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Coexpression cluster:C2528: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:22, 8 August 2012


Full id: C2528_left_heart_skeletal_salivary_parotid_melanoma_tongue



Phase1 CAGE Peaks

Hg19::chr1:153600869..153600926,+p1@S100A1
Hg19::chr1:153603063..153603085,+p2@S100A1
Hg19::chr3:42744146..42744193,-p1@HHATL
Hg19::chr3:48057890..48057923,-p6@MAP4


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:0048155S100 alpha binding0.00953642375842857
GO:0051117ATPase binding0.00953642375842857
GO:0048154S100 beta binding0.00953642375842857
GO:0007026negative regulation of microtubule depolymerization0.0198552699367001
GO:0031114regulation of microtubule depolymerization0.0198552699367001
GO:0007019microtubule depolymerization0.0198552699367001
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0198552699367001
GO:0016528sarcoplasm0.0198552699367001
GO:0016529sarcoplasmic reticulum0.0198552699367001
GO:0031110regulation of microtubule polymerization or depolymerization0.0207264605348736
GO:0031109microtubule polymerization or depolymerization0.0207895971926477
GO:0008016regulation of heart contraction0.0223822396814111
GO:0051261protein depolymerization0.0223822396814111
GO:0060047heart contraction0.0223822396814111
GO:0003015heart process0.0223822396814111
GO:0051129negative regulation of cellular component organization and biogenesis0.0232122025618016
GO:0051128regulation of cellular component organization and biogenesis0.039034393714147
GO:0000226microtubule cytoskeleton organization and biogenesis0.039034393714147
GO:0051248negative regulation of protein metabolic process0.039034393714147



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
adult organism5.19e-46115
neural tube1.42e-2857
neural rod1.42e-2857
future spinal cord1.42e-2857
neural keel1.42e-2857
brain8.00e-2669
future brain8.00e-2669
central nervous system1.13e-2582
regional part of brain7.46e-2559
regional part of nervous system1.39e-2294
nervous system1.39e-2294
anterior neural tube6.85e-2142
regional part of forebrain1.82e-2041
forebrain1.82e-2041
future forebrain1.82e-2041
neural plate5.22e-2086
presumptive neural plate5.22e-2086
neurectoderm6.45e-2090
telencephalon9.57e-1734
gray matter1.08e-1634
brain grey matter1.08e-1634
regional part of telencephalon4.13e-1633
cerebral hemisphere1.96e-1532
regional part of cerebral cortex2.59e-1322
pre-chordal neural plate2.14e-1261
neocortex3.65e-1220
cerebral cortex2.15e-1125
pallium2.15e-1125
anterior region of body3.31e-11129
craniocervical region3.31e-11129
head1.01e-10123
ectoderm2.43e-10173
presumptive ectoderm2.43e-10173
ectoderm-derived structure3.69e-10169
posterior neural tube8.21e-0915
chordal neural plate8.21e-0915
segmental subdivision of nervous system1.13e-0713
segmental subdivision of hindbrain3.97e-0712
hindbrain3.97e-0712
presumptive hindbrain3.97e-0712
nucleus of brain5.98e-079
neural nucleus5.98e-079
basal ganglion7.52e-079
nuclear complex of neuraxis7.52e-079
aggregate regional part of brain7.52e-079
collection of basal ganglia7.52e-079
cerebral subcortex7.52e-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)

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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.