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Coexpression cluster:C3043

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Full id: C3043_spinal_medulla_serous_locus_gall_hippocampus_thalamus



Phase1 CAGE Peaks

Hg19::chr10:73848730..73848763,-p4@SPOCK2
Hg19::chr10:73848764..73848795,-p8@SPOCK2
Hg19::chr10:73848845..73848859,-p11@SPOCK2


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
adult organism1.48e-49115
neural tube2.88e-4157
neural rod2.88e-4157
future spinal cord2.88e-4157
neural keel2.88e-4157
regional part of brain2.67e-3459
central nervous system4.63e-3282
regional part of forebrain4.47e-3141
forebrain4.47e-3141
future forebrain4.47e-3141
brain4.26e-3069
future brain4.26e-3069
anterior neural tube5.95e-3042
regional part of nervous system8.39e-3094
nervous system8.39e-3094
neural plate3.22e-2686
presumptive neural plate3.22e-2686
gray matter3.73e-2634
brain grey matter3.73e-2634
telencephalon7.75e-2634
neurectoderm6.38e-2590
regional part of telencephalon7.02e-2533
cerebral hemisphere4.14e-2432
regional part of cerebral cortex1.22e-2122
neocortex1.29e-1920
cerebral cortex5.34e-1825
pallium5.34e-1825
pre-chordal neural plate1.02e-1761
anterior region of body1.30e-14129
craniocervical region1.30e-14129
head1.34e-12123
posterior neural tube3.40e-1215
chordal neural plate3.40e-1215
ectoderm-derived structure6.18e-11169
ectoderm1.30e-10173
presumptive ectoderm1.30e-10173
segmental subdivision of nervous system5.50e-1013
nucleus of brain9.53e-109
neural nucleus9.53e-109
basal ganglion1.23e-099
nuclear complex of neuraxis1.23e-099
aggregate regional part of brain1.23e-099
collection of basal ganglia1.23e-099
cerebral subcortex1.23e-099
segmental subdivision of hindbrain2.91e-0912
hindbrain2.91e-0912
presumptive hindbrain2.91e-0912
tube4.13e-09194
temporal lobe3.63e-087
telencephalic nucleus1.12e-077
brainstem2.35e-078
gyrus4.55e-076


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
CEBPB#105137.971147625824820.001974187055288560.0114896696498903
MAX#414936.452555509007120.003721913834265510.018565838417006
MYC#460935.22228187160940.007020843755740150.029314752368998



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.