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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C333_Fibroblast_Smooth_Preadipocyte_Adipocyte_Ewing_Placental_sacrococcigeal
|full_id=C333_Fibroblast_Smooth_Preadipocyte_Adipocyte_Ewing_Placental_sacrococcigeal
|id=C333
|id=C333

Revision as of 16:14, 12 September 2012


Full id: C333_Fibroblast_Smooth_Preadipocyte_Adipocyte_Ewing_Placental_sacrococcigeal



Phase1 CAGE Peaks

Hg19::chr3:112317985..112318004,-p@chr3:112317985..112318004
-
Hg19::chr3:112318598..112318609,-p@chr3:112318598..112318609
-
Hg19::chr3:112320772..112320784,-p@chr3:112320772..112320784
-
Hg19::chr3:112324034..112324048,-p@chr3:112324034..112324048
-
Hg19::chr3:112356995..112357025,+p@chr3:112356995..112357025
+
Hg19::chr3:112357199..112357228,+p@chr3:112357199..112357228
+
Hg19::chr3:112357559..112357568,-p@chr3:112357559..112357568
-
Hg19::chr3:112357575..112357598,-p@chr3:112357575..112357598
-
Hg19::chr3:112357721..112357731,-p@chr3:112357721..112357731
-
Hg19::chr3:112357721..112357832,+p@chr3:112357721..112357832
+
Hg19::chr3:112357766..112357771,-p@chr3:112357766..112357771
-
Hg19::chr3:112357848..112357858,-p@chr3:112357848..112357858
-
Hg19::chr3:112358008..112358018,-p25@CCDC80
Hg19::chr3:112358055..112358066,-p24@CCDC80
Hg19::chr3:112358125..112358137,-p22@CCDC80
Hg19::chr3:112358228..112358239,-p31@CCDC80
Hg19::chr3:112358263..112358270,-p35@CCDC80
Hg19::chr3:112358632..112358646,-p5@CCDC80
Hg19::chr3:112359190..112359239,-p9@CCDC80
Hg19::chr3:112359295..112359306,-p19@CCDC80
Hg19::chr3:112359358..112359370,-p26@CCDC80
Hg19::chr3:112359375..112359386,-p27@CCDC80
Hg19::chr3:112359471..112359488,-p21@CCDC80
Hg19::chr3:112359502..112359520,-p13@CCDC80
Hg19::chr3:112359529..112359540,-p23@CCDC80
Hg19::chr3:112359550..112359569,-p7@CCDC80
Hg19::chr3:112359574..112359583,-p30@CCDC80
Hg19::chr3:112359611..112359633,-p18@CCDC80
Hg19::chr3:112359634..112359653,-p10@CCDC80
Hg19::chr3:112359654..112359671,-p15@CCDC80
Hg19::chr3:112359698..112359713,-p17@CCDC80
Hg19::chr3:112359729..112359753,+p@chr3:112359729..112359753
+
Hg19::chr3:112359880..112359894,-p2@CCDC80
Hg19::chr3:112359959..112359972,-p3@CCDC80
Hg19::chr3:112359975..112359997,-p1@CCDC80


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
somite9.01e-1983
paraxial mesoderm9.01e-1983
presomitic mesoderm9.01e-1983
presumptive segmental plate9.01e-1983
trunk paraxial mesoderm9.01e-1983
presumptive paraxial mesoderm9.01e-1983
dermomyotome6.68e-1870
muscle tissue1.97e-1763
musculature1.97e-1763
musculature of body1.97e-1763
skeletal muscle tissue3.63e-1761
striated muscle tissue3.63e-1761
myotome3.63e-1761
multilaminar epithelium4.50e-1782
organism subdivision1.33e-15365
splanchnic layer of lateral plate mesoderm6.38e-1584
trunk mesenchyme2.82e-13143
multi-cellular organism8.65e-13659
multi-tissue structure2.32e-12347
cell layer1.22e-11312
epithelium4.29e-11309
trunk4.32e-11216
unilaminar epithelium1.61e-10138
organ component layer3.27e-1057
vasculature6.78e-1079
vascular system6.78e-1079
surface structure7.75e-1095
anatomical system1.65e-09625
heart1.79e-0924
primitive heart tube1.79e-0924
primary heart field1.79e-0924
anterior lateral plate mesoderm1.79e-0924
heart tube1.79e-0924
heart primordium1.79e-0924
cardiac mesoderm1.79e-0924
cardiogenic plate1.79e-0924
heart rudiment1.79e-0924
primary circulatory organ2.41e-0927
anatomical group2.91e-09626
mesenchyme5.10e-09238
entire embryonic mesenchyme5.10e-09238
blood vessel8.57e-0960
epithelial tube open at both ends8.57e-0960
blood vasculature8.57e-0960
vascular cord8.57e-0960
artery9.39e-0942
arterial blood vessel9.39e-0942
arterial system9.39e-0942
integument1.15e-0845
integumental system1.15e-0845
anatomical cluster1.43e-08286
epithelial tube1.84e-08118
circulatory system4.79e-08113
systemic artery5.34e-0833
systemic arterial system5.34e-0833
cardiovascular system7.55e-08110
vessel8.59e-0869
skin of body4.73e-0740
adipose tissue5.75e-0714


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
BCLAF1#977474.330529522024370.0009588178195446460.00689893036551314
EP300#2033112.128953113955860.009755139762610230.0366824023067347
MAFK#7975107.743066610808553.65307166813718e-071.80133688360991e-05
NR2C2#718287.45476820691228.71584813982768e-060.000235334659740296
POU2F2#545292.341574757705220.01145632032383210.0419113996882691
TRIM28#10155157.967367876541081.04717244445614e-101.13097872726531e-08



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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