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Coexpression cluster:C740: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0060163!subpallium neuron fate commitment!0.00152646717464803!429$GO:0014017!neuroblast fate commitment!0.00152646717464803!429$GO:0014016!neuroblast differentiation!0.00152646717464803!429$GO:0007400!neuroblast fate determination!0.00152646717464803!429$GO:0060165!regulation of timing of subpallium neuron differentiation!0.00152646717464803!429$GO:0060164!regulation of timing of neuron differentiation!0.00152646717464803!429$GO:0004608!phosphatidylethanolamine N-methyltransferase activity!0.00152646717464803!10400$GO:0021544!subpallium development!0.00400674043006203!429$GO:0048505!regulation of timing of cell differentiation!0.00427373064729577!429$GO:0040034!regulation of development, heterochronic!0.00427373064729577!429$GO:0006656!phosphatidylcholine biosynthetic process!0.00485636913446346!10400$GO:0046470!phosphatidylcholine metabolic process!0.00623197345720764!10400$GO:0021537!telencephalon development!0.0090387212307888!429$GO:0048663!neuron fate commitment!0.0106811816718229!429$GO:0008283!cell proliferation!0.0113477532025367!10400;429$GO:0007405!neuroblast proliferation!0.0113477532025367!429$GO:0045664!regulation of neuron differentiation!0.0162956577304724!429$GO:0010001!glial cell differentiation!0.0162956577304724!429$GO:0001709!cell fate determination!0.0162956577304724!429$GO:0042063!gliogenesis!0.0182987399358394!429$GO:0001764!neuron migration!0.0182987399358394!429$GO:0030900!forebrain development!0.0213397299517958!429$GO:0046474!glycerophospholipid biosynthetic process!0.0213397299517958!10400$GO:0008170!N-methyltransferase activity!0.0213397299517958!10400$GO:0007219!Notch signaling pathway!0.0213397299517958!429$GO:0045165!cell fate commitment!0.0291189221451797!429$GO:0008757!S-adenosylmethionine-dependent methyltransferase activity!0.0339494755587485!10400$GO:0008654!phospholipid biosynthetic process!0.0350147803328724!10400$GO:0006650!glycerophospholipid metabolic process!0.0371047763843612!10400$GO:0046467!membrane lipid biosynthetic process!0.0401153013644764!10400$GO:0007389!pattern specification process!0.0425865120099492!429$GO:0007420!brain development!0.0462258483643068!429$GO:0045595!regulation of cell differentiation!0.0464306336375757!429$GO:0048666!neuron development!0.0481803368997648!429
|gostat_on_coexpression_clusters=GO:0060163!subpallium neuron fate commitment!0.00152646717464803!429$GO:0014017!neuroblast fate commitment!0.00152646717464803!429$GO:0014016!neuroblast differentiation!0.00152646717464803!429$GO:0007400!neuroblast fate determination!0.00152646717464803!429$GO:0060165!regulation of timing of subpallium neuron differentiation!0.00152646717464803!429$GO:0060164!regulation of timing of neuron differentiation!0.00152646717464803!429$GO:0004608!phosphatidylethanolamine N-methyltransferase activity!0.00152646717464803!10400$GO:0021544!subpallium development!0.00400674043006203!429$GO:0048505!regulation of timing of cell differentiation!0.00427373064729577!429$GO:0040034!regulation of development, heterochronic!0.00427373064729577!429$GO:0006656!phosphatidylcholine biosynthetic process!0.00485636913446346!10400$GO:0046470!phosphatidylcholine metabolic process!0.00623197345720764!10400$GO:0021537!telencephalon development!0.0090387212307888!429$GO:0048663!neuron fate commitment!0.0106811816718229!429$GO:0008283!cell proliferation!0.0113477532025367!10400;429$GO:0007405!neuroblast proliferation!0.0113477532025367!429$GO:0045664!regulation of neuron differentiation!0.0162956577304724!429$GO:0010001!glial cell differentiation!0.0162956577304724!429$GO:0001709!cell fate determination!0.0162956577304724!429$GO:0042063!gliogenesis!0.0182987399358394!429$GO:0001764!neuron migration!0.0182987399358394!429$GO:0030900!forebrain