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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1544_caudate_globus_optic_locus_spinal_hippocampus_thalamus
|full_id=C1544_caudate_globus_optic_locus_spinal_hippocampus_thalamus
|id=C1544
|id=C1544

Revision as of 14:07, 12 September 2012


Full id: C1544_caudate_globus_optic_locus_spinal_hippocampus_thalamus



Phase1 CAGE Peaks

Hg19::chr8:68864042..68864056,+p11@PREX2
Hg19::chr8:68864487..68864512,+p4@PREX2
Hg19::chr8:68864580..68864596,+p5@PREX2
Hg19::chr8:68864598..68864664,+p1@PREX2
Hg19::chr8:68864670..68864683,+p14@PREX2
Hg19::chr8:69143730..69143734,+p@chr8:69143730..69143734
+


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 organism2.31e-53115
neural tube8.95e-4157
neural rod8.95e-4157
future spinal cord8.95e-4157
neural keel8.95e-4157
central nervous system1.23e-3982
regional part of nervous system9.20e-3594
nervous system9.20e-3594
regional part of brain8.46e-3359
anterior neural tube1.08e-3142
regional part of forebrain1.64e-3141
forebrain1.64e-3141
future forebrain1.64e-3141
brain5.05e-3169
future brain5.05e-3169
neural plate1.06e-3086
presumptive neural plate1.06e-3086
neurectoderm1.66e-2990
gray matter8.49e-2734
brain grey matter8.49e-2734
telencephalon1.19e-2634
regional part of telencephalon7.04e-2633
cerebral hemisphere5.61e-2532
pre-chordal neural plate2.19e-2161
cerebral cortex3.91e-1925
pallium3.91e-1925
regional part of cerebral cortex1.07e-1722
anterior region of body2.81e-17129
craniocervical region2.81e-17129
anatomical conduit3.88e-17241
tube3.98e-17194
ectoderm-derived structure6.08e-17169
head9.24e-17123
ectoderm1.21e-16173
presumptive ectoderm1.21e-16173
neocortex5.83e-1620
anatomical cluster5.02e-15286
multi-cellular organism5.63e-14659
anatomical system1.16e-11625
anatomical group1.60e-11626
posterior neural tube4.61e-1015
chordal neural plate4.61e-1015
endothelium6.66e-1018
blood vessel endothelium6.66e-1018
cardiovascular system endothelium6.66e-1018
epithelium1.35e-09309
organ2.77e-09511
cell layer3.78e-09312
nucleus of brain3.82e-099
neural nucleus3.82e-099
embryo4.75e-09612
basal ganglion4.77e-099
nuclear complex of neuraxis4.77e-099
aggregate regional part of brain4.77e-099
collection of basal ganglia4.77e-099
cerebral subcortex4.77e-099
segmental subdivision of nervous system1.25e-0813
organ part1.51e-08219
simple squamous epithelium8.52e-0822
segmental subdivision of hindbrain8.64e-0812
hindbrain8.64e-0812
presumptive hindbrain8.64e-0812
brainstem1.30e-078
telencephalic nucleus1.97e-077
organism subdivision4.47e-07365
embryonic structure4.96e-07605
developing anatomical structure4.96e-07605
temporal lobe7.66e-077
germ layer8.78e-07604
embryonic tissue8.78e-07604
presumptive structure8.78e-07604
epiblast (generic)8.78e-07604
squamous epithelium9.44e-0725


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
CTCF#1066443.573504248716680.01316635007238510.0466160565194193



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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