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Coexpression cluster:C4718: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.55e-10!106;DOID:0050687!1.84e-07!143
|ontology_enrichment_disease=DOID:305!1.55e-10!106;DOID:0050687!1.84e-07!143
|ontology_enrichment_uberon=UBERON:0007023!2.48e-33!115;UBERON:0001049!3.65e-24!57;UBERON:0005068!3.65e-24!57;UBERON:0006241!3.65e-24!57;UBERON:0007135!3.65e-24!57;UBERON:0005743!2.33e-21!86;UBERON:0001017!1.55e-20!82;UBERON:0000033!2.57e-20!123;UBERON:0000955!3.49e-20!69;UBERON:0006238!3.49e-20!69;UBERON:0003075!3.98e-20!86;UBERON:0007284!3.98e-20!86;UBERON:0002616!1.35e-19!59;UBERON:0000153!2.09e-19!129;UBERON:0007811!2.09e-19!129;UBERON:0000073!1.55e-18!94;UBERON:0001016!1.55e-18!94;UBERON:0003080!2.53e-18!42;UBERON:0002346!3.75e-18!90;UBERON:0004121!6.77e-18!169;UBERON:0002780!1.11e-17!41;UBERON:0001890!1.11e-17!41;UBERON:0006240!1.11e-17!41;UBERON:0000481!1.39e-17!347;UBERON:0000475!2.50e-17!365;UBERON:0000924!1.05e-16!173;UBERON:0006601!1.05e-16!173;UBERON:0002020!5.49e-16!34;UBERON:0003528!5.49e-16!34;UBERON:0001893!1.54e-15!34;UBERON:0000064!2.14e-15!219;UBERON:0001869!3.53e-15!32;UBERON:0002791!5.35e-15!33;UBERON:0003056!5.82e-15!61;UBERON:0000477!9.89e-15!286;UBERON:0002619!4.99e-14!22;UBERON:0001007!1.91e-13!155;UBERON:0001555!1.91e-13!155;UBERON:0007026!1.91e-13!155;UBERON:0004111!3.85e-13!241;UBERON:0001950!5.64e-13!20;UBERON:0004119!2.16e-12!169;UBERON:0000925!2.16e-12!169;UBERON:0006595!2.16e-12!169;UBERON:0000062!2.72e-12!511;UBERON:0000956!4.29e-12!25;UBERON:0000203!4.29e-12!25;UBERON:0004921!1.17e-11!129;UBERON:0004185!1.17e-11!129;UBERON:0000077!2.19e-09!130;UBERON:0000025!6.68e-09!194;UBERON:0001004!9.46e-09!72;UBERON:0001041!1.22e-08!98;UBERON:0000063!3.11e-08!97;UBERON:0005177!4.93e-08!107;UBERON:0008947!5.18e-08!38;UBERON:0003258!5.18e-08!38;UBERON:0000483!5.68e-08!309;UBERON:0000119!1.11e-07!312;UBERON:0003076!4.78e-07!15;UBERON:0003057!4.78e-07!15
|ontology_enrichment_uberon=UBERON:0007023!2.48e-33!115;UBERON:0001049!3.65e-24!57;UBERON:0005068!3.65e-24!57;UBERON:0006241!3.65e-24!57;UBERON:0007135!3.65e-24!57;UBERON:0005743!2.33e-21!86;UBERON:0001017!1.55e-20!82;UBERON:0000033!2.57e-20!123;UBERON:0000955!3.49e-20!69;UBERON:0006238!3.49e-20!69;UBERON:0003075!3.98e-20!86;UBERON:0007284!3.98e-20!86;UBERON:0002616!1.35e-19!59;UBERON:0000153!2.09e-19!129;UBERON:0007811!2.09e-19!129;UBERON:0000073!1.55e-18!94;UBERON:0001016!1.55e-18!94;UBERON:0003080!2.53e-18!42;UBERON:0002346!3.75e-18!90;UBERON:0004121!6.77e-18!169;UBERON:0002780!1.11e-17!41;UBERON:0001890!1.11e-17!41;UBERON:0006240!1.11e-17!41;UBERON:0000481!1.39e-17!347;UBERON:0000475!2.50e-17!365;UBERON:0000924!1.05e-16!173;UBERON:0006601!1.05e-16!173;UBERON:0002020!5.49e-16!34;UBERON:0003528!5.49e-16!34;UBERON:0001893!1.54e-15!34;UBERON:0000064!2.14e-15!219;UBERON:0001869!3.53e-15!32;UBERON:0002791!5.35e-15!33;UBERON:0003056!5.82e-15!61;UBERON:0000477!9.89e-15!286;UBERON:0002619!4.99e-14!22;UBERON:0001007!1.91e-13!155;UBERON:0001555!1.91e-13!155;UBERON:0007026!1.91e-13!155;UBERON:0004111!3.85e-13!241;UBERON:0001950!5.64e-13!20;UBERON:0004119!2.16e-12!169;UBERON:0000925!2.16e-12!169;UBERON:0006595!2.16e-12!169;UBERON:0000062!2.72e-12!511;UBERON:0000956!4.29e-12!25;UBERON:0000203!4.29e-12!25;UBERON:0004921!1.17e-11!129;UBERON:0004185!1.17e-11!129;UBERON:0000077!2.19e-09!130;UBERON:0000025!6.68e-09!194;UBERON:0001004!9.46e-09!72;UBERON:0001041!1.22e-08!98;UBERON:0000063!3.11e-08!97;UBERON:0005177!4.93e-08!107;UBERON:0008947!5.18e-08!38;UBERON:0003258!5.18e-08!38;UBERON:0000483!5.68e-08!309;UBERON:0000119!1.11e-07!312;UBERON:0003076!4.78e-07!15;UBERON:0003057!4.78e-07!15
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}}
}}

