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Coexpression cluster:C4709: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0030326!embryonic limb morphogenesis!1.67356575388897e-05!1750;1749$GO:0035113!embryonic appendage morphogenesis!1.67356575388897e-05!1750;1749$GO:0048736!appendage development!1.67356575388897e-05!1750;1749$GO:0060173!limb development!1.67356575388897e-05!1750;1749$GO:0035107!appendage morphogenesis!1.67356575388897e-05!1750;1749$GO:0035108!limb morphogenesis!1.67356575388897e-05!1750;1749$GO:0048598!embryonic morphogenesis!9.21430411214545e-05!1750;1749$GO:0001501!skeletal development!0.000409646680478949!1750;1749$GO:0009790!embryonic development!0.000460607511543315!1750;1749$GO:0045669!positive regulation of osteoblast differentiation!0.00256078176098444!1749$GO:0007399!nervous system development!0.00350845721558526!1750;1749$GO:0045667!regulation of osteoblast differentiation!0.00426765549395418!1749$GO:0043565!sequence-specific DNA binding!0.00440434259482924!1750;1749$GO:0009653!anatomical structure morphogenesis!0.0058971223235539!1750;1749$GO:0048513!organ development!0.00653715891505568!1750;1749$GO:0001649!osteoblast differentiation!0.0080000871954273!1749$GO:0042472!inner ear morphogenesis!0.00813161387655096!1749$GO:0042471!ear morphogenesis!0.0088170948994528!1749$GO:0003700!transcription factor activity!0.00890942448432714!1750;1749$GO:0048731!system development!0.00926308952311787!1750;1749$GO:0048839!inner ear development!0.00926308952311787!1749$GO:0043583!ear development!0.00977220537817819!1749$GO:0045597!positive regulation of cell differentiation!0.0104593336467374!1749$GO:0048856!anatomical structure development!0.0126209096667435!1750;1749$GO:0051094!positive regulation of developmental process!0.0139177346613956!1749$GO:0007275!multicellular organismal development!0.0153181195105723!1750;1749$GO:0007423!sensory organ development!0.0155223093697608!1749$GO:0031214!biomineral formation!0.0155223093697608!1749$GO:0001503!ossification!0.0155223093697608!1749$GO:0046849!bone remodeling!0.0163670509123034!1749$GO:0048771!tissue remodeling!0.0173216973689242!1749$GO:0007409!axonogenesis!0.0180455087640718!1749$GO:0048667!neuron morphogenesis during differentiation!0.0180455087640718!1749$GO:0048812!neurite morphogenesis!0.0180455087640718!1749$GO:0000904!cellular morphogenesis during differentiation!0.0184047906051062!1749$GO:0031175!neurite development!0.019169112608058!1749$GO:0045595!regulation of cell differentiation!0.0198917898403947!1749$GO:0048666!neuron development!0.0207102889155031!1749$GO:0032502!developmental process!0.0212452500808942!1750;1749$GO:0006355!regulation of transcription, DNA-dependent!0.0212452500808942!1750;1749$GO:0006351!transcription, DNA-dependent!0.0212833840104711!1750;1749$GO:0032774!RNA biosynthetic process!0.0212833840104711!1750;1749$GO:0003677!DNA binding!0.0212936828766488!1750;1749$GO:0045449!regulation of transcription!0.0212936828766488!1750;1749$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0212936828766488!1750;1749$GO:0032990!cell part morphogenesis!0.0212936828766488!1749$GO:0030030!cell projection organization and biogenesis!0.0212936828766488!1749$GO:0048858!cell projection morphogenesis!0.0212936828766488!1749$GO:0030182!neuron differentiation!0.0212936828766488!1749$GO:0006350!transcription!0.0212936828766488!1750;1749$GO:0032501!multicellular organismal process!0.0212936828766488!1750;1749$GO:0010468!regulation of gene expression!0.0212936828766488!1750;1749$GO:0031323!regulation of cellular metabolic process!0.0219963890198013!1750;1749$GO:0050793!regulation of developmental process!0.0223070232679849!1749$GO:0048699!generation of neurons!0.0224562671377371!1749$GO:0019222!regulation of metabolic process!0.022827190887131!1750;1749$GO:0016070!RNA metabolic