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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
neural tube3.47e-4856
neural rod3.47e-4856
future spinal cord3.47e-4856
neural keel3.47e-4856
regional part of nervous system3.41e-4453
regional part of brain3.41e-4453
adult organism7.34e-39114
regional part of forebrain3.99e-3641
forebrain3.99e-3641
anterior neural tube3.99e-3641
future forebrain3.99e-3641
central nervous system8.15e-3581
brain9.00e-3468
future brain9.00e-3468
nervous system1.88e-3389
neural plate1.14e-3182
presumptive neural plate1.14e-3182
brain grey matter3.28e-3134
gray matter3.28e-3134
telencephalon6.43e-3134
neurectoderm2.24e-2986
cerebral hemisphere1.44e-2832
regional part of telencephalon1.72e-2832
regional part of cerebral cortex2.58e-2422
pre-chordal neural plate4.34e-2361
ecto-epithelium2.64e-22104
neocortex1.10e-2120
cerebral cortex1.27e-2025
pallium1.27e-2025
structure with developmental contribution from neural crest4.15e-17132
posterior neural tube7.85e-1315
chordal neural plate7.85e-1315
organ system subdivision9.49e-13223
neural nucleus2.42e-129
nucleus of brain2.42e-129
basal ganglion3.21e-129
nuclear complex of neuraxis3.21e-129
aggregate regional part of brain3.21e-129
collection of basal ganglia3.21e-129
cerebral subcortex3.21e-129
ectoderm-derived structure1.38e-11171
ectoderm1.38e-11171
presumptive ectoderm1.38e-11171
tube2.99e-11192
segmental subdivision of nervous system3.54e-1013
brainstem5.98e-106
telencephalic nucleus1.42e-097
segmental subdivision of hindbrain3.57e-0912
hindbrain3.57e-0912
presumptive hindbrain3.57e-0912
gyrus5.44e-096
limbic system3.35e-085
occipital lobe1.59e-075
temporal lobe2.41e-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.