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Coexpression cluster:C384: Difference between revisions

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|tf_chipseq_enrich=CTCFL#140690;6:4.23138736263736:0.00241671280905517:0.0136196346354907!SPI1#6688;11:3.22312709263393:0.00025658527320966:0.00276149107056303
|tf_chipseq_enrich=CTCFL#140690;6:4.23138736263736:0.00241671280905517:0.0136196346354907!SPI1#6688;11:3.22312709263393:0.00025658527320966:0.00276149107056303
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}}
}}

Revision as of 14:10, 26 November 2012


Full id: C384_Adipocyte_smooth_bladder_left_aorta_Osteoblast_colon



Phase1 CAGE Peaks

Hg19::chr11:117075220..117075249,+p1@uc001pqq.1
Hg19::chr1:201869414..201869432,+p@chr1:201869414..201869432
+
Hg19::chr20:35173246..35173275,+p3@MYL9
Hg19::chr20:35173334..35173350,+p6@MYL9
Hg19::chr20:35173392..35173405,+p8@MYL9
Hg19::chr20:35173425..35173448,+p4@MYL9
Hg19::chr20:35176429..35176448,+p@chr20:35176429..35176448
+
Hg19::chr20:35176459..35176471,+p@chr20:35176459..35176471
+
Hg19::chr20:35176468..35176476,-p@chr20:35176468..35176476
-
Hg19::chr20:35176474..35176493,+p@chr20:35176474..35176493
+
Hg19::chr20:35176518..35176542,+p@chr20:35176518..35176542
+
Hg19::chr20:35176544..35176572,+p@chr20:35176544..35176572
+
Hg19::chr20:35177479..35177514,+p@chr20:35177479..35177514
+
Hg19::chr20:35177539..35177547,+p@chr20:35177539..35177547
+
Hg19::chr20:35177588..35177615,-p@chr20:35177588..35177615
-
Hg19::chr20:35177596..35177615,+p@chr20:35177596..35177615
+
Hg19::chr20:35177635..35177755,-p@chr20:35177635..35177755
-
Hg19::chr20:35177642..35177704,+p@chr20:35177642..35177704
+
Hg19::chr20:35177709..35177724,+p@chr20:35177709..35177724
+
Hg19::chr20:35177756..35177772,+p@chr20:35177756..35177772
+
Hg19::chr20:35177820..35177829,+p@chr20:35177820..35177829
+
Hg19::chr20:35177847..35177864,+p@chr20:35177847..35177864
+
Hg19::chr20:35177969..35177986,+p@chr20:35177969..35177986
+
Hg19::chr20:35178012..35178028,+p@chr20:35178012..35178028
+
Hg19::chr20:35178034..35178046,+p@chr20:35178034..35178046
+
Hg19::chr20:35178050..35178086,-p@chr20:35178050..35178086
-
Hg19::chr20:35178057..35178112,+p@chr20:35178057..35178112
+
Hg19::chr20:35178101..35178139,-p@chr20:35178101..35178139
-


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


GO IDGO nameFDR corrected p-value
GO:0005859muscle myosin complex0.0105086541858001
GO:0016460myosin II complex0.0105086541858001
GO:0006937regulation of muscle contraction0.0105086541858001
GO:0008307structural constituent of muscle0.0105086541858001
GO:0044449contractile fiber part0.0106754582204953
GO:0043292contractile fiber0.0106754582204953
GO:0016459myosin complex0.0152983128963348
GO:0003012muscle system process0.0183484438164763
GO:0006936muscle contraction0.0183484438164763
GO:0051239regulation of multicellular organismal process0.0269312696017041
GO:0015629actin cytoskeleton0.0269312696017041



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
mesenchyme2.85e-16160
entire embryonic mesenchyme2.85e-16160
trunk mesenchyme6.69e-15122
muscle tissue2.33e-1464
musculature2.33e-1464
musculature of body2.33e-1464
epithelial vesicle9.75e-1478
dense mesenchyme tissue1.14e-1373
skeletal muscle tissue2.64e-1362
striated muscle tissue2.64e-1362
myotome2.64e-1362
paraxial mesoderm4.00e-1372
presumptive paraxial mesoderm4.00e-1372
somite4.10e-1371
presomitic mesoderm4.10e-1371
presumptive segmental plate4.10e-1371
dermomyotome4.10e-1371
trunk paraxial mesoderm4.10e-1371
multilaminar epithelium1.23e-1083
trunk1.06e-09199
mesoderm1.45e-09315
mesoderm-derived structure1.45e-09315
presumptive mesoderm1.45e-09315
organism subdivision3.85e-09264
multi-tissue structure1.76e-08342
splanchnic layer of lateral plate mesoderm8.30e-0883
primary circulatory organ3.42e-0727
artery5.62e-0742
arterial blood vessel5.62e-0742
arterial system5.62e-0742
intermediate mesoderm6.12e-0728
systemic artery6.55e-0733
systemic arterial system6.55e-0733
adipose tissue6.83e-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
CTCFL#14069064.231387362637360.002416712809055170.0136196346354907
SPI1#6688113.223127092633930.000256585273209660.00276149107056303



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.