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Coexpression cluster:C4651: Difference between revisions

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|ontology_enrichment_disease=DOID:305!2.38e-20!106;DOID:0050687!7.80e-08!143;DOID:299!8.91e-07!25
|ontology_enrichment_disease=DOID:305!2.38e-20!106;DOID:0050687!7.80e-08!143;DOID:299!8.91e-07!25
|ontology_enrichment_uberon=UBERON:0005743!2.20e-12!86;UBERON:0001017!4.86e-11!82;UBERON:0007023!6.08e-11!115;UBERON:0003075!4.75e-10!86;UBERON:0007284!4.75e-10!86;UBERON:0001049!4.98e-10!57;UBERON:0005068!4.98e-10!57;UBERON:0006241!4.98e-10!57;UBERON:0007135!4.98e-10!57;UBERON:0003056!1.12e-09!61;UBERON:0000073!3.98e-09!94;UBERON:0001016!3.98e-09!94;UBERON:0000064!4.42e-09!219;UBERON:0002616!5.13e-09!59;UBERON:0004119!6.31e-09!169;UBERON:0000925!6.31e-09!169;UBERON:0006595!6.31e-09!169;UBERON:0002780!1.21e-08!41;UBERON:0001890!1.21e-08!41;UBERON:0006240!1.21e-08!41;UBERON:0003080!1.29e-08!42;UBERON:0000153!1.35e-08!129;UBERON:0007811!1.35e-08!129;UBERON:0000033!1.98e-08!123;UBERON:0002346!2.30e-08!90;UBERON:0000955!3.75e-08!69;UBERON:0006238!3.75e-08!69;UBERON:0004921!4.06e-08!129;UBERON:0004185!4.06e-08!129;UBERON:0001007!4.19e-08!155;UBERON:0001555!4.19e-08!155;UBERON:0007026!4.19e-08!155;UBERON:0004121!1.90e-07!169;UBERON:0001893!1.95e-07!34;UBERON:0001869!2.45e-07!32;UBERON:0000063!2.56e-07!97;UBERON:0002791!2.63e-07!33;UBERON:0000065!2.85e-07!53;UBERON:0002020!3.38e-07!34;UBERON:0003528!3.38e-07!34;UBERON:0008947!5.60e-07!38;UBERON:0003258!5.60e-07!38;UBERON:0001004!6.56e-07!72
|ontology_enrichment_uberon=UBERON:0005743!2.20e-12!86;UBERON:0001017!4.86e-11!82;UBERON:0007023!6.08e-11!115;UBERON:0003075!4.75e-10!86;UBERON:0007284!4.75e-10!86;UBERON:0001049!4.98e-10!57;UBERON:0005068!4.98e-10!57;UBERON:0006241!4.98e-10!57;UBERON:0007135!4.98e-10!57;UBERON:0003056!1.12e-09!61;UBERON:0000073!3.98e-09!94;UBERON:0001016!3.98e-09!94;UBERON:0000064!4.42e-09!219;UBERON:0002616!5.13e-09!59;UBERON:0004119!6.31e-09!169;UBERON:0000925!6.31e-09!169;UBERON:0006595!6.31e-09!169;UBERON:0002780!1.21e-08!41;UBERON:0001890!1.21e-08!41;UBERON:0006240!1.21e-08!41;UBERON:0003080!1.29e-08!42;UBERON:0000153!1.35e-08!129;UBERON:0007811!1.35e-08!129;UBERON:0000033!1.98e-08!123;UBERON:0002346!2.30e-08!90;UBERON:0000955!3.75e-08!69;UBERON:0006238!3.75e-08!69;UBERON:0004921!4.06e-08!129;UBERON:0004185!4.06e-08!129;UBERON:0001007!4.19e-08!155;UBERON:0001555!4.19e-08!155;UBERON:0007026!4.19e-08!155;UBERON:0004121!1.90e-07!169;UBERON:0001893!1.95e-07!34;UBERON:0001869!2.45e-07!32;UBERON:0000063!2.56e-07!97;UBERON:0002791!2.63e-07!33;UBERON:0000065!2.85e-07!53;UBERON:0002020!3.38e-07!34;UBERON:0003528!3.38e-07!34;UBERON:0008947!5.60e-07!38;UBERON:0003258!5.60e-07!38;UBERON:0001004!6.56e-07!72
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}}
}}

