Personal tools

Coexpression cluster:C311: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.36439152281912,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C311_rectal_heart_choriocarcinoma_placenta_chorionic_lung_ductal
|full_id=C311_rectal_heart_choriocarcinoma_placenta_chorionic_lung_ductal
|id=C311
|id=C311

Revision as of 15:59, 12 September 2012


Full id: C311_rectal_heart_choriocarcinoma_placenta_chorionic_lung_ductal



Phase1 CAGE Peaks

Hg19::chr11:118826999..118827014,+p1@UPK2
Hg19::chr11:86502063..86502074,+p26@PRSS23
Hg19::chr11:86502085..86502118,+p13@PRSS23
Hg19::chr11:89901127..89901133,+p@chr11:89901127..89901133
+
Hg19::chr12:31632584..31632589,-p20@DENND5B
Hg19::chr12:31632597..31632607,-p13@DENND5B
Hg19::chr12:57410306..57410318,-p1@TAC3
Hg19::chr15:54134723..54134734,+p@chr15:54134723..54134734
+
Hg19::chr1:172421915..172421926,+p4@C1orf105
Hg19::chr1:172421997..172422007,+p3@C1orf105
Hg19::chr1:172422026..172422039,+p2@C1orf105
Hg19::chr1:172422041..172422055,+p1@C1orf105
Hg19::chr1:43533230..43533270,+p@chr1:43533230..43533270
+
Hg19::chr1:90420182..90420201,+p@chr1:90420182..90420201
+
Hg19::chr20:3999149..3999160,-p@chr20:3999149..3999160
-
Hg19::chr2:191384421..191384433,-p@chr2:191384421..191384433
-
Hg19::chr2:191384465..191384471,-p@chr2:191384465..191384471
-
Hg19::chr2:197124712..197124735,+p2@ENST00000430904
Hg19::chr2:209864821..209864831,-p@chr2:209864821..209864831
-
Hg19::chr4:10048437..10048443,+p@chr4:10048437..10048443
+
Hg19::chr4:175309496..175309506,+p@chr4:175309496..175309506
+
Hg19::chr6:125540918..125540931,+p6@TPD52L1
Hg19::chr6:31683061..31683070,+p5@LY6G6D
Hg19::chr6:31683080..31683091,+p2@LY6G6D
Hg19::chr6:31683117..31683130,+p1@LY6G6D
Hg19::chr6:31683157..31683167,+p3@LY6G6D
Hg19::chr7:12007288..12007295,-p@chr7:12007288..12007295
-
Hg19::chr7:12125449..12125453,-p@chr7:12125449..12125453
-
Hg19::chr7:12134329..12134354,-p@chr7:12134329..12134354
-
Hg19::chr7:12134356..12134370,-p@chr7:12134356..12134370
-
Hg19::chr7:12134371..12134377,-p@chr7:12134371..12134377
-
Hg19::chr7:12134400..12134410,-p@chr7:12134400..12134410
-
Hg19::chr7:12250342..12250347,+p@chr7:12250342..12250347
+
Hg19::chr7:16873035..16873059,-p6@AGR2
Hg19::chr7:27282288..27282293,-p2@ENST00000519050
Hg19::chr7:27282416..27282426,+p1@EVX1
Hg19::chr8:120164231..120164239,+p@chr8:120164231..120164239
+
Hg19::chr9:20732373..20732384,+p@chr9:20732373..20732384
+
Hg19::chr9:286553..286563,+p@chr9:286553..286563
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
endo-epithelial cell1.20e-0743
Uber Anatomy
Ontology termp-valuen
adult organism8.44e-23115
regional part of forebrain7.03e-1341
forebrain7.03e-1341
future forebrain7.03e-1341
telencephalon1.08e-1234
gray matter1.52e-1234
brain grey matter1.52e-1234
cerebral hemisphere1.77e-1232
regional part of telencephalon3.32e-1233
neural tube3.95e-1257
neural rod3.95e-1257
future spinal cord3.95e-1257
neural keel3.95e-1257
anterior neural tube4.56e-1242
central nervous system3.30e-1182
regional part of nervous system1.86e-1094
nervous system1.86e-1094
regional part of cerebral cortex2.03e-1022
cerebral cortex8.96e-1025
pallium8.96e-1025
neocortex1.19e-0920
neural plate1.24e-0986
presumptive neural plate1.24e-0986
pre-chordal neural plate1.36e-0961
neurectoderm3.82e-0990
organ8.35e-09511
regional part of brain1.59e-0859
brain1.94e-0869
future brain1.94e-0869
anterior region of body2.25e-08129
craniocervical region2.25e-08129
ectoderm-derived structure7.97e-08169
ectoderm1.35e-07173
presumptive ectoderm1.35e-07173
organ part1.65e-07219
head1.79e-07123
embryo8.16e-07612
Disease
Ontology termp-valuen
carcinoma3.03e-08106


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
TAL1#688653.829309830441050.009376508648130890.0353860369553423



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:C311&oldid=2137874"