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Coexpression cluster:C939: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0030902!hindbrain development!0.0428039440196433!4760$GO:0004143!diacylglycerol kinase activity!0.0428039440196433!375298$GO:0043010!camera-type eye development!0.0428039440196433!4760$GO:0007205!protein kinase C activation!0.0428039440196433!375298$GO:0001654!eye development!0.0428039440196433!4760$GO:0009952!anterior/posterior pattern formation!0.0428039440196433!4760$GO:0032147!activation of protein kinase activity!0.0428039440196433!375298$GO:0045165!cell fate commitment!0.0428039440196433!4760$GO:0007423!sensory organ development!0.0428039440196433!4760$GO:0003002!regionalization!0.0428039440196433!4760$GO:0007200!G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)!0.0428039440196433!375298$GO:0007389!pattern specification process!0.0436576993985432!4760$GO:0048015!phosphoinositide-mediated signaling!0.0436576993985432!375298$GO:0007420!brain development!0.0436576993985432!4760$GO:0045944!positive regulation of transcription from RNA polymerase II promoter!0.0436576993985432!4760$GO:0045860!positive regulation of protein kinase activity!0.0436576993985432!375298$GO:0033674!positive regulation of kinase activity!0.0436576993985432!375298$GO:0051347!positive regulation of transferase activity!0.0436576993985432!375298$GO:0032501!multicellular organismal process!0.0496195203628137!4760;375298$GO:0007601!visual perception!0.0496195203628137!375298$GO:0050953!sensory perception of light stimulus!0.0496195203628137!375298$GO:0045893!positive regulation of transcription, DNA-dependent!0.0496195203628137!4760$GO:0007417!central nervous system development!0.0496195203628137!4760$GO:0045859!regulation of protein kinase activity!0.0496195203628137!375298$GO:0043549!regulation of kinase activity!0.0496195203628137!375298$GO:0051338!regulation of transferase activity!0.0496195203628137!375298$GO:0043085!positive regulation of catalytic activity!0.0496195203628137!375298$GO:0019932!second-messenger-mediated signaling!0.0496195203628137!375298$GO:0003702!RNA polymerase II transcription factor activity!0.0496195203628137!4760$GO:0045941!positive regulation of transcription!0.0496195203628137!4760$GO:0045935!positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0497326468379995!4760
|gostat_on_coexpression_clusters=GO:0030902!hindbrain development!0.0428039440196433!4760$GO:0004143!diacylglycerol kinase activity!0.0428039440196433!375298$GO:0043010!camera-type eye development!0.0428039440196433!4760$GO:0007205!protein kinase C activation!0.0428039440196433!375298$GO:0001654!eye development!0.0428039440196433!4760$GO:0009952!anterior/posterior pattern formation!0.0428039440196433!4760$GO:0032147!activation of protein kinase activity!0.0428039440196433!375298$GO:0045165!cell fate commitment!0.0428039440196433!4760$GO:0007423!sensory organ development!0.0428039440196433!4760$GO:0003002!regionalization!0.0428039440196433!4760$GO:0007200!G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)!0.0428039440196433!375298$GO:0007389!pattern specification process!0.0436576993985432!4760$GO:0048015!phosphoinositide-mediated signaling!0.0436576993985432!375298$GO:0007420!brain development!0.0436576993985432!4760$GO:0045944!positive regulation of transcription from RNA polymerase II promoter!0.0436576993985432!4760$GO:0045860!positive regulation of protein kinase activity!0.0436576993985432!375298$GO:0033674!positive regulation of kinase activity!0.0436576993985432!375298$GO:0051347!positive regulation of transferase activity!0.0436576993985432!375298$GO:0032501!multicellular organismal process!0.0496195203628137!4760;375298$GO:0007601!visual perception!0.0496195203628137!375298$GO:0050953!sensory perception of light stimulus!0.0496195203628137!375298$GO:0045893!positive regulation of transcription, DNA-dependent!0.0496195203628137!4760$GO:0007417!central nervous system development!0.0496195203628137!4760$GO:0045859!regulation of protein kinase activity!0.0496195203628137!375298$GO:0043549!regulation of kinase activity!0.0496195203628137!375298$GO:0051338!regulation of transferase activity!0.0496195203628137!375298$GO:0043085!positive regulation of catalytic activity!0.0496195203628137!375298$GO:0019932!second-messenger-mediated signaling!0.0496195203628137!375298$GO:0003702!RNA polymerase II transcription factor activity!0.0496195203628137!4760$GO:0045941!positive regulation of transcription!0.0496195203628137!4760$GO:0045935!positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0497326468379995!4760
|id=C939
|id=C939
|ontology_enrichment_celltype=CL:0002319!4.73e-07!25
|ontology_enrichment_celltype=CL:0000540!3.93e-07!6;CL:0000031!3.93e-07!6;CL:0000404!3.93e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.08e-56!82;UBERON:0005743!1.33e-55!86;UBERON:0000073!6.12e-53!94;UBERON:0001016!6.12e-53!94;UBERON:0001049!1.22e-52!57;UBERON:0005068!1.22e-52!57;UBERON:0006241!1.22e-52!57;UBERON:0007135!1.22e-52!57;UBERON:0000955!8.28e-48!69;UBERON:0006238!8.28e-48!69;UBERON:0002616!5.88e-46!59;UBERON:0003075!7.11e-41!86;UBERON:0007284!7.11e-41!86;UBERON:0002780!2.48e-40!41;UBERON:0001890!2.48e-40!41;UBERON:0006240!2.48e-40!41;UBERON:0002346!3.95e-40!90;UBERON:0003080!3.96e-39!42;UBERON:0002619!2.01e-37!22;UBERON:0000956!4.58e-35!25;UBERON:0000203!4.58e-35!25;UBERON:0001950!4.03e-34!20;UBERON:0001893!2.93e-33!34;UBERON:0002020!3.99e-33!34;UBERON:0003528!3.99e-33!34;UBERON:0002791!8.34e-32!33;UBERON:0003056!3.62e-31!61;UBERON:0001869!6.38e-31!32;UBERON:0007023!6.02e-30!115;UBERON:0000924!3.80e-27!173;UBERON:0006601!3.80e-27!173;UBERON:0004121!4.23e-27!169;UBERON:0000153!1.31e-25!129;UBERON:0007811!1.31e-25!129;UBERON:0000033!2.44e-25!123;UBERON:0001871!2.61e-14!7;UBERON:0003076!3.72e-14!15;UBERON:0003057!3.72e-14!15;UBERON:0004733!3.40e-13!12;UBERON:0002028!3.40e-13!12;UBERON:0007277!3.40e-13!12;UBERON:0004732!5.48e-12!13;UBERON:0002680!9.60e-12!9;UBERON:0001895!9.60e-12!9;UBERON:0010092!9.60e-12!9;UBERON:0000200!1.19e-10!6;UBERON:0000349!1.48e-09!5;UBERON:0002021!2.59e-09!5;UBERON:0001872!3.03e-09!5;UBERON:0000025!3.39e-09!194;UBERON:0001894!2.19e-08!7;UBERON:0006222!2.19e-08!7;UBERON:0002037!6.46e-08!6;UBERON:0006215!6.46e-08!6;UBERON:0000064!7.28e-08!219;UBERON:0003296!9.03e-08!4;UBERON:0010133!9.03e-08!4;UBERON:0002298!6.14e-07!8
