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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!4.88e-61!82;UBERON:0005743!2.21e-60!86;UBERON:0000073!1.05e-57!94;UBERON:0001016!1.05e-57!94;UBERON:0001049!2.54e-57!57;UBERON:0005068!2.54e-57!57;UBERON:0006241!2.54e-57!57;UBERON:0007135!2.54e-57!57;UBERON:0002346!1.10e-53!90;UBERON:0003075!3.47e-53!86;UBERON:0007284!3.47e-53!86;UBERON:0002616!1.04e-49!59;UBERON:0000955!1.30e-48!69;UBERON:0006238!1.30e-48!69;UBERON:0007023!9.40e-46!115;UBERON:0002780!4.03e-45!41;UBERON:0001890!4.03e-45!41;UBERON:0006240!4.03e-45!41;UBERON:0003080!1.16e-43!42;UBERON:0003056!1.83e-40!61;UBERON:0001893!2.10e-37!34;UBERON:0002020!2.12e-37!34;UBERON:0003528!2.12e-37!34;UBERON:0000924!1.84e-36!173;UBERON:0006601!1.84e-36!173;UBERON:0002791!2.80e-36!33;UBERON:0001869!9.67e-36!32;UBERON:0004121!1.76e-35!169;UBERON:0000153!1.71e-33!129;UBERON:0007811!1.71e-33!129;UBERON:0000033!3.15e-32!123;UBERON:0000956!1.08e-28!25;UBERON:0000203!1.08e-28!25;UBERON:0002619!1.84e-26!22;UBERON:0001950!1.93e-24!20;UBERON:0003076!2.89e-14!15;UBERON:0003057!2.89e-14!15;UBERON:0000025!2.26e-12!194;UBERON:0004733!1.26e-11!12;UBERON:0002028!1.26e-11!12;UBERON:0007277!1.26e-11!12;UBERON:0004111!6.90e-11!241;UBERON:0000477!7.36e-11!286;UBERON:0000064!1.00e-10!219;UBERON:0004732!1.88e-10!13;UBERON:0002420!2.19e-10!9;UBERON:0007245!2.19e-10!9;UBERON:0010009!2.19e-10!9;UBERON:0010011!2.19e-10!9;UBERON:0000454!2.19e-10!9;UBERON:0001871!2.79e-10!7;UBERON:0000922!3.62e-10!612;UBERON:0002308!4.65e-10!9;UBERON:0000125!4.65e-10!9;UBERON:0000481!3.96e-09!347;UBERON:0000483!4.10e-09!309;UBERON:0002680!4.25e-09!9;UBERON:0001895!4.25e-09!9;UBERON:0010092!4.25e-09!9;UBERON:0001894!5.51e-09!7;UBERON:0006222!5.51e-09!7;UBERON:0000119!8.57e-09!312;UBERON:0009663!3.56e-08!7;UBERON:0000475!3.75e-08!365;UBERON:0000200!4.17e-08!6;UBERON:0000923!5.60e-08!604;UBERON:0005291!5.60e-08!604;UBERON:0006598!5.60e-08!604;UBERON:0002532!5.60e-08!604;UBERON:0002050!6.73e-08!605;UBERON:0005423!6.73e-08!605;UBERON:0000468!1.86e-07!659;UBERON:0001872!4.81e-07!5;UBERON:0002021!5.56e-07!5;UBERON:0000349!6.82e-07!5
|ontology_enrichment_uberon=UBERON:0001017!4.88e-61!82;UBERON:0005743!2.21e-60!86;UBERON:0000073!1.05e-57!94;UBERON:0001016!1.05e-57!94;UBERON:0001049!2.54e-57!57;UBERON:0005068!2.54e-57!57;UBERON:0006241!2.54e-57!57;UBERON:0007135!2.54e-57!57;UBERON:0002346!1.10e-53!90;UBERON:0003075!3.47e-53!86;UBERON:0007284!3.47e-53!86;UBERON:0002616!1.04e-49!59;UBERON:0000955!1.30e-48!69;UBERON:0006238!1.30e-48!69;UBERON:0007023!9.40e-46!115;UBERON:0002780!4.03e-45!41;UBERON:0001890!4.03e-45!41;UBERON:0006240!4.03e-45!41;UBERON:0003080!1.16e-43!42;UBERON:0003056!1.83e-40!61;UBERON:0001893!2.10e-37!34;UBERON:0002020!2.12e-37!34;UBERON:0003528!2.12e-37!34;UBERON:0000924!1.84e-36!173;UBERON:0006601!1.84e-36!173;UBERON:0002791!2.80e-36!33;UBERON:0001869!9.67e-36!32;UBERON:0004121!1.76e-35!169;UBERON:0000153!1.71e-33!129;UBERON:0007811!1.71e-33!129;UBERON:0000033!3.15e-32!123;UBERON:0000956!1.08e-28!25;UBERON:0000203!1.08e-28!25;UBERON:0002619!1.84e-26!22;UBERON:0001950!1.93e-24!20;UBERON:0003076!2.89e-14!15;UBERON:0003057!2.89e-14!15;UBERON:0000025!2.26e-12!194;UBERON:0004733!1.26e-11!12;UBERON:0002028!1.26e-11!12;UBERON:0007277!1.26e-11!12;UBERON:0004111!6.90e-11!241;UBERON:0000477!7.36e-11!286;UBERON:0000064!1.00e-10!219;UBERON:0004732!1.88e-10!13;UBERON:0002420!2.19e-10!9;UBERON:0007245!2.19e-10!9;UBERON:0010009!2.19e-10!9;UBERON:0010011!2.19e-10!9;UBERON:0000454!2.19e-10!9;UBERON:0001871!2.79e-10!7;UBERON:0000922!3.62e-10!612;UBERON:0002308!4.65e-10!9;UBERON:0000125!4.65e-10!9;UBERON:0000481!3.96e-09!347;UBERON:0000483!4.10e-09!309;UBERON:0002680!4.25e-09!9;UBERON:0001895!4.25e-09!9;UBERON:0010092!4.25e-09!9;UBERON:0001894!5.51e-09!7;UBERON:0006222!5.51e-09!7;UBERON:0000119!8.57e-09!312;UBERON:0009663!3.56e-08!7;UBERON:0000475!3.75e-08!365;UBERON:0000200!4.17e-08!6;UBERON:0000923!5.60e-08!604;UBERON:0005291!5.60e-08!604;UBERON:0006598!5.60e-08!604;UBERON:0002532!5.60e-08!604;UBERON:0002050!6.73e-08!605;UBERON:0005423!6.73e-08!605;UBERON:0000468!1.86e-07!659;UBERON:0001872!4.81e-07!5;UBERON:0002021!5.56e-07!5;UBERON:0000349!6.82e-07!5
|tf_chipseq_enrich=CTCF#10664;6:5.36025637307503:4.21437267579784e-05:0.000755224550253347!EP300#2033;6:6.7739417262232:1.03454107484288e-05:0.000269576934419949!JUND#3727;6:6.99466394187103:8.53468650061654e-06:0.000232123469645284!MAX#4149;6:6.45255550900712:1.3848964723355e-05:0.000334498618580591!MYC#4609;6:5.2222818716094:4.92821127172503e-05:0.000854127874224512!NRF1#4899;6:12.2102794477109:3.01474934717981e-07:1.51958208045421e-05!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380282639606716!RAD21#5885;6:10.3550338954563:8.10515055094479e-07:3.54181513970763e-05!REST#5978;6:9.65002871612802:1.23743801704917e-06:4.98983741554435e-05!SRF#6722;6:13.7971782621678:1.44812893459755e-07:8.17078000002344e-06!TCF12#6938;6:10.6344649021864:6.9082259011154e-07:3.11254618156424e-05!USF2#7392;5:10.8268311542247:1.51592052313491e-05:0.000358517263396031!ZNF143#7702;6:13.5008765522279:1.64963374888971e-07:9.12049227635216e-06
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}}
}}

