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Coexpression cluster:C3681: Difference between revisions

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|id=C3681
|id=C3681
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:171!3.48e-08!10
|ontology_enrichment_disease=DOID:171!4.85e-09!10
|ontology_enrichment_uberon=UBERON:0001049!3.59e-56!57;UBERON:0005068!3.59e-56!57;UBERON:0006241!3.59e-56!57;UBERON:0007135!3.59e-56!57;UBERON:0002346!1.24e-53!90;UBERON:0000073!6.61e-53!94;UBERON:0001016!6.61e-53!94;UBERON:0003075!1.66e-50!86;UBERON:0007284!1.66e-50!86;UBERON:0005743!2.00e-48!86;UBERON:0002616!7.04e-48!59;UBERON:0001017!2.10e-47!82;UBERON:0000955!6.26e-45!69;UBERON:0006238!6.26e-45!69;UBERON:0002780!5.61e-39!41;UBERON:0001890!5.61e-39!41;UBERON:0006240!5.61e-39!41;UBERON:0003080!8.17e-38!42;UBERON:0007023!2.28e-37!115;UBERON:0003056!3.01e-35!61;UBERON:0002020!1.47e-33!34;UBERON:0003528!1.47e-33!34;UBERON:0001893!1.68e-33!34;UBERON:0000924!6.80e-33!173;UBERON:0006601!6.80e-33!173;UBERON:0002791!6.31e-32!33;UBERON:0004121!2.03e-30!169;UBERON:0001869!4.26e-30!32;UBERON:0000033!1.56e-28!123;UBERON:0000153!1.83e-26!129;UBERON:0007811!1.83e-26!129;UBERON:0002619!7.76e-23!22;UBERON:0001950!8.48e-20!20;UBERON:0000956!1.53e-19!25;UBERON:0000203!1.53e-19!25;UBERON:0003076!3.64e-19!15;UBERON:0003057!3.64e-19!15;UBERON:0002308!7.96e-17!9;UBERON:0000125!7.96e-17!9;UBERON:0000025!3.10e-16!194;UBERON:0004732!5.67e-16!13;UBERON:0004733!3.28e-14!12;UBERON:0002028!3.28e-14!12;UBERON:0007277!3.28e-14!12;UBERON:0000119!5.10e-14!312;UBERON:0000483!1.07e-13!309;UBERON:0009663!2.77e-13!7;UBERON:0002420!6.18e-13!9;UBERON:0007245!6.18e-13!9;UBERON:0010009!6.18e-13!9;UBERON:0010011!6.18e-13!9;UBERON:0000454!6.18e-13!9;UBERON:0002298!4.34e-12!8;UBERON:0000200!2.48e-11!6;UBERON:0004111!3.63e-11!241;UBERON:0000477!1.49e-10!286;UBERON:0000475!9.21e-10!365;UBERON:0002680!2.55e-09!9;UBERON:0001895!2.55e-09!9;UBERON:0010092!2.55e-09!9;UBERON:0000064!5.15e-09!219;UBERON:0000369!7.73e-08!4;UBERON:0002435!7.73e-08!4;UBERON:0000204!7.73e-08!4;UBERON:0010082!7.73e-08!4;UBERON:0000062!2.31e-07!511;UBERON:0000922!2.49e-07!612;UBERON:0006331!5.00e-07!3;UBERON:0000988!5.51e-07!3;UBERON:0001896!6.92e-07!3;UBERON:0005290!6.92e-07!3;UBERON:0010096!6.92e-07!3;UBERON:0000923!7.05e-07!604;UBERON:0005291!7.05e-07!604;UBERON:0006598!7.05e-07!604;UBERON:0002532!7.05e-07!604;UBERON:0001894!7.69e-07!7;UBERON:0006222!7.69e-07!7;UBERON:0002050!7.95e-07!605;UBERON:0005423!7.95e-07!605;UBERON:0002240!8.68e-07!3;UBERON:0000481!9.98e-07!347
