103352595..103352622
+
Hg19::chr3:179754677..179754701,-p5@PEX5L


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


GO IDGO nameFDR corrected p-value
GO:0060163subpallium neuron fate commitment0.000804584167353507
GO:0014017neuroblast fate commitment0.000804584167353507
GO:0014016neuroblast differentiation0.000804584167353507
GO:0007400neuroblast fate determination0.000804584167353507
GO:0060165regulation of timing of subpallium neuron differentiation0.000804584167353507
GO:0060164regulation of timing of neuron differentiation0.000804584167353507
GO:0021544subpallium development0.00206886981320192
GO:0048505regulation of timing of cell differentiation0.00214546304184275
GO:0040034regulation of development, heterochronic0.00214546304184275
GO:0021537telencephalon development0.00530947391795865
GO:0048663neuron fate commitment0.00614292166841388
GO:0007405neuroblast proliferation0.0068373548804725
GO:0045664regulation of neuron differentiation0.00932932998797643
GO:0010001glial cell differentiation0.00932932998797643
GO:0001709cell fate determination0.00932932998797643
GO:0042063gliogenesis0.0102176854681714
GO:0001764neuron migration0.0102176854681714
GO:0030900forebrain development0.0123287861003839
GO:0007219Notch signaling pathway0.0126947983978901
GO:0045165cell fate commitment0.0171199860133783
GO:0007389pattern specification process0.0284536626285139
GO:0007420brain development0.0301607648054761
GO:0045595regulation of cell differentiation0.0301607648054761
GO:0048666neuron development0.0309067338413351
GO:0030182neuron differentiation0.0401418013441119
GO:0016477cell migration0.0401418013441119
GO:0007417central nervous system development0.0401418013441119
GO:0050793regulation of developmental process0.0401418013441119
GO:0048699generation of neurons0.0401418013441119
GO:0022008neurogenesis0.0419982514204205



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
neural cell2.38e-1025
neuronal stem cell1.75e-088
neurectodermal cell2.76e-0759
Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.13e-6094
nervous system3.13e-6094
central nervous system7.45e-5982
neural tube1.26e-5457
neural rod1.26e-5457
future spinal cord1.26e-5457
neural keel1.26e-5457
brain5.26e-4669
future brain5.26e-4669
regional part of brain3.26e-4559
regional part of forebrain2.98e-4441
forebrain2.98e-4441
future forebrain2.98e-4441
anterior neural tube7.70e-4342
neural plate3.77e-4286
presumptive neural plate3.77e-4286
neurectoderm1.37e-4090
telencephalon3.92e-3734
gray matter4.48e-3734
brain grey matter4.48e-3734
regional part of telencephalon6.59e-3633
cerebral hemisphere4.48e-3532
pre-chordal neural plate4.65e-3261
ectoderm-derived structure5.92e-30169
ectoderm1.77e-29173
presumptive ectoderm1.77e-29173
cerebral cortex1.00e-2725
pallium1.00e-2725
adult organism8.11e-27115
regional part of cerebral cortex2.29e-2522
neocortex4.26e-2320
head1.22e-22123
anterior region of body1.41e-22129
craniocervical region1.41e-22129
posterior neural tube1.39e-1215
chordal neural plate1.39e-1215
tube9.71e-11194
nucleus of brain1.10e-109
neural nucleus1.10e-109
basal ganglion1.38e-109
nuclear complex of neuraxis1.38e-109
aggregate regional part of brain1.38e-109
collection of basal ganglia1.38e-109
cerebral subcortex1.38e-109
segmental subdivision of nervous system1.80e-1013
segmental subdivision of hindbrain1.82e-0912
hindbrain1.82e-0912
presumptive hindbrain1.82e-0912
gyrus1.00e-086
telencephalic nucleus1.78e-087
diencephalon2.13e-087
future diencephalon2.13e-087
organ part3.49e-08219
temporal lobe4.00e-087
brainstem7.56e-088
occipital lobe2.23e-075
parietal lobe2.88e-075
limbic system4.20e-075
epithelium5.78e-07309


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


No analysis results for this cluster

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.