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Coexpression cluster:C2132

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Full id: C2132_cerebellum_putamen_pituitary_merkel_gastrointestinal_brain_iPS



Phase1 CAGE Peaks

Hg19::chr11:45907236..45907257,+p3@MAPK8IP1
Hg19::chr8:104511921..104511933,+p@chr8:104511921..104511933
+
Hg19::chr8:104511965..104511977,+p@chr8:104511965..104511977
+
Hg19::chr8:104512000..104512015,+p@chr8:104512000..104512015
+


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.10e-4294
nervous system3.10e-4294
central nervous system5.29e-4282
neural tube9.73e-3857
neural rod9.73e-3857
future spinal cord9.73e-3857
neural keel9.73e-3857
brain1.93e-3369
future brain1.93e-3369
regional part of brain4.61e-3359
regional part of forebrain4.01e-3241
forebrain4.01e-3241
future forebrain4.01e-3241
anterior neural tube6.59e-3142
neural plate3.95e-2886
presumptive neural plate3.95e-2886
ectoderm-derived structure5.19e-28169
ectoderm8.96e-28173
presumptive ectoderm8.96e-28173
neurectoderm2.22e-2790
gray matter1.26e-2634
brain grey matter1.26e-2634
telencephalon1.45e-2634
adult organism2.21e-26115
regional part of telencephalon1.06e-2533
cerebral hemisphere1.68e-2532
head1.75e-24123
anterior region of body4.71e-24129
craniocervical region4.71e-24129
pre-chordal neural plate8.87e-2461
regional part of cerebral cortex1.09e-1922
cerebral cortex1.32e-1925
pallium1.32e-1925
neocortex3.16e-1820
organism subdivision5.74e-09365
basal ganglion1.14e-089
nuclear complex of neuraxis1.14e-089
aggregate regional part of brain1.14e-089
collection of basal ganglia1.14e-089
cerebral subcortex1.14e-089
nucleus of brain1.87e-089
neural nucleus1.87e-089
organ2.26e-08511
posterior neural tube4.16e-0815
chordal neural plate4.16e-0815
multi-cellular organism4.64e-08659
temporal lobe9.27e-087
embryo1.88e-07612
organ part2.79e-07219
telencephalic nucleus4.57e-077
diencephalon6.18e-077
future diencephalon6.18e-077
anatomical system7.32e-07625
segmental subdivision of nervous system7.40e-0713
anatomical group9.20e-07626


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
CTCF#1066445.360256373075030.001211145381643620.00815753982416344
JUND#372735.245997956403270.01043432751748420.0386655808827183



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.