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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:54, 8 August 2012


Full id: C3109_skeletal_occipital_temporal_postcentral_paracentral_insula_parietal



Phase1 CAGE Peaks

Hg19::chr11:123525613..123525633,-p6@SCN3B
Hg19::chr17:37353856..37353900,-p1@CACNB1
Hg19::chr17:37353907..37353930,-p2@CACNB1


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:0022843voltage-gated cation channel activity0.00153206738976007
GO:0005244voltage-gated ion channel activity0.00153206738976007
GO:0022832voltage-gated channel activity0.00153206738976007
GO:0005261cation channel activity0.00187461200335429
GO:0046873metal ion transmembrane transporter activity0.00187461200335429
GO:0022836gated channel activity0.00187461200335429
GO:0005216ion channel activity0.00195450256590777
GO:0030001metal ion transport0.00195450256590777
GO:0022838substrate specific channel activity0.00195450256590777
GO:0015267channel activity0.00195450256590777
GO:0022803passive transmembrane transporter activity0.00195450256590777
GO:0006812cation transport0.00257593431578316
GO:0008324cation transmembrane transporter activity0.00257593431578316
GO:0005248voltage-gated sodium channel activity0.0047167129409244
GO:0015075ion transmembrane transporter activity0.00513488797003193
GO:0006811ion transport0.00513488797003193
GO:0022891substrate-specific transmembrane transporter activity0.00600986352552187
GO:0005891voltage-gated calcium channel complex0.00616847909776799
GO:0022857transmembrane transporter activity0.00621379523318357
GO:0022892substrate-specific transporter activity0.00688725467743432
GO:0005272sodium channel activity0.00814285141353296
GO:0005245voltage-gated calcium channel activity0.00913501136980657
GO:0031402sodium ion binding0.0125145366795723
GO:0005262calcium channel activity0.014861404268176
GO:0003012muscle system process0.0190081598302255
GO:0006936muscle contraction0.0190081598302255
GO:0006814sodium ion transport0.0191893628056703
GO:0006816calcium ion transport0.0195707371948487
GO:0005886plasma membrane0.0221460263117811
GO:0031420alkali metal ion binding0.0221460263117811
GO:0006810transport0.0228914222139489
GO:0015674di-, tri-valent inorganic cation transport0.0228914222139489
GO:0051234establishment of localization0.0228914222139489
GO:0051179localization0.0260924446112384
GO:0015672monovalent inorganic cation transport0.0449431125566352



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
central nervous system2.52e-2382
regional part of nervous system1.29e-2194
nervous system1.29e-2194
neural tube1.31e-2157
neural rod1.31e-2157
future spinal cord1.31e-2157
neural keel1.31e-2157
brain4.56e-2069
future brain4.56e-2069
regional part of brain1.12e-1859
ectoderm-derived structure2.29e-17169
regional part of forebrain3.32e-1741
forebrain3.32e-1741
future forebrain3.32e-1741
adult organism4.60e-17115
neural plate5.72e-1786
presumptive neural plate5.72e-1786
telencephalon6.63e-1734
gray matter7.42e-1734
brain grey matter7.42e-1734
anterior neural tube8.59e-1742
cerebral hemisphere1.32e-1632
ectoderm1.61e-16173
presumptive ectoderm1.61e-16173
regional part of telencephalon3.03e-1633
anterior region of body3.94e-16129
craniocervical region3.94e-16129
neurectoderm1.24e-1590
head2.26e-14123
regional part of cerebral cortex1.08e-1322
cerebral cortex9.28e-1325
pallium9.28e-1325
organism subdivision1.25e-12365
neocortex1.63e-1220
pre-chordal neural plate2.00e-1161
epithelium1.47e-08309
cell layer2.99e-08312
multi-tissue structure4.38e-07347
organ part8.73e-07219


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.