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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1652_normal_brain_cerebellum_occipital_postcentral_temporal_amygdala
|full_id=C1652_normal_brain_cerebellum_occipital_postcentral_temporal_amygdala
|id=C1652
|id=C1652

Revision as of 14:14, 12 September 2012


Full id: C1652_normal_brain_cerebellum_occipital_postcentral_temporal_amygdala



Phase1 CAGE Peaks

Hg19::chr12:101188502..101188513,+p13@ANO4
Hg19::chr12:101188514..101188532,+p8@ANO4
Hg19::chr12:101188547..101188565,+p5@ANO4
Hg19::chr12:101188608..101188621,+p7@ANO4
Hg19::chr5:137774709..137774806,+p1@REEP2


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
regional part of nervous system1.34e-4294
nervous system1.34e-4294
neurectoderm1.54e-4090
central nervous system3.83e-4082
neural plate1.20e-3986
presumptive neural plate1.20e-3986
neural tube1.12e-3457
neural rod1.12e-3457
future spinal cord1.12e-3457
neural keel1.12e-3457
brain1.56e-3469
future brain1.56e-3469
regional part of brain2.67e-3359
ectoderm3.04e-33173
presumptive ectoderm3.04e-33173
pre-chordal neural plate1.64e-3261
ectoderm-derived structure3.89e-32169
head1.74e-31123
organism subdivision1.34e-29365
anterior region of body5.17e-29129
craniocervical region5.17e-29129
multi-tissue structure8.32e-29347
cell layer2.71e-28312
epithelium6.47e-28309
regional part of forebrain1.09e-2641
forebrain1.09e-2641
future forebrain1.09e-2641
anterior neural tube1.87e-2642
telencephalon9.89e-2334
gray matter1.02e-2234
brain grey matter1.02e-2234
regional part of telencephalon4.63e-2233
cerebral hemisphere1.35e-2132
tube1.02e-20194
anatomical cluster3.46e-19286
anatomical conduit4.10e-19241
cerebral cortex2.22e-1725
pallium2.22e-1725
regional part of cerebral cortex9.16e-1622
embryo3.72e-15612
organ part9.33e-15219
neocortex1.75e-1420
multi-cellular organism2.33e-14659
embryonic structure1.05e-13605
developing anatomical structure1.05e-13605
germ layer2.46e-13604
embryonic tissue2.46e-13604
presumptive structure2.46e-13604
epiblast (generic)2.46e-13604
anatomical system1.11e-11625
anatomical group1.18e-11626
adult organism3.36e-11115
posterior neural tube2.92e-0915
chordal neural plate2.92e-0915
visual system1.91e-0821
segmental subdivision of nervous system4.00e-0813
eye5.19e-0820
trunk mesenchyme6.07e-08143
somite8.06e-0883
paraxial mesoderm8.06e-0883
presomitic mesoderm8.06e-0883
presumptive segmental plate8.06e-0883
trunk paraxial mesoderm8.06e-0883
presumptive paraxial mesoderm8.06e-0883
segmental subdivision of hindbrain1.09e-0712
hindbrain1.09e-0712
presumptive hindbrain1.09e-0712
sensory system1.30e-0724
entire sense organ system1.30e-0724
camera-type eye1.57e-0719
simple eye1.57e-0719
ocular region1.57e-0719
optic cup1.57e-0719
eye primordium1.57e-0719
optic vesicle1.57e-0719
sense organ3.41e-0723
dermomyotome4.59e-0770
muscle tissue6.67e-0763
musculature6.67e-0763
musculature of body6.67e-0763
basal ganglion7.14e-079
nuclear complex of neuraxis7.14e-079
aggregate regional part of brain7.14e-079
collection of basal ganglia7.14e-079


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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