Revision as of 13:59, 5 September 2012


Full id: C4718_cerebellum_pancreas_occipital_pharyngeal_Hepatocyte_cervical_rectal



Phase1 CAGE Peaks

Hg19::chr8:110656917..110656960,-p4@SYBU
Hg19::chr8:110656962..110656982,-p3@SYBU
Hg19::chr8:110656995..110657075,-p1@SYBU


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell2.64e-09254
endodermal cell3.83e-0759
Uber Anatomy
Ontology termp-valuen
adult organism2.48e-33115
neural tube3.65e-2457
neural rod3.65e-2457
future spinal cord3.65e-2457
neural keel3.65e-2457
central nervous system1.55e-2082
head2.57e-20123
brain3.49e-2069
future brain3.49e-2069
neural plate3.98e-2086
presumptive neural plate3.98e-2086
regional part of brain1.35e-1959
anterior region of body2.09e-19129
craniocervical region2.09e-19129
regional part of nervous system1.55e-1894
nervous system1.55e-1894
anterior neural tube2.53e-1842
neurectoderm3.75e-1890
ectoderm-derived structure6.77e-18169
regional part of forebrain1.11e-1741
forebrain1.11e-1741
future forebrain1.11e-1741
multi-tissue structure1.39e-17347
organism subdivision2.50e-17365
ectoderm1.05e-16173
presumptive ectoderm1.05e-16173
gray matter5.49e-1634
brain grey matter5.49e-1634
telencephalon1.54e-1534
organ part2.14e-15219
cerebral hemisphere3.53e-1532
regional part of telencephalon5.35e-1533
pre-chordal neural plate5.82e-1561
anatomical cluster9.89e-15286
regional part of cerebral cortex4.99e-1422
digestive system1.91e-13155
digestive tract1.91e-13155
primitive gut1.91e-13155
anatomical conduit3.85e-13241
neocortex5.64e-1320
endoderm-derived structure2.16e-12169
endoderm2.16e-12169
presumptive endoderm2.16e-12169
organ2.72e-12511
cerebral cortex4.29e-1225
pallium4.29e-1225
subdivision of digestive tract1.17e-11129
endodermal part of digestive tract1.17e-11129
mixed endoderm/mesoderm-derived structure2.19e-09130
tube6.68e-09194
respiratory system9.46e-0972
foregut1.22e-0898
organ segment3.11e-0897
trunk region element4.93e-08107
respiratory primordium5.18e-0838
endoderm of foregut5.18e-0838
epithelium5.68e-08309
cell layer1.11e-07312
posterior neural tube4.78e-0715
chordal neural plate4.78e-0715
Disease
Ontology termp-valuen
carcinoma1.55e-10106
cell type cancer1.84e-07143


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
CCNT2#90536.336201576962630.003930750035764890.0191216918806302
CTCF#1066435.360256373075030.0064925092527670.0281380684641768
E2F1#186934.907389214879320.008460985347239390.0327826692146294
E2F6#187635.017155731697390.00791769806886330.0324433642739334
EGR1#195834.988179094810140.008056488137383440.0322590025909669
EP300#203336.77394172622320.003216880500103790.0168523165404464
ESR1#2099330.76860329615453.43136389821584e-050.000679371022115192
HMGN3#932438.178547723350590.001827766942164210.010925489450131
MAX#414936.452555509007120.003721913834265510.0187439945480208
MXI1#460139.96157162875930.001011470541259020.0072354090314076
MYC#460935.22228187160940.007020843755740150.0296142932554825
NRF1#4899312.21027944771090.0005492172401020010.00473616541483056
PAX5#507936.669565531177830.003370290999677260.0173710616253908
RAD21#5885310.35503389545630.0009004912073565420.00668845752116562
SIN3A#2594235.408884726815140.006318961977991520.0278340814010737
SMC3#9126315.04493284493280.0002935825420371870.00310905162318209
SRF#6722313.79717826216780.0003806615025800190.00376547704754258
TCF7L2#6934310.77017656313730.0008003181298398380.00617542853064964
TFAP2A#7020316.5186343730450.0002218033880766340.00249487604171627
TFAP2C#7022310.80922860986020.0007916746575753130.00618921398027608
USF1#739136.361499277207960.00388404057290560.0191233883364929
USF2#7392312.99219738506960.0004558979393427810.00423306586833399
YY1#752834.911170749853860.008441455341808260.0331322918727916
ZEB1#6935316.88843201754390.0002075486917327580.00243826522113358



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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