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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3673_neuroblastoma_brain_small_cerebellum_occipital_temporal_duodenum
|full_id=C3673_neuroblastoma_brain_small_cerebellum_occipital_temporal_duodenum
|gostat_on_coexpression_clusters=GO:0004994!somatostatin receptor activity!0.0164831929442676!6752$GO:0007193!G-protein signaling, adenylate cyclase inhibiting pathway!0.0219727381701648!6752$GO:0030165!PDZ domain binding!0.0219727381701648!6752$GO:0007584!response to nutrient!0.0269051121052268!6752$GO:0008188!neuropeptide receptor activity!0.0269051121052268!6752$GO:0042923!neuropeptide binding!0.0269051121052268!6752$GO:0031667!response to nutrient levels!0.0270486413620883!6752$GO:0009991!response to extracellular stimulus!0.0270486413620883!6752$GO:0007188!G-protein signaling, coupled to cAMP nucleotide second messenger!0.0270486413620883!6752$GO:0019933!cAMP-mediated signaling!0.0270486413620883!6752$GO:0007586!digestion!0.0270486413620883!6752$GO:0007187!G-protein signaling, coupled to cyclic nucleotide second messenger!0.0270486413620883!6752$GO:0019935!cyclic-nucleotide-mediated signaling!0.0270486413620883!6752$GO:0019904!protein domain specific binding!0.0270486413620883!6752$GO:0030594!neurotransmitter receptor activity!0.0270486413620883!6752$GO:0042165!neurotransmitter binding!0.0270486413620883!6752$GO:0001653!peptide receptor activity!0.0270486413620883!6752$GO:0008528!peptide receptor activity, G-protein coupled!0.0270486413620883!6752$GO:0007218!neuropeptide signaling pathway!0.0290792892439112!6752$GO:0042277!peptide binding!0.0341825969867575!6752$GO:0008285!negative regulation of cell proliferation!0.0352067492146173!6752$GO:0019932!second-messenger-mediated signaling!0.0400035891161309!6752
|gostat_on_coexpression_clusters=GO:0004994!somatostatin receptor activity!0.0164831929442676!6752$GO:0007193!G-protein signaling, adenylate cyclase inhibiting pathway!0.0219727381701648!6752$GO:0030165!PDZ domain binding!0.0219727381701648!6752$GO:0007584!response to nutrient!0.0269051121052268!6752$GO:0008188!neuropeptide receptor activity!0.0269051121052268!6752$GO:0042923!neuropeptide binding!0.0269051121052268!6752$GO:0031667!response to nutrient levels!0.0270486413620883!6752$GO:0009991!response to extracellular stimulus!0.0270486413620883!6752$GO:0007188!G-protein signaling, coupled to cAMP nucleotide second messenger!0.0270486413620883!6752$GO:0019933!cAMP-mediated signaling!0.0270486413620883!6752$GO:0007586!digestion!0.0270486413620883!6752$GO:0007187!G-protein signaling, coupled to cyclic nucleotide second messenger!0.0270486413620883!6752$GO:0019935!cyclic-nucleotide-mediated signaling!0.0270486413620883!6752$GO:0019904!protein domain specific binding!0.0270486413620883!6752$GO:0030594!neurotransmitter receptor activity!0.0270486413620883!6752$GO:0042165!neurotransmitter binding!0.0270486413620883!6752$GO:0001653!peptide receptor activity!0.0270486413620883!6752$GO:0008528!peptide receptor activity, G-protein coupled!0.0270486413620883!6752$GO:0007218!neuropeptide signaling pathway!0.0290792892439112!6752$GO:0042277!peptide binding!0.0341825969867575!6752$GO:0008285!negative regulation of cell proliferation!0.0352067492146173!6752$GO:0019932!second-messenger-mediated signaling!0.0400035891161309!6752

Revision as of 16:38, 12 September 2012


Full id: C3673_neuroblastoma_brain_small_cerebellum_occipital_temporal_duodenum



Phase1 CAGE Peaks

Hg19::chr17:71161200..71161204,+p3@SSTR2
Hg19::chr1:244215672..244215678,+p@chr1:244215672..244215678
+
Hg19::chr20:30555945..30555984,+p1@XKR7


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:0004994somatostatin receptor activity0.0164831929442676
GO:0007193G-protein signaling, adenylate cyclase inhibiting pathway0.0219727381701648
GO:0030165PDZ domain binding0.0219727381701648
GO:0007584response to nutrient0.0269051121052268
GO:0008188neuropeptide receptor activity0.0269051121052268
GO:0042923neuropeptide binding0.0269051121052268
GO:0031667response to nutrient levels0.0270486413620883
GO:0009991response to extracellular stimulus0.0270486413620883
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0270486413620883
GO:0019933cAMP-mediated signaling0.0270486413620883
GO:0007586digestion0.0270486413620883
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0270486413620883
GO:0019935cyclic-nucleotide-mediated signaling0.0270486413620883
GO:0019904protein domain specific binding0.0270486413620883
GO:0030594neurotransmitter receptor activity0.0270486413620883
GO:0042165neurotransmitter binding0.0270486413620883
GO:0001653peptide receptor activity0.0270486413620883
GO:0008528peptide receptor activity, G-protein coupled0.0270486413620883
GO:0007218neuropeptide signaling pathway0.0290792892439112
GO:0042277peptide binding0.0341825969867575
GO:0008285negative regulation of cell proliferation0.0352067492146173
GO:0019932second-messenger-mediated signaling0.0400035891161309



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>


Cell Type
Ontology termp-valuen
CD14-positive, CD16-negative classical monocyte1.21e-1242
classical monocyte4.16e-1145
neuronal stem cell1.60e-088
neuron6.57e-076
neuroblast6.57e-076
electrically signaling cell6.57e-076
Uber Anatomy
Ontology termp-valuen
central nervous system2.06e-4482
regional part of nervous system7.64e-4294
nervous system7.64e-4294
neural tube1.34e-3757
neural rod1.34e-3757
future spinal cord1.34e-3757
neural keel1.34e-3757
brain4.48e-3469
future brain4.48e-3469
regional part of brain4.65e-3259
regional part of forebrain2.68e-2941
forebrain2.68e-2941
future forebrain2.68e-2941
anterior neural tube3.20e-2842
neural plate3.65e-2686
presumptive neural plate3.65e-2686
neurectoderm7.02e-2690
gray matter3.77e-2434
brain grey matter3.77e-2434
telencephalon4.40e-2434
cerebral hemisphere3.39e-2332
regional part of telencephalon3.54e-2333
regional part of cerebral cortex1.73e-2122
pre-chordal neural plate5.88e-2061
neocortex6.01e-2020
adult organism2.65e-19115
ectoderm5.55e-18173
presumptive ectoderm5.55e-18173
cerebral cortex7.51e-1825
pallium7.51e-1825
ectoderm-derived structure7.67e-18169
head7.80e-15123
anterior region of body3.80e-14129
craniocervical region3.80e-14129
posterior neural tube2.43e-1015
chordal neural plate2.43e-1015
segmental subdivision of hindbrain1.40e-0812
hindbrain1.40e-0812
presumptive hindbrain1.40e-0812
temporal lobe1.91e-087
basal ganglion4.36e-089
nuclear complex of neuraxis4.36e-089
aggregate regional part of brain4.36e-089
collection of basal ganglia4.36e-089
cerebral subcortex4.36e-089
nucleus of brain9.52e-089
neural nucleus9.52e-089
segmental subdivision of nervous system1.21e-0713


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.