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Coexpression cluster:C4597: Difference between revisions

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|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322244098111979
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322244098111979
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}}
}}

Revision as of 16:50, 26 November 2012


Full id: C4597_putamen_caudate_nucleus_left_insula_heart_temporal



Phase1 CAGE Peaks

Hg19::chr6:36807213..36807231,-p3@CPNE5
Hg19::chr6:36807240..36807269,-p4@CPNE5
Hg19::chr6:36807270..36807282,-p7@CPNE5


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 organism6.70e-52114
neural tube2.33e-4256
neural rod2.33e-4256
future spinal cord2.33e-4256
neural keel2.33e-4256
telencephalon5.40e-4134
regional part of nervous system1.04e-4053
regional part of brain1.04e-4053
brain grey matter1.99e-4034
gray matter1.99e-4034
cerebral hemisphere1.53e-3832
regional part of telencephalon7.11e-3832
regional part of forebrain1.25e-3741
forebrain1.25e-3741
anterior neural tube1.25e-3741
future forebrain1.25e-3741
central nervous system4.69e-3581
brain2.90e-3468
future brain2.90e-3468
neocortex1.13e-3120
regional part of cerebral cortex1.87e-3122
neural plate2.16e-3182
presumptive neural plate2.16e-3182
nervous system3.93e-3089
neurectoderm2.80e-2986
cerebral cortex5.34e-2725
pallium5.34e-2725
tube3.09e-26192
ecto-epithelium3.51e-24104
pre-chordal neural plate1.28e-2361
anatomical conduit1.30e-21240
structure with developmental contribution from neural crest1.20e-20132
blood vessel endothelium1.94e-1918
endothelium1.94e-1918
cardiovascular system endothelium1.94e-1918
anatomical cluster1.03e-18373
basal ganglion1.20e-159
nuclear complex of neuraxis1.20e-159
aggregate regional part of brain1.20e-159
collection of basal ganglia1.20e-159
cerebral subcortex1.20e-159
simple squamous epithelium4.38e-1522
neural nucleus4.42e-159
nucleus of brain4.42e-159
squamous epithelium1.96e-1425
ectoderm-derived structure2.00e-14171
ectoderm2.00e-14171
presumptive ectoderm2.00e-14171
epithelium8.73e-14306
cell layer1.87e-13309
endothelial tube1.93e-139
arterial system endothelium1.93e-139
endothelium of artery1.93e-139
telencephalic nucleus1.18e-127
organ system subdivision5.00e-12223
gyrus1.97e-116
organ part4.18e-11218
multi-cellular organism2.55e-10656
parietal lobe6.30e-105
anatomical system1.37e-09624
anatomical group1.57e-09625
occipital lobe2.53e-095
temporal lobe2.54e-096
corpus striatum7.06e-094
striatum7.06e-094
ventral part of telencephalon7.06e-094
future corpus striatum7.06e-094
embryo8.09e-09592
vessel3.46e-0868
developing anatomical structure4.56e-08581
embryonic structure1.02e-07564
epithelial tube open at both ends1.24e-0759
blood vessel1.24e-0759
blood vasculature1.24e-0759
vascular cord1.24e-0759
germ layer1.74e-07560
germ layer / neural crest1.74e-07560
embryonic tissue1.74e-07560
presumptive structure1.74e-07560
germ layer / neural crest derived structure1.74e-07560
epiblast (generic)1.74e-07560
splanchnic layer of lateral plate mesoderm2.72e-0783
caudate-putamen4.69e-073
dorsal striatum4.69e-073
posterior neural tube7.41e-0715
chordal neural plate7.41e-0715


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
EGR1#195834.988179094810140.008056488137383440.0322244098111979



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.