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Coexpression cluster:C2053: Difference between revisions

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|full_id=C2053_Fibroblast_tridermal_tenocyte_transitionalcell_normal_Pancreatic_Synoviocyte
|full_id=C2053_Fibroblast_tridermal_tenocyte_transitionalcell_normal_Pancreatic_Synoviocyte
|id=C2053
|id=C2053
|ontology_enrichment_celltype=CL:0002620!2.13e-09!23;CL:0000057!2.87e-08!75;CL:0000499!9.43e-07!27
|ontology_enrichment_celltype=CL:0002620!3.29e-10!23;CL:0000057!5.18e-10!76;CL:0000499!6.34e-08!28;CL:0002556!1.21e-07!6;CL:0002552!7.96e-07!5
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:17!5.17e-07!5;DOID:450!5.17e-07!5;DOID:66!5.17e-07!5;DOID:423!5.17e-07!5;DOID:0080000!5.17e-07!5;DOID:11722!5.17e-07!5
|ontology_enrichment_uberon=UBERON:0007023!2.67e-21!115;UBERON:0001049!9.50e-17!57;UBERON:0005068!9.50e-17!57;UBERON:0006241!9.50e-17!57;UBERON:0007135!9.50e-17!57;UBERON:0000033!1.77e-15!123;UBERON:0000153!7.50e-15!129;UBERON:0007811!7.50e-15!129;UBERON:0000475!1.63e-14!365;UBERON:0002346!4.39e-14!90;UBERON:0000955!6.31e-14!69;UBERON:0006238!6.31e-14!69;UBERON:0003075!8.89e-14!86;UBERON:0007284!8.89e-14!86;UBERON:0002616!1.18e-13!59;UBERON:0005743!1.69e-13!86;UBERON:0001017!4.50e-13!82;UBERON:0000073!4.40e-12!94;UBERON:0001016!4.40e-12!94;UBERON:0000924!1.13e-11!173;UBERON:0006601!1.13e-11!173;UBERON:0004121!2.64e-11!169;UBERON:0003080!3.94e-11!42;UBERON:0002020!9.41e-11!34;UBERON:0003528!9.41e-11!34;UBERON:0002780!1.13e-10!41;UBERON:0001890!1.13e-10!41;UBERON:0006240!1.13e-10!41;UBERON:0001893!1.58e-10!34;UBERON:0000062!3.00e-10!511;UBERON:0002791!6.13e-10!33;UBERON:0001869!7.46e-10!32;UBERON:0000468!1.12e-09!659;UBERON:0001950!8.75e-09!20;UBERON:0003102!9.82e-09!95;UBERON:0000481!1.49e-08!347;UBERON:0002619!3.75e-08!22;UBERON:0003056!5.33e-08!61;UBERON:0000956!3.21e-07!25;UBERON:0000203!3.21e-07!25;UBERON:0000075!3.40e-07!13;UBERON:0005944!3.40e-07!13;UBERON:0004288!3.40e-07!13;UBERON:0003089!3.40e-07!13;UBERON:0001737!3.77e-07!9;UBERON:0003076!3.83e-07!15;UBERON:0003057!3.83e-07!15
|ontology_enrichment_uberon=UBERON:0007023!5.87e-20!114;UBERON:0001049!1.28e-16!56;UBERON:0005068!1.28e-16!56;UBERON:0006241!1.28e-16!56;UBERON:0007135!1.28e-16!56;UBERON:0000073!6.15e-15!53;UBERON:0002616!6.15e-15!53;UBERON:0000955!2.15e-13!68;UBERON:0006238!2.15e-13!68;UBERON:0001017!3.04e-13!81;UBERON:0002780!3.28e-13!41;UBERON:0001890!3.28e-13!41;UBERON:0003080!3.28e-13!41;UBERON:0006240!3.28e-13!41;UBERON:0001950!1.02e-12!20;UBERON:0001016!1.53e-12!89;UBERON:0003528!2.91e-12!34;UBERON:0002020!2.91e-12!34;UBERON:0003075!3.34e-12!82;UBERON:0007284!3.34e-12!82;UBERON:0001893!3.91e-12!34;UBERON:0002619!4.01e-11!22;UBERON:0002346!4.60e-11!86;UBERON:0001869!4.65e-11!32;UBERON:0002791!6.55e-11!32;UBERON:0011216!1.22e-10!223;UBERON:0010314!3.60e-10!132;UBERON:0004121!9.08e-10!171;UBERON:0000924!9.08e-10!171;UBERON:0006601!9.08e-10!171;UBERON:0000956!3.24e-09!25;UBERON:0000203!3.24e-09!25;UBERON:0003056!4.39e-09!61;UBERON:0001737!2.32e-08!9;UBERON:0003129!4.26e-08!7;UBERON:0010371!1.09e-07!104;UBERON:0001758!1.21e-07!6;UBERON:0003672!1.21e-07!6;UBERON:0000468!2.47e-07!656;UBERON:0003102!2.59e-07!99;UBERON:0000200!6.21e-07!6
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}}
}}

Revision as of 12:00, 19 October 2012


Full id: C2053_Fibroblast_tridermal_tenocyte_transitionalcell_normal_Pancreatic_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr10:28034739..28034756,-p1@MKX
Hg19::chr10:28035112..28035130,-p5@MKX
Hg19::chr10:28035133..28035148,-p3@MKX
Hg19::chr10:28035155..28035166,-p8@MKX


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>disease_data<br>


Cell Type
Ontology termp-valuen
skin fibroblast3.29e-1023
fibroblast5.18e-1076
stromal cell6.34e-0828
fibroblast of periodontium1.21e-076
fibroblast of gingiva7.96e-075
Uber Anatomy
Ontology termp-valuen
adult organism5.87e-20114
neural tube1.28e-1656
neural rod1.28e-1656
future spinal cord1.28e-1656
neural keel1.28e-1656
regional part of nervous system6.15e-1553
regional part of brain6.15e-1553
brain2.15e-1368
future brain2.15e-1368
central nervous system3.04e-1381
regional part of forebrain3.28e-1341
forebrain3.28e-1341
anterior neural tube3.28e-1341
future forebrain3.28e-1341
neocortex1.02e-1220
nervous system1.53e-1289
brain grey matter2.91e-1234
gray matter2.91e-1234
neural plate3.34e-1282
presumptive neural plate3.34e-1282
telencephalon3.91e-1234
regional part of cerebral cortex4.01e-1122
neurectoderm4.60e-1186
cerebral hemisphere4.65e-1132
regional part of telencephalon6.55e-1132
organ system subdivision1.22e-10223
structure with developmental contribution from neural crest3.60e-10132
ectoderm-derived structure9.08e-10171
ectoderm9.08e-10171
presumptive ectoderm9.08e-10171
cerebral cortex3.24e-0925
pallium3.24e-0925
pre-chordal neural plate4.39e-0961
larynx2.32e-089
skull4.26e-087
ecto-epithelium1.09e-07104
periodontium1.21e-076
dentition1.21e-076
multi-cellular organism2.47e-07656
surface structure2.59e-0799
gyrus6.21e-076
Disease
Ontology termp-valuen
musculoskeletal system disease5.17e-075
myotonic disease5.17e-075
muscle tissue disease5.17e-075
myopathy5.17e-075
muscular disease5.17e-075
myotonic dystrophy5.17e-075


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.