development!0.0213397299517958!429$GO:0046474!glycerophospholipid biosynthetic process!0.0213397299517958!10400$GO:0008170!N-methyltransferase activity!0.0213397299517958!10400$GO:0007219!Notch signaling pathway!0.0213397299517958!429$GO:0045165!cell fate commitment!0.0291189221451797!429$GO:0008757!S-adenosylmethionine-dependent methyltransferase activity!0.0339494755587485!10400$GO:0008654!phospholipid biosynthetic process!0.0350147803328724!10400$GO:0006650!glycerophospholipid metabolic process!0.0371047763843612!10400$GO:0046467!membrane lipid biosynthetic process!0.0401153013644764!10400$GO:0007389!pattern specification process!0.0425865120099492!429$GO:0007420!brain development!0.0462258483643068!429$GO:0045595!regulation of cell differentiation!0.0464306336375757!429$GO:0048666!neuron development!0.0481803368997648!429
|id=C740
|id=C740
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0000080!2.77e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!6.40e-40!82;UBERON:0005743!3.93e-38!86;UBERON:0001049!5.56e-38!57;UBERON:0005068!5.56e-38!57;UBERON:0006241!5.56e-38!57;UBERON:0007135!5.56e-38!57;UBERON:0007023!8.04e-38!115;UBERON:0000073!1.83e-37!94;UBERON:0001016!1.83e-37!94;UBERON:0000955!1.09e-31!69;UBERON:0006238!1.09e-31!69;UBERON:0002780!1.87e-30!41;UBERON:0001890!1.87e-30!41;UBERON:0006240!1.87e-30!41;UBERON:0002616!2.19e-30!59;UBERON:0003080!2.84e-29!42;UBERON:0003075!3.73e-29!86;UBERON:0007284!3.73e-29!86;UBERON:0002346!1.20e-27!90;UBERON:0002020!1.90e-25!34;UBERON:0003528!1.90e-25!34;UBERON:0001893!2.62e-25!34;UBERON:0002791!1.05e-24!33;UBERON:0001869!6.71e-24!32;UBERON:0003056!2.10e-22!61;UBERON:0000956!1.72e-19!25;UBERON:0000203!1.72e-19!25;UBERON:0004121!9.18e-19!169;UBERON:0000924!3.33e-18!173;UBERON:0006601!3.33e-18!173;UBERON:0002619!6.88e-18!22;UBERON:0000153!1.44e-16!129;UBERON:0007811!1.44e-16!129;UBERON:0001950!1.53e-16!20;UBERON:0000033!1.82e-15!123;UBERON:0000064!1.33e-12!219;UBERON:0000025!1.01e-09!194;UBERON:0003076!1.04e-09!15;UBERON:0003057!1.04e-09!15;UBERON:0000475!5.90e-09!365;UBERON:0000481!1.49e-08!347;UBERON:0004732!4.47e-08!13;UBERON:0000483!6.14e-08!309;UBERON:0000119!1.48e-07!312;UBERON:0002308!2.18e-07!9;UBERON:0000125!2.18e-07!9;UBERON:0001871!2.21e-07!7;UBERON:0004733!2.23e-07!12;UBERON:0002028!2.23e-07!12;UBERON:0007277!2.23e-07!12;UBERON:0002420!2.64e-07!9;UBERON:0007245!2.64e-07!9;UBERON:0010009!2.64e-07!9;UBERON:0010011!2.64e-07!9;UBERON:0000454!2.64e-07!9
|ontology_enrichment_uberon=UBERON:0001049!1.07e-30!56;UBERON:0005068!1.07e-30!56;UBERON:0006241!1.07e-30!56;UBERON:0007135!1.07e-30!56;UBERON:0001017!1.19e-23!81;UBERON:0000073!1.51e-23!53;UBERON:0002616!1.51e-23!53;UBERON:0001016!6.35e-23!89;UBERON:0003075!1.77e-21!82;UBERON:0007284!1.77e-21!82;UBERON:0002346!3.06e-20!86;UBERON:0000955!3.46e-19!68;UBERON:0006238!3.46e-19!68;UBERON:0002780!4.04e-19!41;UBERON:0001890!4.04e-19!41;UBERON:0003080!4.04e-19!41;UBERON:0006240!4.04e-19!41;UBERON:0010371!1.49e-17!104;UBERON:0001893!1.21e-14!34;UBERON:0002240!3.45e-14!3;UBERON:0005174!3.45e-14!3;UBERON:0001137!3.45e-14!3;UBERON:0003056!1.11e-13!61;UBERON:0003076!3.04e-13!15;UBERON:0003057!3.04e-13!15;UBERON:0002619!3.10e-13!22;UBERON:0002791!3.84e-13!32;UBERON:0001869!3.84e-13!32;UBERON:0007023!1.26e-12!114;UBERON:0003528!2.88e-12!34;UBERON:0002020!2.88e-12!34;UBERON:0001950!1.49e-11!20;UBERON:0000956!1.58e-11!25;UBERON:0000203!1.58e-11!25;UBERON:0004121!1.64e-11!171;UBERON:0000924!1.64e-11!171;UBERON:0006601!1.64e-11!171;UBERON:0010314!2.13e-11!132;UBERON:0011216!5.90e-11!223;UBERON:0000007!4.34e-10!2;UBERON:0000025!5.52e-08!192;UBERON:0002298!7.58e-07!6;UBERON:0000200!7.73e-07!6
|tf_chipseq_enrich=CTBP2#1488;2:11.4030909707869:0.0127037060978319:0.0458357756218981!SPI1#6688;5:3.72923795841942:0.00657139769228244:0.0280848796326998!SUZ12#23512;4:18.2239203312956:4.66826240794143e-05:0.000816664418128969
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}}
}}

