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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C382_dura_Preadipocyte_Adipocyte_Astrocyte_trachea_diaphragm_vein
|full_id=C382_dura_Preadipocyte_Adipocyte_Astrocyte_trachea_diaphragm_vein
|gostat_on_coexpression_clusters=GO:0005515!protein binding!0.018939282072879!93166;3778;3488;1052;83938;6423$GO:0051150!regulation of smooth muscle cell differentiation!0.018939282072879!93166$GO:0051151!negative regulation of smooth muscle cell differentiation!0.018939282072879!93166$GO:0051148!negative regulation of muscle cell differentiation!0.018939282072879!93166$GO:0051147!regulation of muscle cell differentiation!0.0202004141903781!93166$GO:0051145!smooth muscle cell differentiation!0.0336574476799169!93166$GO:0046983!protein dimerization activity!0.0344695852545456!93166;1052
|gostat_on_coexpression_clusters=GO:0005515!protein binding!0.018939282072879!93166;3778;3488;1052;83938;6423$GO:0051150!regulation of smooth muscle cell differentiation!0.018939282072879!93166$GO:0051151!negative regulation of smooth muscle cell differentiation!0.018939282072879!93166$GO:0051148!negative regulation of muscle cell differentiation!0.018939282072879!93166$GO:0051147!regulation of muscle cell differentiation!0.0202004141903781!93166$GO:0051145!smooth muscle cell differentiation!0.0336574476799169!93166$GO:0046983!protein dimerization activity!0.0344695852545456!93166;1052

Revision as of 16:48, 12 September 2012


Full id: C382_dura_Preadipocyte_Adipocyte_Astrocyte_trachea_diaphragm_vein



Phase1 CAGE Peaks

Hg19::chr10:78078199..78078208,+p8@C10orf11
Hg19::chr10:79398656..79398666,-p25@KCNMA1
Hg19::chr1:110626157..110626165,+p@chr1:110626157..110626165
+
Hg19::chr2:217560615..217560623,-p73@IGFBP5
Hg19::chr2:45234395..45234400,-p@chr2:45234395..45234400
-
Hg19::chr2:45715445..45715482,-p@chr2:45715445..45715482
-
Hg19::chr3:112931366..112931373,-p@chr3:112931366..112931373
-
Hg19::chr3:112931383..112931390,-p@chr3:112931383..112931390
-
Hg19::chr3:112931404..112931414,-p@chr3:112931404..112931414
-
Hg19::chr3:112931435..112931445,-p@chr3:112931435..112931445
-
Hg19::chr3:112931478..112931524,-p@chr3:112931478..112931524
-
Hg19::chr3:112931527..112931557,-p@chr3:112931527..112931557
-
Hg19::chr4:154709612..154709627,+p@chr4:154709612..154709627
+
Hg19::chr4:154710210..154710243,-p1@SFRP2
Hg19::chr4:154711058..154711075,+p@chr4:154711058..154711075
+
Hg19::chr4:154712764..154712772,-p@chr4:154712764..154712772
-
Hg19::chr5:122434917..122434927,+p@chr5:122434917..122434927
+
Hg19::chr5:122434947..122434959,+p4@PRDM6
Hg19::chr5:39892092..39892099,+p@chr5:39892092..39892099
+
Hg19::chr5:39892121..39892134,+p@chr5:39892121..39892134
+
Hg19::chr7:115135068..115135092,-p@chr7:115135068..115135092
-
Hg19::chr8:43349758..43349771,+p@chr8:43349758..43349771
+
Hg19::chr8:43349794..43349803,+p@chr8:43349794..43349803
+
Hg19::chr8:43349847..43349852,+p@chr8:43349847..43349852
+
Hg19::chr8:48651813..48651830,-p14@CEBPD
Hg19::chr9:23524699..23524703,-p@chr9:23524699..23524703
-
Hg19::chr9:23524722..23524736,-p@chr9:23524722..23524736
-
Hg19::chr9:23524772..23524783,-p@chr9:23524772..23524783
-


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:0005515protein binding0.018939282072879
GO:0051150regulation of smooth muscle cell differentiation0.018939282072879
GO:0051151negative regulation of smooth muscle cell differentiation0.018939282072879
GO:0051148negative regulation of muscle cell differentiation0.018939282072879
GO:0051147regulation of muscle cell differentiation0.0202004141903781
GO:0051145smooth muscle cell differentiation0.0336574476799169
GO:0046983protein dimerization activity0.0344695852545456



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
fat cell6.03e-0915
Uber Anatomy
Ontology termp-valuen
adult organism7.34e-41115
central nervous system1.93e-2282
regional part of nervous system7.18e-2294
nervous system7.18e-2294
neurectoderm7.28e-2190
neural plate7.54e-2186
presumptive neural plate7.54e-2186
ectoderm2.14e-20173
presumptive ectoderm2.14e-20173
ectoderm-derived structure3.86e-20169
neural tube1.02e-1857
neural rod1.02e-1857
future spinal cord1.02e-1857
neural keel1.02e-1857
anterior region of body9.60e-18129
craniocervical region9.60e-18129
head2.62e-17123
brain5.34e-1769
future brain5.34e-1769
regional part of brain2.87e-1659
pre-chordal neural plate7.24e-1661
anterior neural tube3.09e-1442
regional part of forebrain1.29e-1341
forebrain1.29e-1341
future forebrain1.29e-1341
organism subdivision1.07e-12365
multi-cellular organism1.52e-12659
telencephalon1.59e-1134
regional part of telencephalon3.28e-1133
gray matter4.94e-1134
brain grey matter4.94e-1134
cerebral hemisphere8.31e-1132
cerebral cortex1.49e-0925
pallium1.49e-0925
regional part of cerebral cortex3.65e-0822
embryo7.47e-08612
organ part8.24e-08219
neocortex2.06e-0720
anatomical system4.87e-07625
anatomical group7.15e-07626


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

No analysis results for this cluster

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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