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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C545_Astrocyte_Neural_Neurons_parietal_neuroectodermal_occipital_temporal
|full_id=C545_Astrocyte_Neural_Neurons_parietal_neuroectodermal_occipital_temporal
|gostat_on_coexpression_clusters=GO:0021545!cranial nerve development!0.00435633654227826!2737$GO:0021776!smoothened signaling pathway involved in spinal cord motor neuron cell fate specification!0.00435633654227826!2737$GO:0021602!cranial nerve morphogenesis!0.00435633654227826!2737$GO:0021520!spinal cord motor neuron cell fate specification!0.00435633654227826!2737$GO:0021554!optic nerve development!0.00435633654227826!2737$GO:0021631!optic nerve morphogenesis!0.00435633654227826!2737$GO:0021521!ventral spinal cord interneuron specification!0.00435633654227826!2737$GO:0021910!smoothened signaling pathway in ventral spinal cord patterning!0.00435633654227826!2737$GO:0048558!embryonic gut morphogenesis!0.00435633654227826!2737$GO:0021514!ventral spinal cord interneuron differentiation!0.00435633654227826!2737$GO:0048557!embryonic digestive tract morphogenesis!0.00435633654227826!2737$GO:0021775!smoothened signaling pathway involved in ventral spinal cord interneuron specification!0.00435633654227826!2737$GO:0008285!negative regulation of cell proliferation!0.00443560970264724!2737;2173$GO:0021522!spinal cord motor neuron differentiation!0.00497823067105098!2737$GO:0007439!ectodermal gut development!0.00497823067105098!2737$GO:0021675!nerve development!0.00497823067105098!2737$GO:0007442!hindgut morphogenesis!0.00497823067105098!2737$GO:0048567!ectodermal gut morphogenesis!0.00497823067105098!2737$GO:0021513!spinal cord dorsal/ventral patterning!0.00497823067105098!2737$GO:0021517!ventral spinal cord development!0.00497823067105098!2737$GO:0048665!neuron fate specification!0.00497823067105098!2737$GO:0048547!gut morphogenesis!0.00544469936992546!2737$GO:0021511!spinal cord patterning!0.00544469936992546!2737$GO:0048546!digestive tract morphogenesis!0.00544469936992546!2737$GO:0009954!proximal/distal pattern formation!0.00603078530159217!2737$GO:0021515!cell differentiation in spinal cord!0.00603078530159217!2737$GO:0048566!embryonic gut development!0.00677502752287089!2737$GO:0042127!regulation of cell proliferation!0.00816524606819734!2737;2173$GO:0017053!transcriptional repressor complex!0.00816524606819734!2737$GO:0001658!ureteric bud branching!0.00816524606819734!2737$GO:0048562!embryonic organ morphogenesis!0.00816524606819734!2737$GO:0021510!spinal cord development!0.00816524606819734!2737$GO:0048565!gut development!0.0087092112142118!2737$GO:0048593!camera-type eye morphogenesis!0.00988482206017364!2737$GO:0007224!smoothened signaling pathway!0.00988482206017364!2737$GO:0048663!neuron fate commitment!0.00988482206017364!2737$GO:0030879!mammary gland development!0.00988482206017364!2737$GO:0001708!cell fate specification!0.0101938987098659!2737$GO:0008250!oligosaccharyl transferase complex!0.0101938987098659!6185$GO:0018279!protein amino acid N-linked glycosylation via asparagine!0.0101938987098659!6185$GO:0018196!peptidyl-asparagine modification!0.0101938987098659!6185$GO:0004579!dolichyl-diphosphooligosaccharide-protein glycotransferase activity!0.0105726691186438!6185$GO:0004576!oligosaccharyl transferase activity!0.0107880368760508!6185$GO:0001657!ureteric bud development!0.0107880368760508!2737$GO:0042475!odontogenesis of dentine-containing teeth!0.0107880368760508!2737$GO:0021915!neural tube development!0.0107880368760508!2737$GO:0005737!cytoplasm!0.0108821882084746!2737;2173;6185;2670$GO:0048568!embryonic organ development!0.0108821882084746!2737$GO:0007399!nervous system development!0.0114905758440886!2737;2173$GO:0000060!protein import into