Personal tools

Coexpression cluster:C406

From FANTOM5_SSTAR

Revision as of 15:38, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C406_Mallassezderived_Mesothelial_mesenchymal_chorionic_Gingival_Placental_Prostate



Phase1 CAGE Peaks

Hg19::chr10:106205466..106205487,+p@chr10:106205466..106205487
+
Hg19::chr10:106205489..106205498,+p@chr10:106205489..106205498
+
Hg19::chr10:106205503..106205518,+p@chr10:106205503..106205518
+
Hg19::chr10:106205565..106205599,+p@chr10:106205565..106205599
+
Hg19::chr10:118187325..118187332,+p5@PNLIPRP3
Hg19::chr12:122380361..122380372,+p@chr12:122380361..122380372
+
Hg19::chr12:56915776..56915787,+p3@RBMS2
Hg19::chr14:81221483..81221489,+p@chr14:81221483..81221489
+
Hg19::chr16:57954525..57954533,-p@chr16:57954525..57954533
-
Hg19::chr16:57954541..57954548,-p@chr16:57954541..57954548
-
Hg19::chr16:79679414..79679446,+p@chr16:79679414..79679446
+
Hg19::chr16:80068152..80068165,-p@chr16:80068152..80068165
-
Hg19::chr17:18343257..18343267,+p2@KRT16P1
Hg19::chr21:44168074..44168079,+p@chr21:44168074..44168079
+
Hg19::chr2:29149934..29149959,+p1@SNORD53
Hg19::chr4:155387574..155387588,-p@chr4:155387574..155387588
-
Hg19::chr4:76481268..76481289,+p1@C4orf26
Hg19::chr5:64454308..64454313,+p@chr5:64454308..64454313
+
Hg19::chr7:137570475..137570486,-p@chr7:137570475..137570486
-
Hg19::chr7:137570496..137570504,-p@chr7:137570496..137570504
-
Hg19::chr9:16094653..16094654,+p@chr9:16094653..16094654
+
Hg19::chr9:27524417..27524425,+p4@IFNK
Hg19::chr9:27524485..27524505,+p2@IFNK
Hg19::chr9:27524537..27524559,+p1@IFNK
Hg19::chr9:27524670..27524673,+p5@IFNK


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:0004420hydroxymethylglutaryl-CoA reductase (NADPH) activity0.0217494896268424
GO:0005132interferon-alpha/beta receptor binding0.0217494896268424
GO:0045089positive regulation of innate immune response0.0217494896268424
GO:0015936coenzyme A metabolic process0.0217494896268424
GO:0045088regulation of innate immune response0.0217494896268424
GO:0004806triacylglycerol lipase activity0.0254136244685966
GO:0030101natural killer cell activation0.0254136244685966



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
gingival epithelium1.49e-593
jaw skeleton1.07e-454
splanchnocranium1.07e-454
primary subdivision of cranial skeletal system9.70e-375
protuberance9.21e-316
pharyngeal arch9.21e-316
embryonic head9.21e-316
epithelium of mucosa6.93e-238
gingiva6.93e-238
cranial skeletal system3.90e-1711
surface structure7.63e-1699
mouth mucosa2.28e-1413
axial skeletal system1.30e-1314
head8.92e-1356
skin epidermis1.78e-1215
outer epithelium1.78e-1215
enveloping layer of ectoderm1.78e-1215
subdivision of skeletal system5.39e-1216
anterior region of body1.56e-1162
craniocervical region1.56e-1162
skin gland2.47e-112
epidermis gland2.47e-112
gland of integumental system2.47e-112
sebaceous gland2.47e-112
skin sebaceous gland2.47e-112
sweat gland2.47e-112
sweat gland placode2.47e-112
sebaceous gland placode2.47e-112
pharyngeal arch system9.85e-1118
mucosa1.44e-0920
oral opening9.43e-0922
respiratory system epithelium5.36e-0728
mouth8.95e-0729
stomodeum8.95e-0729


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
MAFF#2376436.757842778793420.009609650445008780.0361678720972385
STAT3#6774114.628564598747877.15373012922101e-060.000206161264063387



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C406&oldid=2250350"