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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2039_signet_corpus_optic_spinal_globus_thalamus_medulla
|full_id=C2039_signet_corpus_optic_spinal_globus_thalamus_medulla
|gostat_on_coexpression_clusters=GO:0005007!fibroblast growth factor receptor activity!0.0261372497981506!2263$GO:0005922!connexon complex!0.0493500129061144!2705$GO:0005921!gap junction!0.0493500129061144!2705
|gostat_on_coexpression_clusters=GO:0005007!fibroblast growth factor receptor activity!0.0261372497981506!2263$GO:0005922!connexon complex!0.0493500129061144!2705$GO:0005921!gap junction!0.0493500129061144!2705

Revision as of 14:42, 12 September 2012


Full id: C2039_signet_corpus_optic_spinal_globus_thalamus_medulla



Phase1 CAGE Peaks

Hg19::chr10:123357854..123357865,-p6@FGFR2
Hg19::chr9:130713012..130713034,-p5@FAM102A
Hg19::chrX:70443019..70443030,+p6@GJB1
Hg19::chrX:70443050..70443061,+p5@GJB1


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:0005007fibroblast growth factor receptor activity0.0261372497981506
GO:0005922connexon complex0.0493500129061144
GO:0005921gap junction0.0493500129061144



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
melanocyte2.74e-0710
melanoblast2.74e-0710
Uber Anatomy
Ontology termp-valuen
adult organism2.38e-51115
neural tube2.27e-4757
neural rod2.27e-4757
future spinal cord2.27e-4757
neural keel2.27e-4757
central nervous system5.24e-4782
regional part of nervous system3.21e-4294
nervous system3.21e-4294
brain2.37e-4069
future brain2.37e-4069
regional part of brain2.97e-4059
anterior neural tube1.08e-3942
regional part of forebrain6.14e-3941
forebrain6.14e-3941
future forebrain6.14e-3941
gray matter9.37e-3734
brain grey matter9.37e-3734
telencephalon1.00e-3634
regional part of telencephalon1.36e-3533
neural plate4.49e-3586
presumptive neural plate4.49e-3586
cerebral hemisphere3.08e-3432
neurectoderm1.60e-3290
pre-chordal neural plate2.35e-2961
anterior region of body2.15e-27129
craniocervical region2.15e-27129
head6.48e-27123
cerebral cortex1.90e-2625
pallium1.90e-2625
ectoderm-derived structure2.69e-25169
regional part of cerebral cortex1.17e-2422
ectoderm4.44e-24173
presumptive ectoderm4.44e-24173
neocortex1.31e-2220
tube2.90e-12194
nucleus of brain1.10e-119
neural nucleus1.10e-119
basal ganglion3.03e-119
nuclear complex of neuraxis3.03e-119
aggregate regional part of brain3.03e-119
collection of basal ganglia3.03e-119
cerebral subcortex3.03e-119
organ3.22e-11511
anatomical conduit1.55e-10241
brainstem1.98e-108
telencephalic nucleus2.44e-097
temporal lobe3.32e-097
posterior neural tube4.42e-0915
chordal neural plate4.42e-0915
organism subdivision4.62e-09365
organ part6.51e-09219
anatomical cluster6.42e-08286
gyrus8.83e-086
epithelium2.10e-07309
multi-tissue structure2.13e-07347
segmental subdivision of nervous system3.67e-0713
cell layer4.03e-07312
parietal lobe7.04e-075
occipital lobe7.83e-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

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.

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