Personal tools

Coexpression cluster:C3990

From FANTOM5_SSTAR

Revision as of 14:43, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3990_Wilms_choriocarcinoma_chorionic_mature_Amniotic_amniotic_optic



Phase1 CAGE Peaks

Hg19::chr1:62784864..62784917,-p2@KANK4
Hg19::chr1:62784935..62784964,-p3@KANK4
Hg19::chr1:62785054..62785125,-p1@KANK4


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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
endodermal cell2.03e-0859
Uber Anatomy
Ontology termp-valuen
adult organism2.39e-23115
neural tube4.18e-1657
neural rod4.18e-1657
future spinal cord4.18e-1657
neural keel4.18e-1657
regional part of brain3.40e-1359
ectoderm1.36e-12173
presumptive ectoderm1.36e-12173
ectoderm-derived structure1.38e-12169
central nervous system2.63e-1282
brain5.16e-1269
future brain5.16e-1269
regional part of nervous system5.69e-1294
nervous system5.69e-1294
neural plate1.03e-1186
presumptive neural plate1.03e-1186
neurectoderm1.45e-1190
endoderm-derived structure1.58e-11169
endoderm1.58e-11169
presumptive endoderm1.58e-11169
organ8.51e-11511
anterior neural tube1.54e-1042
organ part2.36e-10219
anterior region of body4.11e-10129
craniocervical region4.11e-10129
regional part of forebrain4.57e-1041
forebrain4.57e-1041
future forebrain4.57e-1041
head1.66e-09123
organism subdivision2.99e-09365
extraembryonic membrane4.00e-0914
membranous layer4.00e-0914
gray matter9.03e-0934
brain grey matter9.03e-0934
subdivision of digestive tract1.19e-08129
endodermal part of digestive tract1.19e-08129
telencephalon1.28e-0834
multi-cellular organism1.60e-08659
regional part of telencephalon3.66e-0833
digestive system7.34e-08155
digestive tract7.34e-08155
primitive gut7.34e-08155
mixed endoderm/mesoderm-derived structure9.21e-08130
brainstem1.46e-078
cerebral hemisphere1.87e-0732
chorion2.39e-077
posterior neural tube3.78e-0715
chordal neural plate3.78e-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


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.