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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C991_cerebellum_occipital_thalamus_middle_medial_parietal_hippocampus
|full_id=C991_cerebellum_occipital_thalamus_middle_medial_parietal_hippocampus
|gostat_on_coexpression_clusters=GO:0030981!cortical microtubule cytoskeleton!0.00777076248082068!23332$GO:0051010!microtubule plus-end binding!0.00777076248082068!23332$GO:0043515!kinetochore binding!0.00777076248082068!23332$GO:0005828!kinetochore microtubule!0.00777076248082068!23332$GO:0001578!microtubule bundle formation!0.0103604066223044!23332$GO:0005881!cytoplasmic microtubule!0.0103604066223044!23332$GO:0007271!synaptic transmission, cholinergic!0.0126258162454333!1142$GO:0005892!nicotinic acetylcholine-gated receptor-channel complex!0.0126258162454333!1142$GO:0005876!spindle microtubule!0.012762682403163!23332$GO:0007026!negative regulation of microtubule depolymerization!0.012762682403163!23332$GO:0031114!regulation of microtubule depolymerization!0.012762682403163!23332$GO:0031111!negative regulation of microtubule polymerization or depolymerization!0.012762682403163!23332$GO:0007019!microtubule depolymerization!0.012762682403163!23332$GO:0004889!nicotinic acetylcholine-activated cation-selective channel activity!0.012762682403163!1142$GO:0030863!cortical cytoskeleton!0.0129472675530594!23332$GO:0007163!establishment and/or maintenance of cell polarity!0.0130822061173456!23332$GO:0031110!regulation of microtubule polymerization or depolymerization!0.0130822061173456!23332$GO:0000776!kinetochore!0.0130822061173456!23332$GO:0031109!microtubule polymerization or depolymerization!0.0130822061173456!23332$GO:0044448!cell cortex part!0.0170111473719583!23332$GO:0051261!protein depolymerization!0.0170111473719583!23332$GO:0008017!microtubule binding!0.0172961434962173!23332$GO:0051129!negative regulation of cellular component organization and biogenesis!0.0175562678351748!23332$GO:0005938!cell cortex!0.0207037327184926!23332$GO:0015631!tubulin binding!0.0208063317787594!23332$GO:0005231!excitatory extracellular ligand-gated ion channel activity!0.0214974962065383!1142$GO:0000775!chromosome, pericentric region!0.0216235457381674!23332$GO:0005819!spindle!0.0216235457381674!23332$GO:0051128!regulation of cellular component organization and biogenesis!0.0260312826246814!23332$GO:0000226!microtubule cytoskeleton organization and biogenesis!0.0260312826246814!23332$GO:0051248!negative regulation of protein metabolic process!0.0260312826246814!23332$GO:0043235!receptor complex!0.026670319353467!1142$GO:0043234!protein complex!0.028798453302904!23332;1142$GO:0005813!centrosome!0.0290304848428203!23332$GO:0005230!extracellular ligand-gated ion channel activity!0.0290304848428203!1142$GO:0030594!neurotransmitter receptor activity!0.0296249349141213!1142$GO:0042165!neurotransmitter binding!0.0296249349141213!1142$GO:0005815!microtubule organizing center!0.0296249349141213!23332$GO:0045211!postsynaptic membrane!0.0296249349141213!1142$GO:0044456!synapse part!0.0302715179621065!1142$GO:0015276!ligand-gated ion channel activity!0.0302715179621065!1142$GO:0022834!ligand-gated channel activity!0.0302715179621065!1142$GO:0032991!macromolecular complex!0.0400958062269846!23332;1142$GO:0007067!mitosis!0.0412409419109716!23332$GO:0000087!M phase of mitotic cell cycle!0.0412409419109716!23332$GO:0051301!cell division!0.0412409419109716!23332$GO:0007268!synaptic transmission!0.0477454162708972!1142$GO:0005874!microtubule!0.0480347143358087!23332$GO:0000279!M phase!0.0483119055317247!23332$GO:0007017!microtubule-based process!0.0487317017888626!23332$GO:0000278!mitotic cell cycle!0.0490778226376123!23332$GO:0019226!transmission of nerve impulse!0.0490778226376123!1142
|id=C991
|id=C991
}}
}}