Revision as of 14:17, 5 September 2012


Full id: C4651_argyrophil_colon_Prostate_Intestinal_acute_epidermoid_HES3GFP



Phase1 CAGE Peaks

Hg19::chr7:130126107..130126120,+p4@MEST
Hg19::chr7:130126139..130126152,+p6@MEST
Hg19::chr7:130126165..130126202,+p2@MEST


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 cell2.20e-18254
Uber Anatomy
Ontology termp-valuen
central nervous system4.86e-1182
adult organism6.08e-11115
neural plate4.75e-1086
presumptive neural plate4.75e-1086
neural tube4.98e-1057
neural rod4.98e-1057
future spinal cord4.98e-1057
neural keel4.98e-1057
pre-chordal neural plate1.12e-0961
regional part of nervous system3.98e-0994
nervous system3.98e-0994
organ part4.42e-09219
regional part of brain5.13e-0959
endoderm-derived structure6.31e-09169
endoderm6.31e-09169
presumptive endoderm6.31e-09169
regional part of forebrain1.21e-0841
forebrain1.21e-0841
future forebrain1.21e-0841
anterior neural tube1.29e-0842
anterior region of body1.35e-08129
craniocervical region1.35e-08129
head1.98e-08123
neurectoderm2.30e-0890
brain3.75e-0869
future brain3.75e-0869
subdivision of digestive tract4.06e-08129
endodermal part of digestive tract4.06e-08129
digestive system4.19e-08155
digestive tract4.19e-08155
primitive gut4.19e-08155
ectoderm-derived structure1.90e-07169
telencephalon1.95e-0734
cerebral hemisphere2.45e-0732
organ segment2.56e-0797
regional part of telencephalon2.63e-0733
respiratory tract2.85e-0753
gray matter3.38e-0734
brain grey matter3.38e-0734
respiratory primordium5.60e-0738
endoderm of foregut5.60e-0738
respiratory system6.56e-0772
Disease
Ontology termp-valuen
carcinoma2.38e-20106
cell type cancer7.80e-08143
adenocarcinoma8.91e-0725


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
CEBPB#105137.971147625824820.001974187055288560.0115780616502292
CTCF#1066435.360256373075030.0064925092527670.0281205645854822
E2F6#187635.017155731697390.00791769806886330.0324217396045487
EGR1#195834.988179094810140.008056488137383440.0322379909800839
ELF1#199734.258097958807540.01295179875054610.046482007824758
GTF2F1#2962312.73966087675770.0004835525047438590.0043588589714262
MAX#414936.452555509007120.003721913834265510.0187367665543649
MYC#460935.22228187160940.007020843755740150.0295975579642264
NANOG#79923329.24477848101273.99627955670032e-050.000740932790027029
NR3C1#2908314.9730233311730.0002978331194675480.0031009264444294
NRF1#4899312.21027944771090.0005492172401020010.00473382019798736
RAD21#5885310.35503389545630.0009004912073565420.00668370415785018
SMC3#9126315.04493284493280.0002935825420371870.0031071612391388
TAF7#6879311.43306940492390.0006690181981945830.0054557344890485
TCF12#6938310.63446490218640.0008313523990202070.00631918582250883
TFAP2A#7020316.5186343730450.0002218033880766340.0024943387581927
TFAP2C#7022310.80922860986020.0007916746575753130.0061882875205829
YY1#752834.911170749853860.008441455341808260.0331136250917635
ZEB1#6935211.25895467836260.01010222676646330.0378268486039961



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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