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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1143_parotid_salivary_corpus_optic_temporal_thalamus_globus
|full_id=C1143_parotid_salivary_corpus_optic_temporal_thalamus_globus
|id=C1143
|id=C1143

Revision as of 13:37, 12 September 2012


Full id: C1143_parotid_salivary_corpus_optic_temporal_thalamus_globus



Phase1 CAGE Peaks

Hg19::chr11:49230087..49230098,-p7@FOLH1B
p7@FOLH1
Hg19::chr11:49230144..49230164,-p1@FOLH1B
p1@FOLH1
Hg19::chr11:49230172..49230183,-p6@FOLH1B
p6@FOLH1
Hg19::chr11:49230184..49230198,-p5@FOLH1B
p5@FOLH1
Hg19::chr13:88323717..88323728,+p@chr13:88323717..88323728
+
Hg19::chr15:101402041..101402067,+p1@ENST00000558475
p1@ENST00000558641
p1@ENST00000559673
Hg19::chr3:138022481..138022501,-p@chr3:138022481..138022501
-


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism3.63e-54115
neural tube2.52e-3857
neural rod2.52e-3857
future spinal cord2.52e-3857
neural keel2.52e-3857
regional part of brain1.03e-3059
central nervous system1.17e-3082
neurectoderm3.80e-3090
regional part of nervous system8.48e-3094
nervous system8.48e-3094
neural plate1.16e-2986
presumptive neural plate1.16e-2986
anterior neural tube1.19e-2942
regional part of forebrain4.36e-2941
forebrain4.36e-2941
future forebrain4.36e-2941
brain6.09e-2969
future brain6.09e-2969
telencephalon3.56e-2634
gray matter3.69e-2634
brain grey matter3.69e-2634
regional part of telencephalon2.90e-2533
cerebral hemisphere3.19e-2432
ectoderm3.57e-23173
presumptive ectoderm3.57e-23173
anterior region of body6.58e-23129
craniocervical region6.58e-23129
ectoderm-derived structure1.73e-22169
head5.48e-22123
pre-chordal neural plate1.56e-2061
regional part of cerebral cortex4.68e-2022
neocortex2.48e-1820
cerebral cortex4.28e-1825
pallium4.28e-1825
anatomical cluster4.11e-15286
anatomical conduit3.85e-13241
tube1.46e-12194
organ part1.65e-12219
organ1.72e-11511
multi-tissue structure1.79e-11347
posterior neural tube1.11e-0915
chordal neural plate1.11e-0915
nucleus of brain1.22e-099
neural nucleus1.22e-099
embryo1.95e-09612
basal ganglion2.63e-099
nuclear complex of neuraxis2.63e-099
aggregate regional part of brain2.63e-099
collection of basal ganglia2.63e-099
cerebral subcortex2.63e-099
embryonic structure4.89e-09605
developing anatomical structure4.89e-09605
anatomical group7.56e-09626
organism subdivision7.94e-09365
germ layer1.03e-08604
embryonic tissue1.03e-08604
presumptive structure1.03e-08604
epiblast (generic)1.03e-08604
brainstem1.32e-088
anatomical system1.42e-08625
multi-cellular organism1.86e-08659
segmental subdivision of nervous system4.03e-0813
epithelium5.91e-08309
temporal lobe7.41e-087
telencephalic nucleus8.86e-087
cell layer1.35e-07312
segmental subdivision of hindbrain3.19e-0712
hindbrain3.19e-0712
presumptive hindbrain3.19e-0712


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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