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Coexpression cluster:C3371: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3371_normal_left_heart_lung_diaphragm_aorta_tenocyte
|full_id=C3371_normal_left_heart_lung_diaphragm_aorta_tenocyte
|id=C3371
|id=C3371

Revision as of 16:17, 12 September 2012


Full id: C3371_normal_left_heart_lung_diaphragm_aorta_tenocyte



Phase1 CAGE Peaks

Hg19::chr13:39917684..39917697,-p4@LHFP
Hg19::chr13:40177261..40177339,-p1@LHFP
Hg19::chr13:40177342..40177361,-p2@LHFP


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 cell3.71e-12180
fibroblast9.27e-1175
fat cell2.02e-0715
Uber Anatomy
Ontology termp-valuen
adult organism6.17e-15115
multi-cellular organism8.78e-15659
ectoderm1.23e-13173
presumptive ectoderm1.23e-13173
organism subdivision1.71e-13365
ectoderm-derived structure6.82e-13169
regional part of brain4.55e-1159
regional part of nervous system6.45e-1194
nervous system6.45e-1194
anatomical system7.60e-11625
anatomical group9.27e-11626
central nervous system1.58e-1082
neural tube3.71e-1057
neural rod3.71e-1057
future spinal cord3.71e-1057
neural keel3.71e-1057
neurectoderm4.28e-1090
head4.78e-10123
brain9.61e-1069
future brain9.61e-1069
anterior region of body1.44e-09129
craniocervical region1.44e-09129
neural plate2.28e-0986
presumptive neural plate2.28e-0986
multi-tissue structure4.85e-09347
organ component layer5.43e-0957
cell layer8.77e-09312
organ part1.09e-08219
epithelium3.94e-08309
anatomical cluster5.67e-08286
embryonic structure2.15e-07605
developing anatomical structure2.15e-07605
embryo3.12e-07612
germ layer3.98e-07604
embryonic tissue3.98e-07604
presumptive structure3.98e-07604
epiblast (generic)3.98e-07604


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.