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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1845_spinal_corpus_carcinoid_amygdala_thalamus_brain_globus
|full_id=C1845_spinal_corpus_carcinoid_amygdala_thalamus_brain_globus
|gostat_on_coexpression_clusters=GO:0001637!G-protein chemoattractant receptor activity!0.0207098329063913!2840$GO:0004950!chemokine receptor activity!0.0207098329063913!2840$GO:0019956!chemokine binding!0.0207098329063913!2840$GO:0001608!nucleotide receptor activity, G-protein coupled!0.0207098329063913!2840$GO:0045028!purinergic nucleotide receptor activity, G-protein coupled!0.0207098329063913!2840$GO:0001614!purinergic nucleotide receptor activity!0.0207098329063913!2840$GO:0016502!nucleotide receptor activity!0.0207098329063913!2840$GO:0019955!cytokine binding!0.040739456735913!2840$GO:0001653!peptide receptor activity!0.048687554451759!2840$GO:0008528!peptide receptor activity, G-protein coupled!0.048687554451759!2840
|gostat_on_coexpression_clusters=GO:0001637!G-protein chemoattractant receptor activity!0.0207098329063913!2840$GO:0004950!chemokine receptor activity!0.0207098329063913!2840$GO:0019956!chemokine binding!0.0207098329063913!2840$GO:0001608!nucleotide receptor activity, G-protein coupled!0.0207098329063913!2840$GO:0045028!purinergic nucleotide receptor activity, G-protein coupled!0.0207098329063913!2840$GO:0001614!purinergic nucleotide receptor activity!0.0207098329063913!2840$GO:0016502!nucleotide receptor activity!0.0207098329063913!2840$GO:0019955!cytokine binding!0.040739456735913!2840$GO:0001653!peptide receptor activity!0.048687554451759!2840$GO:0008528!peptide receptor activity, G-protein coupled!0.048687554451759!2840

Revision as of 14:28, 12 September 2012


Full id: C1845_spinal_corpus_carcinoid_amygdala_thalamus_brain_globus



Phase1 CAGE Peaks

Hg19::chr1:20755657..20755668,-p1@LOC339505
Hg19::chr1:21978312..21978363,-p3@RAP1GAP
Hg19::chr20:21493651..21493656,+p@chr20:21493651..21493656
+
Hg19::chr22:18348940..18348949,-p@chr22:18348940..18348949
-
Hg19::chr2:128403563..128403578,+p3@GPR17


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:0001637G-protein chemoattractant receptor activity0.0207098329063913
GO:0004950chemokine receptor activity0.0207098329063913
GO:0019956chemokine binding0.0207098329063913
GO:0001608nucleotide receptor activity, G-protein coupled0.0207098329063913
GO:0045028purinergic nucleotide receptor activity, G-protein coupled0.0207098329063913
GO:0001614purinergic nucleotide receptor activity0.0207098329063913
GO:0016502nucleotide receptor activity0.0207098329063913
GO:0019955cytokine binding0.040739456735913
GO:0001653peptide receptor activity0.048687554451759
GO:0008528peptide receptor activity, G-protein coupled0.048687554451759



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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
central nervous system1.63e-4082
regional part of nervous system8.07e-4094
nervous system8.07e-4094
neural tube1.88e-3957
neural rod1.88e-3957
future spinal cord1.88e-3957
neural keel1.88e-3957
adult organism3.16e-36115
brain1.29e-3269
future brain1.29e-3269
regional part of forebrain2.22e-3241
forebrain2.22e-3241
future forebrain2.22e-3241
regional part of brain1.32e-3159
anterior neural tube4.01e-3142
neurectoderm3.91e-2990
telencephalon1.73e-2734
neural plate2.03e-2786
presumptive neural plate2.03e-2786
gray matter2.15e-2734
brain grey matter2.15e-2734
regional part of telencephalon1.23e-2633
cerebral hemisphere1.04e-2532
ectoderm6.49e-23173
presumptive ectoderm6.49e-23173
ectoderm-derived structure1.99e-21169
regional part of cerebral cortex4.59e-2022
pre-chordal neural plate4.89e-2061
cerebral cortex5.51e-2025
pallium5.51e-2025
neocortex1.93e-1820
anterior region of body3.93e-16129
craniocervical region3.93e-16129
head4.06e-16123
posterior neural tube2.18e-0915
chordal neural plate2.18e-0915
organ part3.55e-09219
tube4.90e-09194
basal ganglion6.69e-099
nuclear complex of neuraxis6.69e-099
aggregate regional part of brain6.69e-099
collection of basal ganglia6.69e-099
cerebral subcortex6.69e-099
nucleus of brain7.57e-099
neural nucleus7.57e-099
organ4.59e-08511
subdivision of digestive tract4.87e-08129
endodermal part of digestive tract4.87e-08129
temporal lobe5.22e-087
multi-tissue structure6.78e-08347
segmental subdivision of nervous system8.00e-0813
anatomical conduit8.76e-08241
telencephalic nucleus3.25e-077
segmental subdivision of hindbrain4.49e-0712
hindbrain4.49e-0712
presumptive hindbrain4.49e-0712
foregut6.59e-0798
anatomical cluster8.37e-07286
Disease
Ontology termp-valuen
cell type cancer5.73e-21143
carcinoma2.61e-18106
cancer3.84e-13235
disease of cellular proliferation3.93e-12239


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.