nucleus, translocation!0.0114905758440886!2737$GO:0008283!cell proliferation!0.012051987083627!2737;2173$GO:0001656!metanephros development!0.012051987083627!2737$GO:0042476!odontogenesis!0.012316738462079!2737$GO:0048592!eye morphogenesis!0.0125716415467752!2737$GO:0048754!branching morphogenesis of a tube!0.0130540131932628!2737$GO:0009953!dorsal/ventral pattern formation!0.0130540131932628!2737$GO:0001763!morphogenesis of a branching structure!0.0145995702918233!2737$GO:0030326!embryonic limb morphogenesis!0.0145995702918233!2737$GO:0035113!embryonic appendage morphogenesis!0.0145995702918233!2737$GO:0043010!camera-type eye development!0.0146305015267709!2737$GO:0001822!kidney development!0.0146305015267709!2737$GO:0060173!limb development!0.0146305015267709!2737$GO:0035107!appendage morphogenesis!0.0146305015267709!2737$GO:0035108!limb morphogenesis!0.0146305015267709!2737$GO:0048589!developmental growth!0.0146305015267709!2737$GO:0048736!appendage development!0.0146305015267709!2737$GO:0001655!urogenital system development!0.0155786231932965!2737$GO:0030324!lung development!0.0161155785367846!2737$GO:0030323!respiratory tube development!0.0162594446306115!2737$GO:0030900!forebrain development!0.0169016180438877!2737$GO:0048732!gland development!0.0169016180438877!2737$GO:0001654!eye development!0.0170284445874101!2737$GO:0006487!protein amino acid N-linked glycosylation!0.0188208178361548!6185$GO:0048523!negative regulation of cellular process!0.0188208178361548!2737;2173$GO:0009952!anterior/posterior pattern formation!0.0188208178361548!2737$GO:0044446!intracellular organelle part!0.0188208178361548!2737;6185;2670$GO:0044422!organelle part!0.0188208178361548!2737;6185;2670$GO:0048519!negative regulation of biological process!0.0197118215554276!2737;2173$GO:0045596!negative regulation of cell differentiation!0.0214462127169151!2737$GO:0045165!cell fate commitment!0.0231269098369947!2737$GO:0051093!negative regulation of developmental process!0.0247650865459521!2737$GO:0035239!tube morphogenesis!0.0266527868964115!2737$GO:0005200!structural constituent of cytoskeleton!0.0266527868964115!2670$GO:0007423!sensory organ development!0.0266527868964115!2737$GO:0003002!regionalization!0.0266527868964115!2737$GO:0048598!embryonic morphogenesis!0.0277650433714627!2737$GO:0007507!heart development!0.0277650433714627!2737$GO:0009792!embryonic development ending in birth or egg hatching!0.0277650433714627!2737$GO:0043009!chordate embryonic development!0.0277650433714627!2737$GO:0006606!protein import into nucleus!0.0277650433714627!2737$GO:0051170!nuclear import!0.0280295383176914!2737$GO:0048731!system development!0.0303011573863702!2737;2173$GO:0035295!tube development!0.0326438729366966!2737$GO:0003682!chromatin binding!0.0326438729366966!2737$GO:0018193!peptidyl-amino acid modification!0.0330414707869852!6185$GO:0017038!protein import!0.0330414707869852!2737$GO:0007389!pattern specification process!0.0332339795160174!2737$GO:0007420!brain development!0.0368496431624614!2737$GO:0045595!regulation of cell differentiation!0.0377812141129488!2737$GO:0048646!anatomical structure formation!0.0395873156007333!2737$GO:0006913!nucleocytoplasmic transport!0.0395873156007333!2737$GO:0051169!nuclear transport!0.0397047760353869!2737$GO:0048856!anatomical structure development!0.0415630502381958!2737;2173$GO:0006486!protein amino acid glycosylation!0.0433999046355241!6185$GO:0043413!biopolymer glycosylation!0.0437219229245242!6185$GO:0044424!intracellular part!0.0441069401277718!2737;2173;6185;2670$GO:0009101!glycoprotein biosynthetic process!0.0441069401277718!6185$GO:0006631!fatty acid metabolic process!0.0458412218466548!2173$GO:0009100!glycoprotein metabolic process!0.0494261849602594!6185$GO:0030182!neuron differentiation!0.0494434162419841!2737
|id=C545
|id=C545
}}
}}