Revision as of 17:42, 18 May 2012


Full id: C991_cerebellum_occipital_thalamus_middle_medial_parietal_hippocampus



Phase1 CAGE Peaks

Hg19::chr11:17760741..17760754,+p@chr11:17760741..17760754
+
Hg19::chr12:50274906..50274914,-p11@AK127601
Hg19::chr17:8030284..8030295,-p@chr17:8030284..8030295
-
Hg19::chr2:122247959..122247960,-p28@CLASP1
Hg19::chr5:87981099..87981108,-p25@LINC00461
Hg19::chr6:123318409..123318423,+p@chr6:123318409..123318423
+
Hg19::chr7:70664156..70664170,+p@chr7:70664156..70664170
+
Hg19::chr8:42552503..42552524,+p1@CHRNB3


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:0030981cortical microtubule cytoskeleton0.00777076248082068
GO:0051010microtubule plus-end binding0.00777076248082068
GO:0043515kinetochore binding0.00777076248082068
GO:0005828kinetochore microtubule0.00777076248082068
GO:0001578microtubule bundle formation0.0103604066223044
GO:0005881cytoplasmic microtubule0.0103604066223044
GO:0007271synaptic transmission, cholinergic0.0126258162454333
GO:0005892nicotinic acetylcholine-gated receptor-channel complex0.0126258162454333
GO:0005876spindle microtubule0.012762682403163
GO:0007026negative regulation of microtubule depolymerization0.012762682403163
GO:0031114regulation of microtubule depolymerization0.012762682403163
GO:0031111negative regulation of microtubule polymerization or depolymerization0.012762682403163
GO:0007019microtubule depolymerization0.012762682403163
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity0.012762682403163
GO:0030863cortical cytoskeleton0.0129472675530594
GO:0007163establishment and/or maintenance of cell polarity0.0130822061173456
GO:0031110regulation of microtubule polymerization or depolymerization0.0130822061173456
GO:0000776kinetochore0.0130822061173456
GO:0031109microtubule polymerization or depolymerization0.0130822061173456
GO:0044448cell cortex part0.0170111473719583
GO:0051261protein depolymerization0.0170111473719583
GO:0008017microtubule binding0.0172961434962173
GO:0051129negative regulation of cellular component organization and biogenesis0.0175562678351748
GO:0005938cell cortex0.0207037327184926
GO:0015631tubulin binding0.0208063317787594
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0214974962065383
GO:0000775chromosome, pericentric region0.0216235457381674
GO:0005819spindle0.0216235457381674
GO:0051128regulation of cellular component organization and biogenesis0.0260312826246814
GO:0000226microtubule cytoskeleton organization and biogenesis0.0260312826246814
GO:0051248negative regulation of protein metabolic process0.0260312826246814
GO:0043235receptor complex0.026670319353467
GO:0043234protein complex0.028798453302904
GO:0005813centrosome0.0290304848428203
GO:0005230extracellular ligand-gated ion channel activity0.0290304848428203
GO:0030594neurotransmitter receptor activity0.0296249349141213
GO:0042165neurotransmitter binding0.0296249349141213
GO:0005815microtubule organizing center0.0296249349141213
GO:0045211postsynaptic membrane0.0296249349141213
GO:0044456synapse part0.0302715179621065
GO:0015276ligand-gated ion channel activity0.0302715179621065
GO:0022834ligand-gated channel activity0.0302715179621065
GO:0032991macromolecular complex0.0400958062269846
GO:0007067mitosis0.0412409419109716
GO:0000087M phase of mitotic cell cycle0.0412409419109716
GO:0051301cell division0.0412409419109716
GO:0007268synaptic transmission0.0477454162708972
GO:0005874microtubule0.0480347143358087
GO:0000279M phase0.0483119055317247
GO:0007017microtubule-based process0.0487317017888626
GO:0000278mitotic cell cycle0.0490778226376123
GO:0019226transmission of nerve impulse0.0490778226376123



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>disease_data<br>


Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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.