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Coexpression cluster:C809: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C809_CD14_Olfactory_Synoviocyte_Monocytederived_Mesothelial_Fibroblast_Smooth
|full_id=C809_CD14_Olfactory_Synoviocyte_Monocytederived_Mesothelial_Fibroblast_Smooth
|id=C809
|id=C809

Revision as of 18:32, 12 September 2012


Full id: C809_CD14_Olfactory_Synoviocyte_Monocytederived_Mesothelial_Fibroblast_Smooth



Phase1 CAGE Peaks

Hg19::chr12:102271087..102271111,+p7@DRAM1
Hg19::chr12:102271201..102271223,+p8@DRAM1
Hg19::chr12:102271229..102271245,+p9@DRAM1
Hg19::chr12:102271249..102271260,+p10@DRAM1
Hg19::chr12:102271313..102271322,+p12@DRAM1
Hg19::chr12:102271348..102271376,+p2@DRAM1
Hg19::chr12:102271387..102271426,+p3@DRAM1
Hg19::chr12:102271436..102271486,+p1@DRAM1
Hg19::chr12:102271492..102271516,+p5@DRAM1
Hg19::chr12:102271520..102271550,+p4@DRAM1


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 mesoderm4.41e-20216
mesoderm6.17e-20448
mesoderm-derived structure6.17e-20448
presumptive mesoderm6.17e-20448
musculoskeletal system1.75e-16167
bone marrow2.43e-1580
hemolymphoid system1.16e-14112
immune system1.51e-13115
skeletal element8.73e-13101
skeletal system8.73e-13101
hematopoietic system1.34e-12102
blood island1.34e-12102
bone element3.66e-1286
vessel3.69e-1069
anatomical group5.05e-10626
anatomical system5.79e-10625
vasculature1.04e-0879
vascular system1.04e-0879
multi-cellular organism1.36e-08659
cardiovascular system1.58e-08110
splanchnic layer of lateral plate mesoderm2.93e-0884
blood vessel3.75e-0860
epithelial tube open at both ends3.75e-0860
blood vasculature3.75e-0860
vascular cord3.75e-0860
circulatory system4.72e-08113
artery1.48e-0742
arterial blood vessel1.48e-0742
arterial system1.48e-0742
systemic artery3.99e-0733
systemic arterial system3.99e-0733


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#90585.068961261570111.27971424775898e-050.000313810932899037
CEBPB#1051107.971147625824829.63949422428846e-108.96472962858827e-08
CTCF#1066484.288205098460024.59406669642002e-050.000807200086990933
CTCFL#140690611.84788461538462.96270758774739e-060.000101350218721503
E2F1#1869104.907389214879321.23333699071511e-077.07738911941182e-06
E2F6#1876105.017155731697399.88551667938738e-085.81980539164903e-06
EGR1#1958104.988179094810141.04750927020086e-076.12546588300717e-06
ELF1#199772.980668571165280.002378202870469130.0134745906574581
EP300#203396.096547553600882.8843323567924e-071.46089615427275e-05
ETS1#211365.83725655332140.0001713587518742850.00208949640245165
GATA1#26231013.56030814380044.74215757032704e-126.21413042016795e-10
GTF2B#2959412.77753197372970.000173128848581580.00210788106983115
HEY1#23462104.040111043105718.62472978604083e-073.74535615020507e-05
HMGN3#932486.542838178680471.78445645847134e-066.69902401388528e-05
MAX#414963.871533305404270.001649602786473820.0103169570283573
MYC#4609105.22228187160946.6214088608781e-084.04405450304824e-06
NFKB1#4790105.488063424193844.03027026544603e-082.66234912240935e-06
PAX5#507996.002608978060053.30907588058665e-071.6559490938792e-05
POLR2A#5430102.147453176558070.0004793377491637920.00436456453225085
SIN3A#2594263.245330836089080.004223840630485730.020101785901449
TAF1#6872103.343046285745295.73229241267096e-060.000172379754473637
TBP#6908103.706770687096392.04059382584877e-067.45426997474013e-05
TCF7L2#69341010.77017656313734.75049080034347e-115.3752601158946e-09
TFAP2A#70201016.5186343730456.58593123034545e-139.48728374849721e-11
TFAP2C#70221010.80922860986024.58158302019868e-115.18976083564566e-09
YY1#7528104.911170749853861.22387217331053e-077.02693710326434e-06
ZBTB7A#5134196.61671837708831.39690928008423e-077.92029361035381e-06
ZNF143#770268.100525931336742.6666044303864e-050.000571511389503642



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.