|ontology_enrichment_uberon=UBERON:0001017!1.86e-41!81;UBERON:0001016!1.51e-39!89;UBERON:0000073!1.94e-38!53;UBERON:0002616!1.94e-38!53;UBERON:0000955!4.39e-37!68;UBERON:0006238!4.39e-37!68;UBERON:0002619!2.13e-36!22;UBERON:0001049!4.14e-36!56;UBERON:0005068!4.14e-36!56;UBERON:0006241!4.14e-36!56;UBERON:0007135!4.14e-36!56;UBERON:0001950!7.52e-35!20;UBERON:0000956!8.39e-32!25;UBERON:0000203!8.39e-32!25;UBERON:0001869!1.53e-31!32;UBERON:0002780!1.26e-30!41;UBERON:0001890!1.26e-30!41;UBERON:0003080!1.26e-30!41;UBERON:0006240!1.26e-30!41;UBERON:0001893!1.63e-29!34;UBERON:0002791!8.26e-28!32;UBERON:0003075!1.22e-27!82;UBERON:0007284!1.22e-27!82;UBERON:0002346!4.39e-26!86;UBERON:0003528!5.22e-26!34;UBERON:0002020!5.22e-26!34;UBERON:0003056!3.39e-24!61;UBERON:0010371!1.97e-22!104;UBERON:0004121!2.99e-20!171;UBERON:0000924!2.99e-20!171;UBERON:0006601!2.99e-20!171;UBERON:0011216!2.74e-17!223;UBERON:0007023!1.11e-16!114;UBERON:0010314!2.39e-16!132;UBERON:0002021!1.84e-13!5;UBERON:0001872!2.92e-13!5;UBERON:0000200!4.89e-11!6;UBERON:0001905!7.90e-10!2;UBERON:0002757!7.90e-10!2;UBERON:0010134!7.90e-10!2;UBERON:0005408!7.90e-10!2;UBERON:0001899!7.90e-10!2;UBERON:0004733!6.61e-09!12;UBERON:0002028!6.61e-09!12;UBERON:0007277!6.61e-09!12;UBERON:0004732!3.39e-08!13;UBERON:0002108!4.10e-08!4;UBERON:0002680!4.68e-08!9;UBERON:0001895!4.68e-08!9;UBERON:0010092!4.68e-08!9;UBERON:0000349!5.12e-08!5;UBERON:0000477!7.34e-08!373;UBERON:0000025!1.24e-07!192;UBERON:0002037!1.76e-07!6;UBERON:0006215!1.76e-07!6;UBERON:0003076!4.66e-07!15;UBERON:0003057!4.66e-07!15;UBERON:0000064!7.76e-07!218
|tf_chipseq_enrich=ATF3#467;4:9.98363312267056:0.000412784327724188:0.00393203050010822!NRF1#4899;4:5.42679086564929:0.00404669891206852:0.0193681860445225!REST#5978;4:4.28890165161245:0.00945702594596283:0.0356705671122255!SUZ12#23512;2:11.1368402024584:0.0130543531390231:0.0463121569172334!TCF12#6938;4:4.72642884541619:0.00668035530260397:0.0284202870768119!USF2#7392;4:5.77430994891982:0.00322324100537492:0.016701332970845!ZNF263#10127;8:7.30830367734282:3.84008362723504e-07:1.8758395413695e-05
|tf_chipseq_enrich=ATF3#467;4:9.98363312267056:0.000412784327724188:0.00393203050010822!NRF1#4899;4:5.42679086564929:0.00404669891206852:0.0193681860445225!REST#5978;4:4.28890165161245:0.00945702594596283:0.0356705671122255!SUZ12#23512;2:11.1368402024584:0.0130543531390231:0.0463121569172334!TCF12#6938;4:4.72642884541619:0.00668035530260397:0.0284202870768119!USF2#7392;4:5.77430994891982:0.00322324100537492:0.016701332970845!ZNF263#10127;8:7.30830367734282:3.84008362723504e-07:1.8758395413695e-05
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}}
}}