Revision as of 16:39, 19 October 2012


Full id: C740_gastrointestinal_smallcell_small_nonsmall_neuroblastoma_temporal_somatostatinoma



Phase1 CAGE Peaks

Hg19::chr11:60466937..60466947,+p6@MS4A8B
Hg19::chr12:103351444..103351461,+p1@ASCL1
Hg19::chr12:103351694..103351704,+p6@ASCL1
Hg19::chr12:103352731..103352740,+p@chr12:103352731..103352740
+
Hg19::chr12:103353138..103353168,+p@chr12:103353138..103353168
+
Hg19::chr12:103353295..103353316,-p@chr12:103353295..103353316
-
Hg19::chr12:103353566..103353596,+p@chr12:103353566..103353596
+
Hg19::chr16:67219381..67219395,-p@chr16:67219381..67219395
-
Hg19::chr17:17421463..17421482,-p5@PEMT
Hg19::chr19:13743837..13743844,-p@chr19:13743837..13743844
-
Hg19::chr1:246383189..246383211,-p@chr1:246383189..246383211
-


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:0060163subpallium neuron fate commitment0.00152646717464803
GO:0014017neuroblast fate commitment0.00152646717464803
GO:0014016neuroblast differentiation0.00152646717464803
GO:0007400neuroblast fate determination0.00152646717464803
GO:0060165regulation of timing of subpallium neuron differentiation0.00152646717464803
GO:0060164regulation of timing of neuron differentiation0.00152646717464803
GO:0004608phosphatidylethanolamine N-methyltransferase activity0.00152646717464803
GO:0021544subpallium development0.00400674043006203
GO:0048505regulation of timing of cell differentiation0.00427373064729577
GO:0040034regulation of development, heterochronic0.00427373064729577
GO:0006656phosphatidylcholine biosynthetic process0.00485636913446346
GO:0046470phosphatidylcholine metabolic process0.00623197345720764
GO:0021537telencephalon development0.0090387212307888
GO:0048663neuron fate commitment0.0106811816718229
GO:0008283cell proliferation0.0113477532025367
GO:0007405neuroblast proliferation0.0113477532025367
GO:0045664regulation of neuron differentiation0.0162956577304724
GO:0010001glial cell differentiation0.0162956577304724
GO:0001709cell fate determination0.0162956577304724
GO:0042063gliogenesis0.0182987399358394
GO:0001764neuron migration0.0182987399358394
GO:0030900forebrain development0.0213397299517958
GO:0046474glycerophospholipid biosynthetic process0.0213397299517958
GO:0008170N-methyltransferase activity0.0213397299517958
GO:0007219Notch signaling pathway0.0213397299517958
GO:0045165cell fate commitment0.0291189221451797
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0339494755587485
GO:0008654phospholipid biosynthetic process0.0350147803328724
GO:0006650glycerophospholipid metabolic process0.0371047763843612
GO:0046467membrane lipid biosynthetic process0.0401153013644764
GO:0007389pattern specification process0.0425865120099492
GO:0007420brain development0.0462258483643068
GO:0045595regulation of cell differentiation0.0464306336375757
GO:0048666neuron development0.0481803368997648



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
circulating cell2.77e-076
Uber Anatomy
Ontology termp-valuen
neural tube1.07e-3056
neural rod1.07e-3056
future spinal cord1.07e-3056
neural keel1.07e-3056
central nervous system1.19e-2381
regional part of nervous system1.51e-2353
regional part of brain1.51e-2353
nervous system6.35e-2389
neural plate1.77e-2182
presumptive neural plate1.77e-2182
neurectoderm3.06e-2086
brain3.46e-1968
future brain3.46e-1968
regional part of forebrain4.04e-1941
forebrain4.04e-1941
anterior neural tube4.04e-1941
future forebrain4.04e-1941
ecto-epithelium1.49e-17104
telencephalon1.21e-1434
spinal cord3.45e-143
dorsal region element3.45e-143
dorsum3.45e-143
pre-chordal neural plate1.11e-1361
posterior neural tube3.04e-1315
chordal neural plate3.04e-1315
regional part of cerebral cortex3.10e-1322
regional part of telencephalon3.84e-1332
cerebral hemisphere3.84e-1332
adult organism1.26e-12114
brain grey matter2.88e-1234
gray matter2.88e-1234
neocortex1.49e-1120
cerebral cortex1.58e-1125
pallium1.58e-1125
ectoderm-derived structure1.64e-11171
ectoderm1.64e-11171
presumptive ectoderm1.64e-11171
structure with developmental contribution from neural crest2.13e-11132
organ system subdivision5.90e-11223
pituitary gland4.34e-102
tube5.52e-08192
brainstem7.58e-076
gyrus7.73e-076


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)

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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
CTBP2#1488211.40309097078690.01270370609783190.0458357756218981
SPI1#668853.729237958419420.006571397692282440.0280848796326998
SUZ12#23512418.22392033129564.66826240794143e-050.000816664418128969



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.