Revision as of 13:32, 5 September 2012


Full id: C1440_gastrointestinal_small_occipital_retinoblastoma_parietal_temporal_carcinoid



Phase1 CAGE Peaks

Hg19::chr18:31804736..31804754,-p@chr18:31804736..31804754
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Hg19::chr18:31804765..31804783,-p@chr18:31804765..31804783
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Hg19::chr18:31804789..31804820,-p@chr18:31804789..31804820
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Hg19::chr18:31804823..31804833,-p@chr18:31804823..31804833
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Hg19::chr18:31804835..31804861,-p@chr18:31804835..31804861
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Hg19::chr18:31804864..31804900,-p@chr18:31804864..31804900
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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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
neural cell4.87e-0925
neuronal stem cell1.48e-088
Uber Anatomy
Ontology termp-valuen
central nervous system4.88e-6182
regional part of nervous system1.05e-5794
nervous system1.05e-5794
neural tube2.54e-5757
neural rod2.54e-5757
future spinal cord2.54e-5757
neural keel2.54e-5757
neurectoderm1.10e-5390
neural plate3.47e-5386
presumptive neural plate3.47e-5386
regional part of brain1.04e-4959
brain1.30e-4869
future brain1.30e-4869
adult organism9.40e-46115
regional part of forebrain4.03e-4541
forebrain4.03e-4541
future forebrain4.03e-4541
anterior neural tube1.16e-4342
pre-chordal neural plate1.83e-4061
telencephalon2.10e-3734
gray matter2.12e-3734
brain grey matter2.12e-3734
ectoderm1.84e-36173
presumptive ectoderm1.84e-36173
regional part of telencephalon2.80e-3633
cerebral hemisphere9.67e-3632
ectoderm-derived structure1.76e-35169
anterior region of body1.71e-33129
craniocervical region1.71e-33129
head3.15e-32123
cerebral cortex1.08e-2825
pallium1.08e-2825
regional part of cerebral cortex1.84e-2622
neocortex1.93e-2420
posterior neural tube2.89e-1415
chordal neural plate2.89e-1415
tube2.26e-12194
segmental subdivision of hindbrain1.26e-1112
hindbrain1.26e-1112
presumptive hindbrain1.26e-1112
anatomical conduit6.90e-11241
anatomical cluster7.36e-11286
organ part1.00e-10219
segmental subdivision of nervous system1.88e-1013
basal ganglion2.19e-109
nuclear complex of neuraxis2.19e-109
aggregate regional part of brain2.19e-109
collection of basal ganglia2.19e-109
cerebral subcortex2.19e-109
temporal lobe2.79e-107
embryo3.62e-10612
nucleus of brain4.65e-109
neural nucleus4.65e-109
multi-tissue structure3.96e-09347
epithelium4.10e-09309
regional part of metencephalon4.25e-099
metencephalon4.25e-099
future metencephalon4.25e-099
diencephalon5.51e-097
future diencephalon5.51e-097
cell layer8.57e-09312
telencephalic nucleus3.56e-087
organism subdivision3.75e-08365
gyrus4.17e-086
germ layer5.60e-08604
embryonic tissue5.60e-08604
presumptive structure5.60e-08604
epiblast (generic)5.60e-08604
embryonic structure6.73e-08605
developing anatomical structure6.73e-08605
multi-cellular organism1.86e-07659
parietal lobe4.81e-075
occipital lobe5.56e-075
limbic system6.82e-075


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
CTCF#1066465.360256373075034.21437267579784e-050.000755224550253347
EP300#203366.77394172622321.03454107484288e-050.000269576934419949
JUND#372766.994663941871038.53468650061654e-060.000232123469645284
MAX#414966.452555509007121.3848964723355e-050.000334498618580591
MYC#460965.22228187160944.92821127172503e-050.000854127874224512
NRF1#4899612.21027944771093.01474934717981e-071.51958208045421e-05
POLR2A#543062.147453176558070.01019570676818780.0380282639606716
RAD21#5885610.35503389545638.10515055094479e-073.54181513970763e-05
REST#597869.650028716128021.23743801704917e-064.98983741554435e-05
SRF#6722613.79717826216781.44812893459755e-078.17078000002344e-06
TCF12#6938610.63446490218646.9082259011154e-073.11254618156424e-05
USF2#7392510.82683115422471.51592052313491e-050.000358517263396031
ZNF143#7702613.50087655222791.64963374888971e-079.12049227635216e-06



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.