|ontology_enrichment_uberon=UBERON:0001049!3.05e-72!56;UBERON:0005068!3.05e-72!56;UBERON:0006241!3.05e-72!56;UBERON:0007135!3.05e-72!56;UBERON:0002346!3.24e-65!86;UBERON:0000073!1.56e-63!53;UBERON:0002616!1.56e-63!53;UBERON:0001016!2.15e-62!89;UBERON:0003075!3.96e-62!82;UBERON:0007284!3.96e-62!82;UBERON:0000955!4.97e-57!68;UBERON:0006238!4.97e-57!68;UBERON:0001017!6.43e-56!81;UBERON:0002780!2.02e-50!41;UBERON:0001890!2.02e-50!41;UBERON:0003080!2.02e-50!41;UBERON:0006240!2.02e-50!41;UBERON:0010371!1.27e-49!104;UBERON:0003528!4.00e-47!34;UBERON:0002020!4.00e-47!34;UBERON:0001893!4.00e-47!34;UBERON:0003056!9.44e-47!61;UBERON:0002791!1.83e-41!32;UBERON:0001869!3.52e-41!32;UBERON:0004121!1.77e-38!171;UBERON:0000924!1.77e-38!171;UBERON:0006601!1.77e-38!171;UBERON:0007023!3.12e-38!114;UBERON:0010314!3.41e-37!132;UBERON:0002619!1.86e-30!22;UBERON:0001950!4.01e-29!20;UBERON:0000956!1.61e-26!25;UBERON:0000203!1.61e-26!25;UBERON:0000125!3.23e-24!9;UBERON:0002308!3.23e-24!9;UBERON:0003076!4.34e-22!15;UBERON:0003057!4.34e-22!15;UBERON:0011216!1.13e-21!223;UBERON:0002298!2.11e-21!6;UBERON:0002420!2.46e-18!9;UBERON:0007245!2.46e-18!9;UBERON:0010009!2.46e-18!9;UBERON:0010011!2.46e-18!9;UBERON:0000454!2.46e-18!9;UBERON:0009663!6.36e-18!7;UBERON:0000025!3.19e-17!192;UBERON:0004732!1.09e-16!13;UBERON:0000119!2.09e-14!309;UBERON:0000200!2.40e-14!6;UBERON:0004733!8.31e-14!12;UBERON:0002028!8.31e-14!12;UBERON:0007277!8.31e-14!12;UBERON:0000483!9.30e-14!306;UBERON:0004111!5.38e-12!240;UBERON:0000477!7.98e-12!373;UBERON:0001896!1.24e-11!3;UBERON:0005290!1.24e-11!3;UBERON:0010096!1.24e-11!3;UBERON:0000988!1.65e-11!3;UBERON:0002240!1.71e-11!3;UBERON:0005174!1.71e-11!3;UBERON:0001137!1.71e-11!3;UBERON:0002021!1.79e-11!5;UBERON:0000064!6.01e-11!218;UBERON:0000481!1.21e-09!342;UBERON:0000966!2.31e-09!6;UBERON:0005388!2.31e-09!6;UBERON:0001802!2.31e-09!6;UBERON:0005162!9.24e-09!2;UBERON:0000122!9.24e-09!2;UBERON:0001897!9.95e-09!2;UBERON:0010225!9.95e-09!2;UBERON:0001875!1.44e-08!2;UBERON:0006514!1.44e-08!2;UBERON:0000369!3.50e-08!4;UBERON:0002435!3.50e-08!4;UBERON:0000204!3.50e-08!4;UBERON:0010082!3.50e-08!4;UBERON:0002148!4.12e-08!2;UBERON:0006331!4.12e-08!2;UBERON:0009662!4.12e-08!2;UBERON:0001871!4.67e-08!6;UBERON:0002771!5.29e-08!2;UBERON:0000013!1.24e-07!5;UBERON:0002410!1.24e-07!5;UBERON:0000923!1.52e-07!560;UBERON:0010316!1.52e-07!560;UBERON:0005291!1.52e-07!560;UBERON:0006598!1.52e-07!560;UBERON:0010317!1.52e-07!560;UBERON:0002532!1.52e-07!560;UBERON:0002050!2.08e-07!564;UBERON:0000010!3.98e-07!8;UBERON:0005423!7.63e-07!581;UBERON:0001872!9.70e-07!5
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167356305130929!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436777835043034!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663513483879708!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329010730871441
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167356305130929!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436777835043034!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663513483879708!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329010730871441
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}}
}}

