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Coexpression cluster:C1473

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Full id: C1473_CD4_cerebellum_thymus_neuroblastoma_CD8_Peripheral_caudate



Phase1 CAGE Peaks

Hg19::chr1:24829320..24829332,+p6@RCAN3
Hg19::chr1:24829340..24829375,+p4@RCAN3
Hg19::chr5:110560072..110560106,+p1@CAMK4
Hg19::chr5:110560211..110560222,+p6@CAMK4
Hg19::chr5:110574533..110574537,+p@chr5:110574533..110574537
+
Hg19::chr5:110576837..110576844,+p@chr5:110576837..110576844
+


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:0007270nerve-nerve synaptic transmission0.0432581913920992
GO:0004683calmodulin-dependent protein kinase activity0.0432581913920992



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>


Uber Anatomy
Ontology termp-valuen
central nervous system2.85e-2282
regional part of nervous system4.24e-2294
nervous system4.24e-2294
adult organism8.96e-22115
neural tube2.83e-2157
neural rod2.83e-2157
future spinal cord2.83e-2157
neural keel2.83e-2157
brain1.12e-1869
future brain1.12e-1869
anterior region of body5.27e-18129
craniocervical region5.27e-18129
regional part of brain5.34e-1859
neural plate8.11e-1886
presumptive neural plate8.11e-1886
ectoderm-derived structure1.07e-17169
regional part of forebrain7.70e-1741
forebrain7.70e-1741
future forebrain7.70e-1741
anterior neural tube1.04e-1642
ectoderm2.12e-16173
presumptive ectoderm2.12e-16173
neurectoderm7.30e-1690
head1.00e-15123
pre-chordal neural plate1.17e-1561
gray matter5.31e-1434
brain grey matter5.31e-1434
telencephalon5.42e-1434
regional part of telencephalon1.28e-1333
cerebral hemisphere1.58e-1332
regional part of cerebral cortex2.18e-1022
cerebral cortex2.34e-1025
pallium2.34e-1025
neocortex1.04e-0920
blood6.13e-0715
haemolymphatic fluid6.13e-0715
organism substance6.13e-0715


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ZBTB7A#5134144.901272871917260.004079628118843750.019490063634048



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.