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Coexpression cluster:C2707: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000467!5.79e-21!625;UBERON:0000468!1.34e-20!659;UBERON:0000480!1.57e-20!626;UBERON:0002050!2.35e-18!605;UBERON:0005423!2.35e-18!605;UBERON:0000923!2.81e-18!604;UBERON:0005291!2.81e-18!604;UBERON:0006598!2.81e-18!604;UBERON:0002532!2.81e-18!604;UBERON:0002390!1.38e-17!102;UBERON:0003061!1.38e-17!102;UBERON:0002193!1.50e-17!112;UBERON:0000922!1.88e-17!612;UBERON:0000062!3.39e-17!511;UBERON:0002371!4.40e-17!80;UBERON:0002405!1.99e-16!115;UBERON:0001474!4.40e-15!86;UBERON:0004765!2.95e-13!101;UBERON:0001434!2.95e-13!101;UBERON:0003081!5.23e-13!216;UBERON:0007023!7.28e-11!115;UBERON:0000926!1.13e-09!448;UBERON:0004120!1.13e-09!448;UBERON:0006603!1.13e-09!448;UBERON:0002204!9.75e-07!167
|ontology_enrichment_uberon=UBERON:0000467!5.79e-21!625;UBERON:0000468!1.34e-20!659;UBERON:0000480!1.57e-20!626;UBERON:0002050!2.35e-18!605;UBERON:0005423!2.35e-18!605;UBERON:0000923!2.81e-18!604;UBERON:0005291!2.81e-18!604;UBERON:0006598!2.81e-18!604;UBERON:0002532!2.81e-18!604;UBERON:0002390!1.38e-17!102;UBERON:0003061!1.38e-17!102;UBERON:0002193!1.50e-17!112;UBERON:0000922!1.88e-17!612;UBERON:0000062!3.39e-17!511;UBERON:0002371!4.40e-17!80;UBERON:0002405!1.99e-16!115;UBERON:0001474!4.40e-15!86;UBERON:0004765!2.95e-13!101;UBERON:0001434!2.95e-13!101;UBERON:0003081!5.23e-13!216;UBERON:0007023!7.28e-11!115;UBERON:0000926!1.13e-09!448;UBERON:0004120!1.13e-09!448;UBERON:0006603!1.13e-09!448;UBERON:0002204!9.75e-07!167
|tf_chipseq_enrich=BRCA1#672;3:15.1381729824178:0.000468218442143119:0.00430308569860834!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106642484589261!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161155643328409!EP300#2033;3:5.0804562946674:0.0114429840539824:0.0419066488398157!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186401184016915!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.000794721111179061!STAT1#6772;3:15.5299406228994:0.00043408865517555:0.00405145532241995!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322819936816796!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244680144467759
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}}
}}

Revision as of 14:22, 5 September 2012


Full id: C2707_Neutrophils_Eosinophils_CD14_Mesenchymal_blood_Whole_heart



Phase1 CAGE Peaks

Hg19::chr2:96931679..96931756,-p1@TMEM127
Hg19::chr3:122513887..122513992,+p1@DIRC2
Hg19::chr3:122513994..122514005,+p6@DIRC2
Hg19::chr9:33817124..33817197,+p1@UBE2R2


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>


Uber Anatomy
Ontology termp-valuen
anatomical system5.79e-21625
multi-cellular organism1.34e-20659
anatomical group1.57e-20626
embryonic structure2.35e-18605
developing anatomical structure2.35e-18605
germ layer2.81e-18604
embryonic tissue2.81e-18604
presumptive structure2.81e-18604
epiblast (generic)2.81e-18604
hematopoietic system1.38e-17102
blood island1.38e-17102
hemolymphoid system1.50e-17112
embryo1.88e-17612
organ3.39e-17511
bone marrow4.40e-1780
immune system1.99e-16115
bone element4.40e-1586
skeletal element2.95e-13101
skeletal system2.95e-13101
lateral plate mesoderm5.23e-13216
adult organism7.28e-11115
mesoderm1.13e-09448
mesoderm-derived structure1.13e-09448
presumptive mesoderm1.13e-09448
musculoskeletal system9.75e-07167


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
BRCA1#672315.13817298241780.0004682184421431190.00430308569860834
E2F1#186944.907389214879320.001724022357361790.0106642484589261
ELF1#199744.258097958807540.003041525565781240.0161155643328409
EP300#203335.08045629466740.01144298405398240.0419066488398157
HEY1#2346244.040111043105710.00375304636917980.0186401184016915
NRF1#4899412.21027944771094.49717228915276e-050.000794721111179061
STAT1#6772315.52994062289940.000434088655175550.00405145532241995
TAF1#687243.343046285745290.008005664898701650.0322819936816796
TBP#690843.706770687096390.005296377814784350.0244680144467759



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.