Revision as of 17:40, 18 May 2012


Full id: C545_Astrocyte_Neural_Neurons_parietal_neuroectodermal_occipital_temporal



Phase1 CAGE Peaks

Hg19::chr17:42988599..42988605,-p46@GFAP
Hg19::chr18:56248019..56248037,-p@chr18:56248019..56248037
-
Hg19::chr18:56248051..56248065,-p@chr18:56248051..56248065
-
Hg19::chr1:39874999..39875038,+p5@KIAA0754
Hg19::chr20:35856764..35856768,+p25@RPN2
Hg19::chr2:104096987..104096993,-p@chr2:104096987..104096993
-
Hg19::chr2:104490710..104490719,+p2@ENST00000537492
Hg19::chr2:104490735..104490784,+p1@ENST00000537492
Hg19::chr2:104490799..104490827,+p1@ENST00000544869
Hg19::chr2:104517092..104517093,+p@chr2:104517092..104517093
+
Hg19::chr2:104580974..104580979,+p@chr2:104580974..104580979
+
Hg19::chr5:71479431..71479458,+p@chr5:71479431..71479458
+
Hg19::chr5:71479469..71479482,+p@chr5:71479469..71479482
+
Hg19::chr6:123100819..123100828,+p3@FABP7
Hg19::chr6:123100853..123100874,+p1@FABP7
Hg19::chr7:42192043..42192057,-p10@GLI3
Hg19::chr7:42192092..42192108,-p13@GLI3