process!0.022827190887131!1750;1749$GO:0022008!neurogenesis!0.0230478209014503!1749$GO:0009888!tissue development!0.0263589672780351!1749$GO:0009887!organ morphogenesis!0.0307377263448293!1749$GO:0010467!gene expression!0.0367545070308573!1750;1749$GO:0000902!cell morphogenesis!0.0383171077563499!1749$GO:0032989!cellular structure morphogenesis!0.0383171077563499!1749$GO:0050794!regulation of cellular process!0.0383171077563499!1750;1749$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0396567305998326!1750;1749$GO:0005634!nucleus!0.0419114525788757!1750;1749$GO:0050789!regulation of biological process!0.0424112436476964!1750;1749$GO:0003676!nucleic acid binding!0.0450760257742571!1750;1749$GO:0065007!biological regulation!0.049492041671133!1750;1749
|gostat_on_coexpression_clusters=GO:0030326!embryonic limb morphogenesis!1.67356575388897e-05!1750;1749$GO:0035113!embryonic appendage morphogenesis!1.67356575388897e-05!1750;1749$GO:0048736!appendage development!1.67356575388897e-05!1750;1749$GO:0060173!limb development!1.67356575388897e-05!1750;1749$GO:0035107!appendage morphogenesis!1.67356575388897e-05!1750;1749$GO:0035108!limb morphogenesis!1.67356575388897e-05!1750;1749$GO:0048598!embryonic morphogenesis!9.21430411214545e-05!1750;1749$GO:0001501!skeletal development!0.000409646680478949!1750;1749$GO:0009790!embryonic development!0.000460607511543315!1750;1749$GO:0045669!positive regulation of osteoblast differentiation!0.00256078176098444!1749$GO:0007399!nervous system development!0.00350845721558526!1750;1749$GO:0045667!regulation of osteoblast differentiation!0.00426765549395418!1749$GO:0043565!sequence-specific DNA binding!0.00440434259482924!1750;1749$GO:0009653!anatomical structure morphogenesis!0.0058971223235539!1750;1749$GO:0048513!organ development!0.00653715891505568!1750;1749$GO:0001649!osteoblast differentiation!0.0080000871954273!1749$GO:0042472!inner ear morphogenesis!0.00813161387655096!1749$GO:0042471!ear morphogenesis!0.0088170948994528!1749$GO:0003700!transcription factor activity!0.00890942448432714!1750;1749$GO:0048731!system development!0.00926308952311787!1750;1749$GO:0048839!inner ear development!0.00926308952311787!1749$GO:0043583!ear development!0.00977220537817819!1749$GO:0045597!positive regulation of cell differentiation!0.0104593336467374!1749$GO:0048856!anatomical structure development!0.0126209096667435!1750;1749$GO:0051094!positive regulation of developmental process!0.0139177346613956!1749$GO:0007275!multicellular organismal development!0.0153181195105723!1750;1749$GO:0007423!sensory organ development!0.0155223093697608!1749$GO:0031214!biomineral formation!0.0155223093697608!1749$GO:0001503!ossification!0.0155223093697608!1749$GO:0046849!bone remodeling!0.0163670509123034!1749$GO:0048771!tissue remodeling!0.0173216973689242!1749$GO:0007409!axonogenesis!0.0180455087640718!1749$GO:0048667!neuron morphogenesis during differentiation!0.0180455087640718!1749$GO:0048812!neurite morphogenesis!0.0180455087640718!1749$GO:0000904!cellular morphogenesis during differentiation!0.0184047906051062!1749$GO:0031175!neurite development!0.019169112608058!1749$GO:0045595!regulation of cell differentiation!0.0198917898403947!1749$GO:0048666!neuron development!0.0207102889155031!1749$GO:0032502!developmental process!0.0212452500808942!1750;1749$GO:0006355!regulation of transcription, DNA-dependent!0.0212452500808942!1750;1749$GO:0006351!transcription, DNA-dependent!0.0212833840104711!1750;1749$GO:0032774!RNA biosynthetic process!0.0212833840104711!1750;1749$GO:0003677!DNA binding!0.0212936828766488!1750;1749$GO:0045449!regulation of transcription!0.0212936828766488!1750;1749$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0212936828766488!1750;1749$GO:0032990!cell part morphogenesis!0.0212936828766488!1749$GO:0030030!cell projection organization and biogenesis!0.0212936828766488!1749$GO:0048858!cell