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Coexpression cluster:C3278: Difference between revisions

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|full_id=C3278_testicular_small_colon_amniotic_seminal_Endothelial_stomach
|full_id=C3278_testicular_small_colon_amniotic_seminal_Endothelial_stomach
|id=C3278
|id=C3278
|ontology_enrichment_celltype=CL:0000066!1.09e-24!254;CL:0002139!7.82e-08!24;CL:0000076!5.33e-07!62
|ontology_enrichment_celltype=CL:0000066!6.53e-15!253
|ontology_enrichment_disease=DOID:305!5.97e-10!106
|ontology_enrichment_disease=DOID:305!4.87e-09!106
|ontology_enrichment_uberon=UBERON:0007023!2.73e-28!115;UBERON:0000468!2.48e-17!659;UBERON:0000062!3.89e-17!511;UBERON:0000922!4.07e-17!612;UBERON:0004111!9.79e-15!241;UBERON:0002050!2.62e-14!605;UBERON:0005423!2.62e-14!605;UBERON:0000467!3.18e-14!625;UBERON:0000480!4.41e-14!626;UBERON:0000923!5.54e-14!604;UBERON:0005291!5.54e-14!604;UBERON:0006598!5.54e-14!604;UBERON:0002532!5.54e-14!604;UBERON:0000477!1.27e-13!286;UBERON:0000064!2.37e-13!219;UBERON:0003075!3.51e-13!86;UBERON:0007284!3.51e-13!86;UBERON:0001049!6.96e-13!57;UBERON:0005068!6.96e-13!57;UBERON:0006241!6.96e-13!57;UBERON:0007135!6.96e-13!57;UBERON:0002616!7.19e-12!59;UBERON:0002346!1.25e-11!90;UBERON:0000025!1.75e-11!194;UBERON:0005743!1.02e-10!86;UBERON:0001017!1.94e-10!82;UBERON:0000033!2.16e-10!123;UBERON:0000153!2.75e-10!129;UBERON:0007811!2.75e-10!129;UBERON:0004121!3.38e-10!169;UBERON:0000955!5.73e-10!69;UBERON:0006238!5.73e-10!69;UBERON:0000481!6.67e-10!347;UBERON:0000483!1.32e-09!309;UBERON:0004119!1.43e-09!169;UBERON:0000925!1.43e-09!169;UBERON:0006595!1.43e-09!169;UBERON:0000466!1.73e-09!126;UBERON:0000119!2.00e-09!312;UBERON:0003080!2.47e-09!42;UBERON:0000924!2.59e-09!173;UBERON:0006601!2.59e-09!173;UBERON:0002780!7.73e-09!41;UBERON:0001890!7.73e-09!41;UBERON:0006240!7.73e-09!41;UBERON:0003056!9.30e-09!61;UBERON:0002020!1.28e-08!34;UBERON:0003528!1.28e-08!34;UBERON:0001893!2.51e-08!34;UBERON:0004921!3.13e-08!129;UBERON:0004185!3.13e-08!129;UBERON:0000464!3.37e-08!104;UBERON:0000073!3.49e-08!94;UBERON:0001016!3.49e-08!94;UBERON:0002791!4.54e-08!33;UBERON:0001007!7.73e-08!155;UBERON:0001555!7.73e-08!155;UBERON:0007026!7.73e-08!155;UBERON:0001869!9.25e-08!32;UBERON:0005177!9.69e-08!107;UBERON:0000077!5.02e-07!130
|ontology_enrichment_uberon=UBERON:0007023!8.59e-25!114;UBERON:0000477!2.67e-13!373;UBERON:0000062!3.62e-12!503;UBERON:0011216!2.20e-10!223;UBERON:0000064!2.41e-10!218;UBERON:0000468!8.22e-10!656;UBERON:0004111!2.17e-09!240;UBERON:0000481!2.23e-09!342;UBERON:0000922!1.04e-08!592;UBERON:0001049!1.55e-08!56;UBERON:0005068!1.55e-08!56;UBERON:0006241!1.55e-08!56;UBERON:0007135!1.55e-08!56;UBERON:0000467!1.59e-08!624;UBERON:0000480!2.11e-08!625;UBERON:0004119!2.70e-08!160;UBERON:0000925!2.70e-08!160;UBERON:0006595!2.70e-08!160;UBERON:0003075!2.74e-08!82;UBERON:0007284!2.74e-08!82;UBERON:0000073!1.90e-07!53;UBERON:0002616!1.90e-07!53;UBERON:0005423!2.10e-07!581;UBERON:0003133!2.12e-07!48;UBERON:0004921!2.58e-07!118;UBERON:0003135!2.89e-07!11;UBERON:0002346!3.26e-07!86;UBERON:0000464!3.41e-07!95;UBERON:0001007!3.44e-07!145;UBERON:0001555!3.44e-07!145;UBERON:0007026!3.44e-07!145;UBERON:0001017!4.23e-07!81;UBERON:0010371!4.71e-07!104;UBERON:0000466!5.80e-07!117;UBERON:0000025!9.15e-07!192
|tf_chipseq_enrich=ESR1#2099;2:20.5124021974363:0.00309974157709518:0.016303263865148!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460200538579241!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329721434258419!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457173762581558
|tf_chipseq_enrich=ESR1#2099;2:20.5124021974363:0.00309974157709518:0.016303263865148!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460200538579241!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329721434258419!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457173762581558
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}}
}}

Revision as of 14:57, 19 October 2012


Full id: C3278_testicular_small_colon_amniotic_seminal_Endothelial_stomach



Phase1 CAGE Peaks

Hg19::chr12:32552434..32552448,+p10@FGD4
Hg19::chr12:32552451..32552508,+p2@FGD4
Hg19::chr12:32555079..32555083,+p@chr12:32555079..32555083
+


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 cell6.53e-15253
Uber Anatomy
Ontology termp-valuen
adult organism8.59e-25114
anatomical cluster2.67e-13373
organ3.62e-12503
organ system subdivision2.20e-10223
organ part2.41e-10218
multi-cellular organism8.22e-10656
anatomical conduit2.17e-09240
multi-tissue structure2.23e-09342
embryo1.04e-08592
neural tube1.55e-0856
neural rod1.55e-0856
future spinal cord1.55e-0856
neural keel1.55e-0856
anatomical system1.59e-08624
anatomical group2.11e-08625
endoderm-derived structure2.70e-08160
endoderm2.70e-08160
presumptive endoderm2.70e-08160
neural plate2.74e-0882
presumptive neural plate2.74e-0882
regional part of nervous system1.90e-0753
regional part of brain1.90e-0753
developing anatomical structure2.10e-07581
reproductive organ2.12e-0748
subdivision of digestive tract2.58e-07118
male reproductive organ2.89e-0711
neurectoderm3.26e-0786
anatomical space3.41e-0795
digestive system3.44e-07145
digestive tract3.44e-07145
primitive gut3.44e-07145
central nervous system4.23e-0781
ecto-epithelium4.71e-07104
immaterial anatomical entity5.80e-07117
tube9.15e-07192
Disease
Ontology termp-valuen
carcinoma4.87e-09106


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
ESR1#2099220.51240219743630.003099741577095180.016303263865148
NR3C1#290829.982015554115360.01278474365547170.0460200538579241
SMARCB1#6598212.16847718743830.008675002221921740.0329721434258419
SMC3#9126210.02995522995520.0126656379767470.0457173762581558



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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