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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3549_testis_Whole_blood_Hepatic_skeletal_Reticulocytes_liver
|full_id=C3549_testis_Whole_blood_Hepatic_skeletal_Reticulocytes_liver
|id=C3549
|id=C3549

Revision as of 16:29, 12 September 2012


Full id: C3549_testis_Whole_blood_Hepatic_skeletal_Reticulocytes_liver



Phase1 CAGE Peaks

Hg19::chr16:28841378..28841383,+p@chr16:28841378..28841383
+
Hg19::chr2:97481875..97481902,-p@chr2:97481875..97481902
-
Hg19::chrX:37061830..37061867,-p1@FTH1P18


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
mature alpha-beta T cell8.52e-0818
alpha-beta T cell8.52e-0818
immature T cell8.52e-0818
mature T cell8.52e-0818
immature alpha-beta T cell8.52e-0818
T cell6.21e-0725
pro-T cell6.21e-0725
Uber Anatomy
Ontology termp-valuen
adult organism9.21e-27115
neural tube1.33e-1457
neural rod1.33e-1457
future spinal cord1.33e-1457
neural keel1.33e-1457
regional part of brain1.85e-1259
neural plate3.32e-1186
presumptive neural plate3.32e-1186
regional part of nervous system4.62e-1194
nervous system4.62e-1194
brain4.64e-1169
future brain4.64e-1169
anterior neural tube8.27e-1142
regional part of forebrain8.41e-1141
forebrain8.41e-1141
future forebrain8.41e-1141
central nervous system9.79e-1182
neurectoderm1.45e-1090
pre-chordal neural plate6.43e-1061
telencephalon1.15e-0934
regional part of telencephalon2.18e-0933
gray matter3.46e-0934
brain grey matter3.46e-0934
anterior region of body4.19e-09129
craniocervical region4.19e-09129
cerebral hemisphere9.92e-0932
cerebral cortex1.09e-0725
pallium1.09e-0725
head1.13e-07123
regional part of cerebral cortex2.11e-0722
tube8.68e-07194
ectoderm-derived structure9.12e-07169


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.