projection morphogenesis!0.0212936828766488!1749$GO:0030182!neuron differentiation!0.0212936828766488!1749$GO:0006350!transcription!0.0212936828766488!1750;1749$GO:0032501!multicellular organismal process!0.0212936828766488!1750;1749$GO:0010468!regulation of gene expression!0.0212936828766488!1750;1749$GO:0031323!regulation of cellular metabolic process!0.0219963890198013!1750;1749$GO:0050793!regulation of developmental process!0.0223070232679849!1749$GO:0048699!generation of neurons!0.0224562671377371!1749$GO:0019222!regulation of metabolic process!0.022827190887131!1750;1749$GO:0016070!RNA metabolic process!0.022827190887131!1750;1749$GO:0022008!neurogenesis!0.0230478209014503!1749$GO:0009888!tissue development!0.0263589672780351!1749$GO:0009887!organ morphogenesis!0.0307377263448293!1749$GO:0010467!gene expression!0.0367545070308573!1750;1749$GO:0000902!cell morphogenesis!0.0383171077563499!1749$GO:0032989!cellular structure morphogenesis!0.0383171077563499!1749$GO:0050794!regulation of cellular process!0.0383171077563499!1750;1749$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0396567305998326!1750;1749$GO:0005634!nucleus!0.0419114525788757!1750;1749$GO:0050789!regulation of biological process!0.0424112436476964!1750;1749$GO:0003676!nucleic acid binding!0.0450760257742571!1750;1749$GO:0065007!biological regulation!0.049492041671133!1750;1749
|id=C4709
|id=C4709
|ontology_enrichment_celltype=CL:0000062!1.11e-13!11;CL:0000375!1.11e-13!11;CL:0000335!1.11e-13!11;CL:0000035!7.03e-09!20
|ontology_enrichment_celltype=CL:0000062!1.52e-19!11;CL:0000375!1.52e-19!11;CL:0000335!1.52e-19!11;CL:0000035!1.10e-12!20;CL:0000047!4.39e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 16:11, 19 October 2012


Full id: C4709_Osteoblast_anaplastic_neuroblastoma_gastric_osteosarcoma_small_temporal



Phase1 CAGE Peaks

Hg19::chr7:96635329..96635357,+p9@DLX6
Hg19::chr7:96651945..96651968,-p@chr7:96651945..96651968
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Hg19::chr7:96654015..96654018,-p3@DLX5


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:0030326embryonic limb morphogenesis1.67356575388897e-05
GO:0035113embryonic appendage morphogenesis1.67356575388897e-05
GO:0048736appendage development1.67356575388897e-05
GO:0060173limb development1.67356575388897e-05
GO:0035107appendage morphogenesis1.67356575388897e-05
GO:0035108limb morphogenesis1.67356575388897e-05
GO:0048598embryonic morphogenesis9.21430411214545e-05
GO:0001501skeletal development0.000409646680478949
GO:0009790embryonic development0.000460607511543315
GO:0045669positive regulation of osteoblast differentiation0.00256078176098444
GO:0007399nervous system development0.00350845721558526
GO:0045667regulation of osteoblast differentiation0.00426765549395418
GO:0043565sequence-specific DNA binding0.00440434259482924
GO:0009653anatomical structure morphogenesis0.0058971223235539
GO:0048513organ development0.00653715891505568
GO:0001649osteoblast differentiation0.0080000871954273
GO:0042472inner ear morphogenesis0.00813161387655096
GO:0042471ear morphogenesis0.0088170948994528
GO:0003700transcription factor activity0.00890942448432714
GO:0048731system development0.00926308952311787
GO:0048839inner ear development0.00926308952311787
GO:0043583ear development0.00977220537817819
GO:0045597positive regulation of cell differentiation0.0104593336467374
GO:0048856anatomical structure development0.0126209096667435
GO:0051094positive regulation of developmental process0.0139177346613956
GO:0007275multicellular organismal development0.0153181195105723
GO:0007423sensory organ development0.0155223093697608
GO:0031214biomineral formation0.0155223093697608
GO:0001503ossification0.0155223093697608
GO:0046849bone remodeling0.0163670509123034
GO:0048771tissue remodeling0.0173216973689242
GO:0007409axonogenesis0.0180455087640718