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:0021545cranial nerve development0.00435633654227826
GO:0021776smoothened signaling pathway involved in spinal cord motor neuron cell fate specification0.00435633654227826
GO:0021602cranial nerve morphogenesis0.00435633654227826
GO:0021520spinal cord motor neuron cell fate specification0.00435633654227826
GO:0021554optic nerve development0.00435633654227826
GO:0021631optic nerve morphogenesis0.00435633654227826
GO:0021521ventral spinal cord interneuron specification0.00435633654227826
GO:0021910smoothened signaling pathway in ventral spinal cord patterning0.00435633654227826
GO:0048558embryonic gut morphogenesis0.00435633654227826
GO:0021514ventral spinal cord interneuron differentiation0.00435633654227826
GO:0048557embryonic digestive tract morphogenesis0.00435633654227826
GO:0021775smoothened signaling pathway involved in ventral spinal cord interneuron specification0.00435633654227826
GO:0008285negative regulation of cell proliferation0.00443560970264724
GO:0021522spinal cord motor neuron differentiation0.00497823067105098
GO:0007439ectodermal gut development0.00497823067105098
GO:0021675nerve development0.00497823067105098
GO:0007442hindgut morphogenesis0.00497823067105098
GO:0048567ectodermal gut morphogenesis0.00497823067105098
GO:0021513spinal cord dorsal/ventral patterning0.00497823067105098
GO:0021517ventral spinal cord development0.00497823067105098
GO:0048665neuron fate specification0.00497823067105098
GO:0048547gut morphogenesis0.00544469936992546
GO:0021511spinal cord patterning0.00544469936992546
GO:0048546digestive tract morphogenesis0.00544469936992546
GO:0009954proximal/distal pattern formation0.00603078530159217
GO:0021515cell differentiation in spinal cord0.00603078530159217
GO:0048566embryonic gut development0.00677502752287089
GO:0042127regulation of cell proliferation0.00816524606819734
GO:0017053transcriptional repressor complex0.00816524606819734
GO:0001658ureteric bud branching0.00816524606819734
GO:0048562embryonic organ morphogenesis0.00816524606819734
GO:0021510spinal cord development0.00816524606819734
GO:0048565gut development0.0087092112142118
GO:0048593camera-type eye morphogenesis0.00988482206017364
GO:0007224smoothened signaling pathway0.00988482206017364
GO:0048663neuron fate commitment0.00988482206017364
GO:0030879mammary gland development0.00988482206017364
GO:0001708cell fate specification0.0101938987098659
GO:0008250oligosaccharyl transferase complex0.0101938987098659
GO:0018279protein amino acid N-linked glycosylation via asparagine0.0101938987098659
GO:0018196peptidyl-asparagine modification0.0101938987098659
GO:0004579dolichyl-diphosphooligosaccharide-protein glycotransferase activity0.0105726691186438
GO:0004576oligosaccharyl transferase activity0.0107880368760508
GO:0001657ureteric bud development0.0107880368760508
GO:0042475odontogenesis of dentine-containing teeth0.0107880368760508
GO:0021915neural tube development0.0107880368760508
GO:0005737cytoplasm0.0108821882084746
GO:0048568embryonic organ development0.0108821882084746
GO:0007399nervous system development0.0114905758440886
GO:0000060protein import into nucleus, translocation0.0114905758440886
GO:0008283cell proliferation0.012051987083627
GO:0001656metanephros development0.012051987083627
GO:0042476odontogenesis0.012316738462079
GO:0048592eye morphogenesis0.0125716415467752
GO:0048754branching morphogenesis of a tube0.0130540131932628
GO:0009953dorsal/ventral pattern formation0.0130540131932628
GO:0001763morphogenesis of a branching structure0.0145995702918233
GO:0030326embryonic limb morphogenesis0.0145995702918233
GO:0035113embryonic appendage morphogenesis0.0145995702918233
GO:0043010camera-type eye development0.0146305015267709
GO:0001822kidney development0.0146305015267709
GO:0060173limb development0.0146305015267709
GO:0035107appendage morphogenesis0.0146305015267709
GO:0035108limb morphogenesis0.0146305015267709
GO:0048589developmental growth0.0146305015267709
GO:0048736appendage development0.0146305015267709
GO:0001655urogenital system development0.0155786231932965
GO:0030324lung development0.0161155785367846
GO:0030323respiratory tube development0.0162594446306115
GO:0030900forebrain development0.0169016180438877
GO:0048732gland development0.0169016180438877
GO:0001654eye development0.0170284445874101
GO:0006487protein amino acid N-linked glycosylation0.0188208178361548
GO:0048523negative regulation of cellular process0.0188208178361548
GO:0009952anterior/posterior pattern formation0.0188208178361548
GO:0044446intracellular organelle part0.0188208178361548
GO:0044422organelle part0.0188208178361548
GO:0048519negative regulation of biological process0.0197118215554276
GO:0045596negative regulation of cell differentiation0.0214462127169151
GO:0045165cell fate commitment0.0231269098369947
GO:0051093negative regulation of developmental process0.0247650865459521
GO:0035239tube morphogenesis0.0266527868964115
GO:0005200structural constituent of cytoskeleton0.0266527868964115
GO:0007423sensory organ development0.0266527868964115
GO:0003002regionalization0.0266527868964115
GO:0048598embryonic morphogenesis0.0277650433714627
GO:0007507heart development0.0277650433714627
GO:0009792embryonic development ending in birth or egg hatching0.0277650433714627
GO:0043009chordate embryonic development0.0277650433714627
GO:0006606protein import into nucleus0.0277650433714627
GO:0051170nuclear import0.0280295383176914
GO:0048731system development0.0303011573863702
GO:0035295tube development0.0326438729366966
GO:0003682chromatin binding0.0326438729366966
GO:0018193peptidyl-amino acid modification0.0330414707869852
GO:0017038protein import0.0330414707869852
GO:0007389pattern specification process0.0332339795160174
GO:0007420brain development0.0368496431624614
GO:0045595regulation of cell differentiation0.0377812141129488
GO:0048646anatomical structure formation0.0395873156007333
GO:0006913nucleocytoplasmic transport0.0395873156007333
GO:0051169nuclear transport0.0397047760353869
GO:0048856anatomical structure development0.0415630502381958
GO:0006486protein amino acid glycosylation0.0433999046355241
GO:0043413biopolymer glycosylation0.0437219229245242
GO:0044424intracellular part0.0441069401277718
GO:0009101glycoprotein biosynthetic process0.0441069401277718
GO:0006631fatty acid metabolic process0.0458412218466548
GO:0009100glycoprotein metabolic process0.0494261849602594
GO:0030182neuron differentiation0.0494434162419841



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.

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