Personal tools

Coexpression cluster:C3130

From FANTOM5_SSTAR

Revision as of 18:55, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3130_amniotic_skeletal_Placental_diaphragm_chorionic_throat_trachea



Phase1 CAGE Peaks

Hg19::chr11:1977212..1977224,+p@chr11:1977212..1977224
+
Hg19::chr11:1977251..1977266,+p@chr11:1977251..1977266
+
Hg19::chr6:12007897..12007910,+p2@ENST00000437559


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>


Uber Anatomy
Ontology termp-valuen
extraembryonic membrane1.96e-2214
membranous layer1.96e-2214
chorion7.09e-167
extraembryonic structure6.35e-1424
sense organ5.84e-1123
eye1.01e-1020
retina1.03e-105
photoreceptor array1.03e-105
posterior segment of eyeball1.03e-105
sensory system2.21e-1024
entire sense organ system2.21e-1024
placenta4.10e-104
allantois4.10e-104
organ component layer4.17e-1057
visual system4.35e-1021
camera-type eye2.73e-0919
simple eye2.73e-0919
ocular region2.73e-0919
optic cup2.73e-0919
eye primordium2.73e-0919
optic vesicle2.73e-0919
amnion8.48e-097
pigment epithelium of eye1.46e-0811
face3.36e-0821
somatic layer of lateral plate mesoderm1.28e-078
acellular anatomical structure1.90e-073
egg chorion1.90e-073
layer of retina6.24e-073
pigmented layer of retina6.24e-073
presumptive retinal pigmented epithelium6.24e-073


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.