GO:0048667neuron morphogenesis during differentiation0.0180455087640718
GO:0048812neurite morphogenesis0.0180455087640718
GO:0000904cellular morphogenesis during differentiation0.0184047906051062
GO:0031175neurite development0.019169112608058
GO:0045595regulation of cell differentiation0.0198917898403947
GO:0048666neuron development0.0207102889155031
GO:0032502developmental process0.0212452500808942
GO:0006355regulation of transcription, DNA-dependent0.0212452500808942
GO:0006351transcription, DNA-dependent0.0212833840104711
GO:0032774RNA biosynthetic process0.0212833840104711
GO:0003677DNA binding0.0212936828766488
GO:0045449regulation of transcription0.0212936828766488
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0212936828766488
GO:0032990cell part morphogenesis0.0212936828766488
GO:0030030cell projection organization and biogenesis0.0212936828766488
GO:0048858cell projection morphogenesis0.0212936828766488
GO:0030182neuron differentiation0.0212936828766488
GO:0006350transcription0.0212936828766488
GO:0032501multicellular organismal process0.0212936828766488
GO:0010468regulation of gene expression0.0212936828766488
GO:0031323regulation of cellular metabolic process0.0219963890198013
GO:0050793regulation of developmental process0.0223070232679849
GO:0048699generation of neurons0.0224562671377371
GO:0019222regulation of metabolic process0.022827190887131
GO:0016070RNA metabolic process0.022827190887131
GO:0022008neurogenesis0.0230478209014503
GO:0009888tissue development0.0263589672780351
GO:0009887organ morphogenesis0.0307377263448293
GO:0010467gene expression0.0367545070308573
GO:0000902cell morphogenesis0.0383171077563499
GO:0032989cellular structure morphogenesis0.0383171077563499
GO:0050794regulation of cellular process0.0383171077563499
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0396567305998326
GO:0005634nucleus0.0419114525788757
GO:0050789regulation of biological process0.0424112436476964
GO:0003676nucleic acid binding0.0450760257742571
GO:0065007biological regulation0.049492041671133



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
osteoblast1.52e-1911
osteoprogenitor cell1.52e-1911
mesenchyme condensation cell1.52e-1911
single fate stem cell1.10e-1220
neuronal stem cell4.39e-078
Uber Anatomy
Ontology termp-valuen
cerebral hemisphere6.07e-2732
telencephalon3.87e-2534
regional part of telencephalon6.97e-2432
regional part of forebrain1.47e-2241
forebrain1.47e-2241
anterior neural tube1.47e-2241
future forebrain1.47e-2241
brain grey matter2.85e-2234
gray matter2.85e-2234
nervous system1.43e-1889
central nervous system1.10e-1781
telencephalic nucleus1.15e-167
regional part of nervous system1.76e-1653
regional part of brain1.76e-1653
neural tube2.30e-1556
neural rod2.30e-1556
future spinal cord2.30e-1556
neural keel2.30e-1556
regional part of cerebral cortex2.64e-1422
corpus striatum7.58e-144
striatum7.58e-144
ventral part of telencephalon7.58e-144
future corpus striatum7.58e-144
pre-chordal neural plate9.49e-1461
neocortex3.89e-1320
brain4.27e-1368
future brain4.27e-1368
basal ganglion8.33e-139
neural nucleus8.33e-139
nuclear complex of neuraxis8.33e-139
nucleus of brain8.33e-139
aggregate regional part of brain8.33e-139
collection of basal ganglia8.33e-139
cerebral subcortex8.33e-139
cerebral cortex2.18e-1225
pallium2.18e-1225
caudate-putamen6.71e-113
dorsal striatum6.71e-113
ectoderm-derived structure6.23e-10171
ectoderm6.23e-10171
presumptive ectoderm6.23e-10171
neural plate3.91e-0982
presumptive neural plate3.91e-0982
organ system subdivision1.02e-08223
adult organism1.07e-08114
neurectoderm1.62e-0886
caudate nucleus8.31e-082
future caudate nucleus8.31e-082
globus pallidus2.03e-072
pallidum2.03e-072
ecto-epithelium3.09e-07104


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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