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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1242_Mast_anaplastic_putamen_caudate_nucleus_occipital_insula
|full_id=C1242_Mast_anaplastic_putamen_caudate_nucleus_occipital_insula
|gostat_on_coexpression_clusters=GO:0007274!neuromuscular synaptic transmission!0.0445020006415389!1960$GO:0007422!peripheral nervous system development!0.0477843731091476!1960$GO:0007623!circadian rhythm!0.0477843731091476!1960
|gostat_on_coexpression_clusters=GO:0007274!neuromuscular synaptic transmission!0.0445020006415389!1960$GO:0007422!peripheral nervous system development!0.0477843731091476!1960$GO:0007623!circadian rhythm!0.0477843731091476!1960

Revision as of 13:44, 12 September 2012


Full id: C1242_Mast_anaplastic_putamen_caudate_nucleus_occipital_insula



Phase1 CAGE Peaks

Hg19::chr19:47105424..47105433,+p32@CALM3
Hg19::chr3:171178035..171178046,-p7@TNIK
Hg19::chr3:71181437..71181451,-p@chr3:71181437..71181451
-
Hg19::chr8:22550045..22550063,-p8@EGR3
Hg19::chr8:22550509..22550526,-p6@EGR3
Hg19::chr8:22550530..22550609,-p2@EGR3
Hg19::chr8:22550700..22550717,-p4@EGR3


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:0007274neuromuscular synaptic transmission0.0445020006415389
GO:0007422peripheral nervous system development0.0477843731091476
GO:0007623circadian rhythm0.0477843731091476



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
CD14-positive, CD16-negative classical monocyte1.26e-0742
Uber Anatomy
Ontology termp-valuen
neural tube1.29e-2257
neural rod1.29e-2257
future spinal cord1.29e-2257
neural keel1.29e-2257
anterior neural tube6.11e-2242
regional part of forebrain1.15e-2141
forebrain1.15e-2141
future forebrain1.15e-2141
adult organism6.91e-21115
central nervous system9.18e-2082
telencephalon1.37e-1934
gray matter2.69e-1934
brain grey matter2.69e-1934
regional part of telencephalon7.57e-1933
cerebral hemisphere1.04e-1832
regional part of brain1.83e-1859
brain1.57e-1669
future brain1.57e-1669
regional part of nervous system2.25e-1694
nervous system2.25e-1694
regional part of cerebral cortex3.94e-1622
neocortex1.05e-1420
neural plate1.81e-1486
presumptive neural plate1.81e-1486
cerebral cortex1.06e-1325
pallium1.06e-1325
neurectoderm1.28e-1390
pre-chordal neural plate5.23e-1261
basal ganglion1.41e-079
nuclear complex of neuraxis1.41e-079
aggregate regional part of brain1.41e-079
collection of basal ganglia1.41e-079
cerebral subcortex1.41e-079
nucleus of brain3.90e-079
neural nucleus3.90e-079


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.