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Coexpression cluster:C2198

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Full id: C2198_amniotic_chorionic_Urothelial_Mallassezderived_Keratinocyte_Sebocyte_Prostate



Phase1 CAGE Peaks

Hg19::chr12:15081950..15081955,-p9@ERP27
Hg19::chr6:125367660..125367682,+p12@RNF217
Hg19::chr6:125367685..125367700,+p16@RNF217
Hg19::chr6:125367708..125367746,+p13@RNF217


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:0042787protein ubiquitination during ubiquitin-dependent protein catabolic process0.0170718784065629



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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
extraembryonic membrane6.37e-2414
membranous layer6.37e-2414
mouth mucosa1.53e-1513
organ component layer3.24e-1466
mucosa of oral region5.41e-144
respiratory system mucosa5.41e-144
extraembryonic structure4.86e-1324
chorion6.23e-137
amnion1.20e-127
acellular anatomical structure5.35e-123
egg chorion5.35e-123
neck2.53e-1110
gingival epithelium2.87e-113
somatic layer of lateral plate mesoderm5.11e-118
mucosa1.29e-0920
oral opening9.74e-0922
jaw skeleton1.11e-084
splanchnocranium1.11e-084
skin gland3.32e-082
epidermis gland3.32e-082
gland of integumental system3.32e-082
sebaceous gland3.32e-082
skin sebaceous gland3.32e-082
sweat gland3.32e-082
sweat gland placode3.32e-082
sebaceous gland placode3.32e-082
mammary gland7.22e-084
mammary bud7.22e-084
mammary ridge7.22e-084
mammary placode7.22e-084
mouth7.51e-0829
stomodeum7.51e-0829
orifice1.57e-0736
endoderm-derived structure1.58e-07160
endoderm1.58e-07160
presumptive endoderm1.58e-07160
anterior region of body1.89e-0762
craniocervical region1.89e-0762
primary subdivision of cranial skeletal system5.19e-075
urothelium5.19e-075
surface structure6.47e-0799
Disease
Ontology termp-valuen
squamous cell carcinoma9.01e-1414


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
GATA1#2623310.17023110785030.001515158168498270.00966006983455169
GATA2#262439.55869880016550.001818151618357440.0108948268328437
STAT3#677437.889598747865680.003190760481680130.0167398319157177
TFAP2C#702238.106921457395170.002947011739866440.0157160416207063
TRIM28#10155313.94289378394690.0005972858184258420.00499199212472603



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.