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Coexpression cluster:C3178: Difference between revisions

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|full_id=C3178_Hepatocyte_mature_left_Adipocyte_pharyngeal_liver_heart
|full_id=C3178_Hepatocyte_mature_left_Adipocyte_pharyngeal_liver_heart
|id=C3178
|id=C3178
|ontology_enrichment_celltype=CL:0000136!4.77e-07!15
|ontology_enrichment_celltype=CL:0000136!3.41e-07!15
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.35e-18!115;UBERON:0003103!3.56e-11!69;UBERON:0000477!3.67e-11!286;UBERON:0003886!1.39e-10!63;UBERON:0000466!6.68e-10!126;UBERON:0000064!1.37e-09!219;UBERON:0002417!1.42e-09!61;UBERON:0000916!1.42e-09!61;UBERON:0002553!1.73e-09!70;UBERON:0005177!4.54e-09!107;UBERON:0004111!1.25e-08!241;UBERON:0009569!1.50e-08!113;UBERON:0000464!1.59e-08!104;UBERON:0005172!4.98e-08!55;UBERON:0005173!4.98e-08!55;UBERON:0000025!6.96e-08!194;UBERON:0004921!1.46e-07!129;UBERON:0004185!1.46e-07!129;UBERON:0003064!1.84e-07!37;UBERON:0001048!1.90e-07!168;UBERON:0000489!3.31e-07!32;UBERON:0000077!4.14e-07!130;UBERON:0000058!4.16e-07!26;UBERON:0000481!5.15e-07!347;UBERON:0001041!9.16e-07!98;UBERON:0004876!9.96e-07!20
|ontology_enrichment_uberon=UBERON:0007023!1.44e-16!114;UBERON:0000477!1.05e-11!373;UBERON:0003103!3.85e-11!68;UBERON:0000064!6.82e-10!218;UBERON:0002417!4.55e-09!60;UBERON:0000916!4.55e-09!60;UBERON:0003886!2.45e-08!54;UBERON:0005177!2.66e-08!101;UBERON:0000466!2.92e-08!117;UBERON:0009569!4.13e-08!112;UBERON:0004111!4.39e-08!240;UBERON:0011216!6.86e-08!223;UBERON:0005172!1.91e-07!54;UBERON:0005173!1.91e-07!54;UBERON:0002553!1.93e-07!61;UBERON:0001048!3.00e-07!160;UBERON:0000025!3.58e-07!192;UBERON:0000464!4.27e-07!95;UBERON:0000062!5.19e-07!503;UBERON:0000489!8.71e-07!31
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.018924242980927!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323790571499884!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320597242900792!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319212248029208!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460249373837456!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00386952764407221!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108361802720645!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156209149945329!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00154489653902355!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.00071894727137062!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00613138372729018!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328092424711813!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139665840663276
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.018924242980927!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323790571499884!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320597242900792!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319212248029208!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460249373837456!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00386952764407221!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108361802720645!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156209149945329!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00154489653902355!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.00071894727137062!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00613138372729018!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328092424711813!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139665840663276
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}}
}}

Revision as of 14:52, 19 October 2012


Full id: C3178_Hepatocyte_mature_left_Adipocyte_pharyngeal_liver_heart



Phase1 CAGE Peaks

Hg19::chr11:63381712..63381727,-p6@PLA2G16
Hg19::chr11:63381737..63381757,-p4@PLA2G16
Hg19::chr11:63381763..63381783,-p5@PLA2G16


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
fat cell3.41e-0715
Uber Anatomy
Ontology termp-valuen
adult organism1.44e-16114
anatomical cluster1.05e-11373
compound organ3.85e-1168
organ part6.82e-10218
abdominal segment of trunk4.55e-0960
abdomen4.55e-0960
body cavity precursor2.45e-0854
trunk region element2.66e-08101
immaterial anatomical entity2.92e-08117
subdivision of trunk4.13e-08112
anatomical conduit4.39e-08240
organ system subdivision6.86e-08223
abdomen element1.91e-0754
abdominal segment element1.91e-0754
anatomical cavity1.93e-0761
primordium3.00e-07160
tube3.58e-07192
anatomical space4.27e-0795
organ5.19e-07503
cavitated compound organ8.71e-0731


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#90536.336201576962630.003930750035764890.018924242980927
E2F1#186934.907389214879320.008460985347239390.0323790571499884
E2F6#187635.017155731697390.00791769806886330.0320597242900792
EGR1#195834.988179094810140.008056488137383440.0319212248029208
ELF1#199734.258097958807540.01295179875054610.0460249373837456
GATA1#2623313.56030814380040.0004009615963782630.00386952764407221
HMGN3#932438.178547723350590.001827766942164210.0108361802720645
JUND#372736.994663941871030.002921845042734990.0156209149945329
STAT1#6772320.70658749719920.0001125992441046670.00154489653902355
TAL1#6886329.86861667744023.75103522793067e-050.00071894727137062
TFAP2C#7022310.80922860986020.0007916746575753130.00613138372729018
YY1#752834.911170749853860.008441455341808260.0328092424711813
ZBTB7A#5134137.35190930787590.002516255860282270.0139665840663276



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.