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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C876_skeletal_spinal_medulla_hippocampus_parietal_thalamus_occipital
|full_id=C876_skeletal_spinal_medulla_hippocampus_parietal_thalamus_occipital
|gostat_on_coexpression_clusters=GO:0001843!neural tube closure!0.010383953248564!56963$GO:0014020!primary neural tube formation!0.010383953248564!56963$GO:0001839!neural plate morphogenesis!0.010383953248564!56963$GO:0001841!neural tube formation!0.010383953248564!56963$GO:0001840!neural plate development!0.010383953248564!56963$GO:0001838!embryonic epithelial tube formation!0.010383953248564!56963$GO:0021915!neural tube development!0.010383953248564!56963$GO:0016331!morphogenesis of embryonic epithelium!0.0105201195496108!56963$GO:0002009!morphogenesis of an epithelium!0.0236325170582736!56963$GO:0007254!JNK cascade!0.0236325170582736!9459$GO:0031098!stress-activated protein kinase signaling pathway!0.0236325170582736!9459$GO:0035239!tube morphogenesis!0.0242021142259976!56963$GO:0048598!embryonic morphogenesis!0.0242021142259976!56963$GO:0009792!embryonic development ending in birth or egg hatching!0.0242021142259976!56963$GO:0043009!chordate embryonic development!0.0242021142259976!56963$GO:0035295!tube development!0.0274244371401497!56963$GO:0048503!GPI anchor binding!0.0274244371401497!56963$GO:0009986!cell surface!0.0274244371401497!56963$GO:0000165!MAPKKK cascade!0.0274244371401497!9459$GO:0005089!Rho guanyl-nucleotide exchange factor activity!0.0274244371401497!9459$GO:0035023!regulation of Rho protein signal transduction!0.0274244371401497!9459$GO:0005088!Ras guanyl-nucleotide exchange factor activity!0.0274244371401497!9459$GO:0032502!developmental process!0.0274244371401497!9459;56963$GO:0007266!Rho protein signal transduction!0.0298931627822005!9459$GO:0009790!embryonic development!0.0358469119443389!56963$GO:0035091!phosphoinositide binding!0.0368062548747997!56963$GO:0005085!guanyl-nucleotide exchange factor activity!0.0435957043134591!9459$GO:0005543!phospholipid binding!0.0441627868691779!56963$GO:0016337!cell-cell adhesion!0.0441627868691779!56963$GO:0005096!GTPase activator activity!0.0441627868691779!9459$GO:0046578!regulation of Ras protein signal transduction!0.044715327201792!9459$GO:0007243!protein kinase cascade!0.044715327201792!9459$GO:0007265!Ras protein signal transduction!0.049776947180899!9459
|id=C876
|id=C876
}}
}}

Revision as of 17:42, 18 May 2012


Full id: C876_skeletal_spinal_medulla_hippocampus_parietal_thalamus_occipital



Phase1 CAGE Peaks

Hg19::chr10:94001015..94001051,-p@chr10:94001015..94001051
-
Hg19::chr15:93632396..93632407,-p3@RGMA
Hg19::chr1:160103394..160103410,+p@chr1:160103394..160103410
+
Hg19::chr1:160103559..160103576,+p@chr1:160103559..160103576
+
Hg19::chr1:160103656..160103669,+p@chr1:160103656..160103669
+
Hg19::chr1:160103687..160103724,+p@chr1:160103687..160103724
+
Hg19::chr1:160103733..160103769,+p@chr1:160103733..160103769
+
Hg19::chr1:160107625..160107629,+p@chr1:160107625..160107629
+
Hg19::chrX:135849340..135849399,-p6@ARHGEF6


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:0001843neural tube closure0.010383953248564
GO:0014020primary neural tube formation0.010383953248564
GO:0001839neural plate morphogenesis0.010383953248564
GO:0001841neural tube formation0.010383953248564
GO:0001840neural plate development0.010383953248564
GO:0001838embryonic epithelial tube formation0.010383953248564
GO:0021915neural tube development0.010383953248564
GO:0016331morphogenesis of embryonic epithelium0.0105201195496108
GO:0002009morphogenesis of an epithelium0.0236325170582736
GO:0007254JNK cascade0.0236325170582736
GO:0031098stress-activated protein kinase signaling pathway0.0236325170582736
GO:0035239tube morphogenesis0.0242021142259976
GO:0048598embryonic morphogenesis0.0242021142259976
GO:0009792embryonic development ending in birth or egg hatching0.0242021142259976
GO:0043009chordate embryonic development0.0242021142259976
GO:0035295tube development0.0274244371401497
GO:0048503GPI anchor binding0.0274244371401497
GO:0009986cell surface0.0274244371401497
GO:0000165MAPKKK cascade0.0274244371401497
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0274244371401497
GO:0035023regulation of Rho protein signal transduction0.0274244371401497
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0274244371401497
GO:0032502developmental process0.0274244371401497
GO:0007266Rho protein signal transduction0.0298931627822005
GO:0009790embryonic development0.0358469119443389
GO:0035091phosphoinositide binding0.0368062548747997
GO:0005085guanyl-nucleotide exchange factor activity0.0435957043134591
GO:0005543phospholipid binding0.0441627868691779
GO:0016337cell-cell adhesion0.0441627868691779
GO:0005096GTPase activator activity0.0441627868691779
GO:0046578regulation of Ras protein signal transduction0.044715327201792
GO:0007243protein kinase cascade0.044715327201792
GO:0007265Ras protein signal transduction0.049776947180899



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.