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Coexpression cluster:C3571: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003081!1.65e-23!216;UBERON:0002371!6.58e-20!80;UBERON:0002390!2.56e-19!102;UBERON:0003061!2.56e-19!102;UBERON:0002193!8.31e-19!112;UBERON:0000467!6.06e-17!625;UBERON:0000480!1.33e-16!626;UBERON:0001474!3.66e-16!86;UBERON:0004765!4.79e-14!101;UBERON:0001434!4.79e-14!101;UBERON:0000468!5.99e-14!659;UBERON:0002405!2.12e-12!115;UBERON:0002204!8.29e-11!167;UBERON:0002050!1.43e-10!605;UBERON:0005423!1.43e-10!605;UBERON:0000923!1.75e-10!604;UBERON:0005291!1.75e-10!604;UBERON:0006598!1.75e-10!604;UBERON:0002532!1.75e-10!604;UBERON:0000922!4.93e-10!612;UBERON:0000062!1.42e-09!511;UBERON:0000926!4.50e-09!448;UBERON:0004120!4.50e-09!448;UBERON:0006603!4.50e-09!448;UBERON:0004535!1.40e-07!110;UBERON:0004872!1.84e-07!84;UBERON:0001009!2.38e-07!113;UBERON:0001637!4.13e-07!42;UBERON:0003509!4.13e-07!42;UBERON:0004572!4.13e-07!42;UBERON:0001981!5.64e-07!60;UBERON:0007500!5.64e-07!60;UBERON:0004537!5.64e-07!60;UBERON:0006965!5.64e-07!60
|ontology_enrichment_uberon=UBERON:0003081!1.65e-23!216;UBERON:0002371!6.58e-20!80;UBERON:0002390!2.56e-19!102;UBERON:0003061!2.56e-19!102;UBERON:0002193!8.31e-19!112;UBERON:0000467!6.06e-17!625;UBERON:0000480!1.33e-16!626;UBERON:0001474!3.66e-16!86;UBERON:0004765!4.79e-14!101;UBERON:0001434!4.79e-14!101;UBERON:0000468!5.99e-14!659;UBERON:0002405!2.12e-12!115;UBERON:0002204!8.29e-11!167;UBERON:0002050!1.43e-10!605;UBERON:0005423!1.43e-10!605;UBERON:0000923!1.75e-10!604;UBERON:0005291!1.75e-10!604;UBERON:0006598!1.75e-10!604;UBERON:0002532!1.75e-10!604;UBERON:0000922!4.93e-10!612;UBERON:0000062!1.42e-09!511;UBERON:0000926!4.50e-09!448;UBERON:0004120!4.50e-09!448;UBERON:0006603!4.50e-09!448;UBERON:0004535!1.40e-07!110;UBERON:0004872!1.84e-07!84;UBERON:0001009!2.38e-07!113;UBERON:0001637!4.13e-07!42;UBERON:0003509!4.13e-07!42;UBERON:0004572!4.13e-07!42;UBERON:0001981!5.64e-07!60;UBERON:0007500!5.64e-07!60;UBERON:0004537!5.64e-07!60;UBERON:0006965!5.64e-07!60
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461458366495508!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127882100062719!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470624379217369!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00614688198368211!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000646110573628335
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}}
}}

Revision as of 12:52, 5 September 2012


Full id: C3571_Neutrophils_Mast_CD14_Eosinophils_Dendritic_thyroid_Prostate



Phase1 CAGE Peaks

Hg19::chr16:55542958..55542972,+p3@LPCAT2
Hg19::chr16:55542976..55543003,+p1@LPCAT2
Hg19::chr16:55543013..55543047,+p2@LPCAT2


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
lateral plate mesoderm1.65e-23216
bone marrow6.58e-2080
hematopoietic system2.56e-19102
blood island2.56e-19102
hemolymphoid system8.31e-19112
anatomical system6.06e-17625
anatomical group1.33e-16626
bone element3.66e-1686
skeletal element4.79e-14101
skeletal system4.79e-14101
multi-cellular organism5.99e-14659
immune system2.12e-12115
musculoskeletal system8.29e-11167
embryonic structure1.43e-10605
developing anatomical structure1.43e-10605
germ layer1.75e-10604
embryonic tissue1.75e-10604
presumptive structure1.75e-10604
epiblast (generic)1.75e-10604
embryo4.93e-10612
organ1.42e-09511
mesoderm4.50e-09448
mesoderm-derived structure4.50e-09448
presumptive mesoderm4.50e-09448
cardiovascular system1.40e-07110
splanchnic layer of lateral plate mesoderm1.84e-0784
circulatory system2.38e-07113
artery4.13e-0742
arterial blood vessel4.13e-0742
arterial system4.13e-0742
blood vessel5.64e-0760
epithelial tube open at both ends5.64e-0760
blood vasculature5.64e-0760
vascular cord5.64e-0760


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
ELF1#199734.258097958807540.01295179875054610.0461458366495508
IRF1#365937.63716375356390.002244692747297240.0127882100062719
NRF1#4899312.21027944771090.0005492172401020010.00470624379217369
TFAP2C#7022310.80922860986020.0007916746575753130.00614688198368211
THAP1#55145331.36914460285133.23800758564397e-050.000646110573628335



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.