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Coexpression cluster:C2696: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2696_Alveolar_Amniotic_Mesenchymal_Mallassezderived_Placental_Adipocyte_Urothelial
|full_id=C2696_Alveolar_Amniotic_Mesenchymal_Mallassezderived_Placental_Adipocyte_Urothelial
|id=C2696
|id=C2696

Revision as of 15:27, 12 September 2012


Full id: C2696_Alveolar_Amniotic_Mesenchymal_Mallassezderived_Placental_Adipocyte_Urothelial



Phase1 CAGE Peaks

Hg19::chr2:24307635..24307660,-p1@TP53I3
Hg19::chr2:24307664..24307682,-p6@TP53I3
Hg19::chr2:24307692..24307711,-p3@TP53I3
Hg19::chr2:24307712..24307742,-p2@TP53I3


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
embryonic cell9.35e-30248
mesodermal cell3.75e-24119
non-terminally differentiated cell1.66e-23180
animal cell3.76e-23679
eukaryotic cell3.76e-23679
somatic cell7.12e-21591
epithelial cell1.95e-14254
contractile cell5.63e-1359
fibroblast6.47e-1375
muscle precursor cell6.18e-1257
myoblast6.18e-1257
multi-potent skeletal muscle stem cell6.18e-1257
lining cell8.63e-1257
barrier cell8.63e-1257
meso-epithelial cell5.46e-1144
muscle cell8.05e-1154
endothelial cell1.79e-1035
electrically responsive cell2.67e-1060
electrically active cell2.67e-1060
native cell8.35e-10722
smooth muscle cell1.65e-0942
smooth muscle myoblast1.65e-0942
endothelial cell of vascular tree9.72e-0924
blood vessel endothelial cell1.69e-0718
embryonic blood vessel endothelial progenitor cell1.69e-0718
vascular associated smooth muscle cell3.67e-0732
epithelial cell of nephron8.53e-0716
preadipocyte8.98e-0712
Uber Anatomy
Ontology termp-valuen
multi-cellular organism4.22e-19659
vasculature4.33e-1879
vascular system4.33e-1879
trunk4.96e-18216
trunk mesenchyme2.73e-16143
anatomical system5.92e-16625
anatomical group9.02e-16626
epithelial tube1.41e-14118
vessel1.67e-1469
mesoderm6.29e-14448
mesoderm-derived structure6.29e-14448
presumptive mesoderm6.29e-14448
multilaminar epithelium7.35e-1482
splanchnic layer of lateral plate mesoderm1.58e-1384
somite1.94e-1383
paraxial mesoderm1.94e-1383
presomitic mesoderm1.94e-1383
presumptive segmental plate1.94e-1383
trunk paraxial mesoderm1.94e-1383
presumptive paraxial mesoderm1.94e-1383
unilaminar epithelium1.95e-13138
mesenchyme4.11e-13238
entire embryonic mesenchyme4.11e-13238
blood vessel9.01e-1360
epithelial tube open at both ends9.01e-1360
blood vasculature9.01e-1360
vascular cord9.01e-1360
embryo1.02e-11612
embryonic structure2.88e-11605
developing anatomical structure2.88e-11605
germ layer3.52e-11604
embryonic tissue3.52e-11604
presumptive structure3.52e-11604
epiblast (generic)3.52e-11604
cardiovascular system3.58e-11110
dermomyotome4.64e-1170
organism subdivision1.07e-10365
circulatory system1.94e-10113
skeletal muscle tissue1.94e-1061
striated muscle tissue1.94e-1061
myotome1.94e-1061
artery2.65e-1042
arterial blood vessel2.65e-1042
arterial system2.65e-1042
muscle tissue2.91e-1063
musculature2.91e-1063
musculature of body2.91e-1063
multi-tissue structure5.53e-09347
cell layer6.75e-09312
subdivision of trunk7.12e-09113
epithelium9.51e-09309
simple squamous epithelium5.11e-0822
systemic artery5.50e-0833
systemic arterial system5.50e-0833
squamous epithelium1.17e-0725
endothelium1.69e-0718
blood vessel endothelium1.69e-0718
cardiovascular system endothelium1.69e-0718
nephron epithelium8.53e-0716
nephron8.53e-0716
uriniferous tubule8.53e-0716
metanephric mesenchyme8.53e-0716
nephrogenic mesenchyme8.53e-0716


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#90546.336201576962630.0006203100587215640.00513023140820569
CTCF#1066445.360256373075030.001211145381643620.00818604792347129
CTCFL#140690419.74647435897446.5732084880439e-060.000193271205316108
EBF1#187948.9064668465690.00015887907472010.00199869569798754
ELF1#199744.258097958807540.003041525565781240.0161147467818906
EP300#203346.77394172622320.0004748459821442640.00434640136101357
ETS1#211349.728760922202340.0001115955317418140.0015469771355964
HEY1#2346244.040111043105710.00375304636917980.0186383456847727
HMGN3#932448.178547723350590.0002234570284440470.00248431217731189
IRF1#365947.63716375356390.0002938853996185490.00307916304682601
JUNB#3726430.61063265982111.13787152942193e-064.6621484763161e-05
RAD21#5885410.35503389545638.6948481184721e-050.00129670318812667
SMARCB1#6598418.25271578115749.00423392720929e-060.000241932901241011
SP2#6668426.15353049384462.13562021071447e-067.75259086502638e-05
TAF1#687243.343046285745290.008005664898701650.0322770088154533
TAF7#6879411.43306940492395.85061525419808e-050.000970663076303722
TBP#690843.706770687096390.005296377814784350.0244647679167741
THAP1#55145431.36914460285131.03171810326891e-064.32043331945877e-05
YY1#752844.911170749853860.00171871838055440.0106973318800191
ZBTB7A#5134147.35190930787590.000342223540015990.00347072094540007



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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