Revision as of 15:18, 19 October 2012


Full id: C3681_neuroblastoma_optic_teratocarcinoma_substantia_diencephalon_corpus_globus



Phase1 CAGE Peaks

Hg19::chr17:74540323..74540336,+p6@PRCD
Hg19::chr17:74540344..74540355,+p8@PRCD
Hg19::chr17:74540357..74540388,+p1@PRCD


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

No GOStat results

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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
neural tube3.05e-7256
neural rod3.05e-7256
future spinal cord3.05e-7256
neural keel3.05e-7256
neurectoderm3.24e-6586
regional part of nervous system1.56e-6353
regional part of brain1.56e-6353
nervous system2.15e-6289
neural plate3.96e-6282
presumptive neural plate3.96e-6282
brain4.97e-5768
future brain4.97e-5768
central nervous system6.43e-5681
regional part of forebrain2.02e-5041
forebrain2.02e-5041
anterior neural tube2.02e-5041
future forebrain2.02e-5041
ecto-epithelium1.27e-49104
brain grey matter4.00e-4734
gray matter4.00e-4734
telencephalon4.00e-4734
pre-chordal neural plate9.44e-4761
regional part of telencephalon1.83e-4132
cerebral hemisphere3.52e-4132
ectoderm-derived structure1.77e-38171
ectoderm1.77e-38171
presumptive ectoderm1.77e-38171
adult organism3.12e-38114
structure with developmental contribution from neural crest3.41e-37132
regional part of cerebral cortex1.86e-3022
neocortex4.01e-2920
cerebral cortex1.61e-2625
pallium1.61e-2625
neural nucleus3.23e-249
nucleus of brain3.23e-249
posterior neural tube4.34e-2215
chordal neural plate4.34e-2215
organ system subdivision1.13e-21223
brainstem2.11e-216
basal ganglion2.46e-189
nuclear complex of neuraxis2.46e-189
aggregate regional part of brain2.46e-189
collection of basal ganglia2.46e-189
cerebral subcortex2.46e-189
telencephalic nucleus6.36e-187
tube3.19e-17192
segmental subdivision of nervous system1.09e-1613
cell layer2.09e-14309
gyrus2.40e-146
segmental subdivision of hindbrain8.31e-1412
hindbrain8.31e-1412
presumptive hindbrain8.31e-1412
epithelium9.30e-14306
anatomical conduit5.38e-12240
anatomical cluster7.98e-12373
medulla oblongata1.24e-113
myelencephalon1.24e-113
future myelencephalon1.24e-113
pons1.65e-113
spinal cord1.71e-113
dorsal region element1.71e-113
dorsum1.71e-113
occipital lobe1.79e-115
organ part6.01e-11218
multi-tissue structure1.21e-09342
retina2.31e-096
photoreceptor array2.31e-096
posterior segment of eyeball2.31e-096
multi cell component structure9.24e-092
neuron projection bundle9.24e-092
dorsal plus ventral thalamus9.95e-092
thalamic complex9.95e-092
globus pallidus1.44e-082
pallidum1.44e-082
corpus striatum3.50e-084
striatum3.50e-084
ventral part of telencephalon3.50e-084
future corpus striatum3.50e-084
locus ceruleus4.12e-082
brainstem nucleus4.12e-082
hindbrain nucleus4.12e-082
temporal lobe4.67e-086
middle temporal gyrus5.29e-082
sympathetic nervous system1.24e-075
autonomic nervous system1.24e-075
germ layer1.52e-07560
germ layer / neural crest1.52e-07560
embryonic tissue1.52e-07560
presumptive structure1.52e-07560
germ layer / neural crest derived structure1.52e-07560
epiblast (generic)1.52e-07560
embryonic structure2.08e-07564
peripheral nervous system3.98e-078
developing anatomical structure7.63e-07581
parietal lobe9.70e-075
Disease
Ontology termp-valuen
neuroectodermal tumor4.85e-0910


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
EP300#203336.77394172622320.003216880500103790.0167356305130929
GATA2#2624312.7449317335540.0004829527704283790.00436777835043034
RAD21#5885310.35503389545630.0009004912073565420.00663513483879708
YY1#752834.911170749853860.008441455341808260.0329010730871441



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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