Revision as of 16:53, 19 October 2012


Full id: C939_neuroblastoma_argyrophil_small_cerebellum_retinoblastoma_pineal_medulloblastoma



Phase1 CAGE Peaks

Hg19::chr2:182543057..182543068,-p1@GQ904713
Hg19::chr2:182543197..182543218,-p4@NEUROD1
Hg19::chr2:182543249..182543261,-p5@NEUROD1
Hg19::chr2:182543547..182543559,-p9@NEUROD1
Hg19::chr2:182545234..182545252,-p1@NEUROD1
Hg19::chr2:182545296..182545307,-p3@NEUROD1
Hg19::chr2:182545330..182545341,-p2@CERKL
Hg19::chr2:182545363..182545372,-p3@CERKL
Hg19::chr6:66194027..66194031,-p@chr6:66194027..66194031
-


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:0030902hindbrain development0.0428039440196433
GO:0004143diacylglycerol kinase activity0.0428039440196433
GO:0043010camera-type eye development0.0428039440196433
GO:0007205protein kinase C activation0.0428039440196433
GO:0001654eye development0.0428039440196433
GO:0009952anterior/posterior pattern formation0.0428039440196433
GO:0032147activation of protein kinase activity0.0428039440196433
GO:0045165cell fate commitment0.0428039440196433
GO:0007423sensory organ development0.0428039440196433
GO:0003002regionalization0.0428039440196433
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0428039440196433
GO:0007389pattern specification process0.0436576993985432
GO:0048015phosphoinositide-mediated signaling0.0436576993985432
GO:0007420brain development0.0436576993985432
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0436576993985432
GO:0045860positive regulation of protein kinase activity0.0436576993985432
GO:0033674positive regulation of kinase activity0.0436576993985432
GO:0051347positive regulation of transferase activity0.0436576993985432
GO:0032501multicellular organismal process0.0496195203628137
GO:0007601visual perception0.0496195203628137
GO:0050953sensory perception of light stimulus0.0496195203628137
GO:0045893positive regulation of transcription, DNA-dependent0.0496195203628137
GO:0007417central nervous system development0.0496195203628137
GO:0045859regulation of protein kinase activity0.0496195203628137
GO:0043549regulation of kinase activity0.0496195203628137
GO:0051338regulation of transferase activity0.0496195203628137
GO:0043085positive regulation of catalytic activity0.0496195203628137
GO:0019932second-messenger-mediated signaling0.0496195203628137
GO:0003702RNA polymerase II transcription factor activity0.0496195203628137
GO:0045941positive regulation of transcription0.0496195203628137
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0497326468379995



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
neuron3.93e-076
neuroblast3.93e-076
electrically signaling cell3.93e-076
Uber Anatomy
Ontology termp-valuen
central nervous system1.86e-4181
nervous system1.51e-3989
regional part of nervous system1.94e-3853
regional part of brain1.94e-3853
brain4.39e-3768
future brain4.39e-3768
regional part of cerebral cortex2.13e-3622
neural tube4.14e-3656
neural rod4.14e-3656
future spinal cord4.14e-3656
neural keel4.14e-3656
neocortex7.52e-3520
cerebral cortex8.39e-3225
pallium8.39e-3225
cerebral hemisphere1.53e-3132
regional part of forebrain1.26e-3041
forebrain1.26e-3041
anterior neural tube1.26e-3041
future forebrain1.26e-3041
telencephalon1.63e-2934
regional part of telencephalon8.26e-2832
neural plate1.22e-2782
presumptive neural plate1.22e-2782
neurectoderm4.39e-2686
brain grey matter5.22e-2634
gray matter5.22e-2634
pre-chordal neural plate3.39e-2461
ecto-epithelium1.97e-22104
ectoderm-derived structure2.99e-20171
ectoderm2.99e-20171
presumptive ectoderm2.99e-20171
organ system subdivision2.74e-17223
adult organism1.11e-16114
structure with developmental contribution from neural crest2.39e-16132
occipital lobe1.84e-135
parietal lobe2.92e-135
gyrus4.89e-116
pineal body7.90e-102
regional part of epithalamus7.90e-102
secretory circumventricular organ7.90e-102
circumventricular organ7.90e-102
epithalamus7.90e-102
segmental subdivision of hindbrain6.61e-0912
hindbrain6.61e-0912
presumptive hindbrain6.61e-0912
segmental subdivision of nervous system3.39e-0813
small intestine4.10e-084
regional part of metencephalon4.68e-089
metencephalon4.68e-089
future metencephalon4.68e-089
limbic system5.12e-085
anatomical cluster7.34e-08373
tube1.24e-07192
cerebellum1.76e-076
rhombic lip1.76e-076
posterior neural tube4.66e-0715
chordal neural plate4.66e-0715
organ part7.76e-07218


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#46749.983633122670560.0004127843277241880.00393203050010822
NRF1#489945.426790865649290.004046698912068520.0193681860445225
REST#597844.288901651612450.009457025945962830.0356705671122255
SUZ12#23512211.13684020245840.01305435313902310.0463121569172334
TCF12#693844.726428845416190.006680355302603970.0284202870768119
USF2#739245.774309948919820.003223241005374920.016701332970845
ZNF263#1012787.308303677342823.84008362723504e-071.8758395413695e-05



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.