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Coexpression cluster:C1108: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1108_Chondrocyte_Adipocyte_tenocyte_Preadipocyte_Osteoblast_mesenchymal_Myoblast
|full_id=C1108_Chondrocyte_Adipocyte_tenocyte_Preadipocyte_Osteoblast_mesenchymal_Myoblast
|id=C1108
|id=C1108

Revision as of 13:34, 12 September 2012


Full id: C1108_Chondrocyte_Adipocyte_tenocyte_Preadipocyte_Osteoblast_mesenchymal_Myoblast



Phase1 CAGE Peaks

Hg19::chr10:124220985..124220996,+p5@HTRA1
Hg19::chr10:124221036..124221047,+p4@HTRA1
Hg19::chr10:124221061..124221080,+p2@HTRA1
Hg19::chr10:124221082..124221140,+p1@HTRA1
Hg19::chr10:124221146..124221166,+p3@HTRA1
Hg19::chr10:124248410..124248428,+p@chr10:124248410..124248428
+
Hg19::chr10:124248461..124248481,+p7@HTRA1


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
non-terminally differentiated cell2.94e-19180
fibroblast1.03e-1375
fat cell5.66e-0915
preadipocyte2.58e-0712
muscle precursor cell3.05e-0757
myoblast3.05e-0757
multi-potent skeletal muscle stem cell3.05e-0757
Uber Anatomy
Ontology termp-valuen
organism subdivision6.35e-26365
multi-cellular organism1.66e-22659
anatomical system9.16e-19625
anatomical group2.15e-18626
cell layer7.11e-15312
epithelium8.21e-15309
multi-tissue structure9.27e-15347
head9.38e-14123
regional part of brain1.82e-1359
ectoderm-derived structure2.76e-13169
embryo4.73e-13612
embryonic structure4.86e-13605
developing anatomical structure4.86e-13605
germ layer6.72e-13604
embryonic tissue6.72e-13604
presumptive structure6.72e-13604
epiblast (generic)6.72e-13604
anatomical cluster8.42e-13286
neural tube9.39e-1357
neural rod9.39e-1357
future spinal cord9.39e-1357
neural keel9.39e-1357
anterior region of body2.26e-12129
craniocervical region2.26e-12129
central nervous system4.96e-1282
ectoderm1.33e-11173
presumptive ectoderm1.33e-11173
brain1.79e-1169
future brain1.79e-1169
anatomical conduit3.87e-11241
organ8.19e-11511
somite1.21e-1083
paraxial mesoderm1.21e-1083
presomitic mesoderm1.21e-1083
presumptive segmental plate1.21e-1083
trunk paraxial mesoderm1.21e-1083
presumptive paraxial mesoderm1.21e-1083
neural plate1.85e-1086
presumptive neural plate1.85e-1086
anterior neural tube3.24e-1042
regional part of forebrain7.55e-1041
forebrain7.55e-1041
future forebrain7.55e-1041
tube1.12e-09194
regional part of nervous system1.39e-0994
nervous system1.39e-0994
surface structure1.50e-0995
adult organism2.32e-09115
multilaminar epithelium7.62e-0982
trunk mesenchyme1.52e-08143
organ part1.68e-08219
neurectoderm1.86e-0890
pre-chordal neural plate2.19e-0861
gray matter3.06e-0834
brain grey matter3.06e-0834
telencephalon3.13e-0834
dermomyotome4.04e-0870
regional part of telencephalon5.86e-0833
integument7.43e-0845
integumental system7.43e-0845
adipose tissue7.63e-0814
trunk8.99e-08216
cerebral hemisphere1.84e-0732
tissue3.80e-07787
skeletal muscle tissue6.17e-0761
striated muscle tissue6.17e-0761
myotome6.17e-0761
muscle tissue6.38e-0763
musculature6.38e-0763
musculature of body6.38e-0763


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
E2F1#186953.505278010628090.005090553587915050.0236826729996107



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.