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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C262_breast_MCF7_skeletal_Reticulocytes_mucinous_hepatoblastoma_Wilms
|full_id=C262_breast_MCF7_skeletal_Reticulocytes_mucinous_hepatoblastoma_Wilms
|gostat_on_coexpression_clusters=GO:0045517!interleukin-20 receptor binding!0.0181900678706479!50604$GO:0031852!mu-type opioid receptor binding!0.0181900678706479!2778$GO:0031628!opioid receptor binding!0.0181900678706479!2778$GO:0045616!regulation of keratinocyte differentiation!0.0181900678706479!50604$GO:0045606!positive regulation of epidermal cell differentiation!0.0181900678706479!50604$GO:0045684!positive regulation of epidermis development!0.0181900678706479!50604$GO:0045618!positive regulation of keratinocyte differentiation!0.0181900678706479!50604$GO:0005737!cytoplasm!0.0181900678706479!4591;6198;84612;2778;10564;80145;9861$GO:0042517!positive regulation of tyrosine phosphorylation of Stat3 protein!0.0218069442542464!50604$GO:0045604!regulation of epidermal cell differentiation!0.0363149639583208!50604$GO:0046427!positive regulation of JAK-STAT cascade!0.0363149639583208!50604$GO:0042531!positive regulation of tyrosine phosphorylation of STAT protein!0.0363149639583208!50604$GO:0045682!regulation of epidermis development!0.0363149639583208!50604$GO:0017022!myosin binding!0.0363149639583208!10564$GO:0006510!ATP-dependent proteolysis!0.0363149639583208!9861$GO:0042516!regulation of tyrosine phosphorylation of Stat3 protein!0.0363149639583208!50604$GO:0032940!secretion by cell!0.0363149639583208!2778;10564$GO:0042503!tyrosine phosphorylation of Stat3 protein!0.0363149639583208!50604$GO:0042509!regulation of tyrosine phosphorylation of STAT protein!0.0447089513687611!50604$GO:0007043!intercellular junction assembly!0.045211431643751!84612$GO:0046425!regulation of JAK-STAT cascade!0.045211431643751!50604$GO:0042383!sarcolemma!0.045211431643751!2778$GO:0046903!secretion!0.045211431643751!2778;10564$GO:0050731!positive regulation of peptidyl-tyrosine phosphorylation!0.045211431643751!50604$GO:0007260!tyrosine phosphorylation of STAT protein!0.045211431643751!50604$GO:0045216!intercellular junction assembly and maintenance!0.045211431643751!84612$GO:0030054!cell junction!0.0494088084778299!6198;84612
|gostat_on_coexpression_clusters=GO:0045517!interleukin-20 receptor binding!0.0181900678706479!50604$GO:0031852!mu-type opioid receptor binding!0.0181900678706479!2778$GO:0031628!opioid receptor binding!0.0181900678706479!2778$GO:0045616!regulation of keratinocyte differentiation!0.0181900678706479!50604$GO:0045606!positive regulation of epidermal cell differentiation!0.0181900678706479!50604$GO:0045684!positive regulation of epidermis development!0.0181900678706479!50604$GO:0045618!positive regulation of keratinocyte differentiation!0.0181900678706479!50604$GO:0005737!cytoplasm!0.0181900678706479!4591;6198;84612;2778;10564;80145;9861$GO:0042517!positive regulation of tyrosine phosphorylation of Stat3 protein!0.0218069442542464!50604$GO:0045604!regulation of epidermal cell differentiation!0.0363149639583208!50604$GO:0046427!positive regulation of JAK-STAT cascade!0.0363149639583208!50604$GO:0042531!positive regulation of tyrosine phosphorylation of STAT protein!0.0363149639583208!50604$GO:0045682!regulation of epidermis development!0.0363149639583208!50604$GO:0017022!myosin binding!0.0363149639583208!10564$GO:0006510!ATP-dependent proteolysis!0.0363149639583208!9861$GO:0042516!regulation of tyrosine phosphorylation of Stat3 protein!0.0363149639583208!50604$GO:0032940!secretion by cell!0.0363149639583208!2778;10564$GO:0042503!tyrosine phosphorylation of Stat3 protein!0.0363149639583208!50604$GO:0042509!regulation of tyrosine phosphorylation of STAT protein!0.0447089513687611!50604$GO:0007043!intercellular junction assembly!0.045211431643751!84612$GO:0046425!regulation of JAK-STAT cascade!0.045211431643751!50604$GO:0042383!sarcolemma!0.045211431643751!2778$GO:0046903!secretion!0.045211431643751!2778;10564$GO:0050731!positive regulation of peptidyl-tyrosine phosphorylation!0.045211431643751!50604$GO:0007260!tyrosine phosphorylation of STAT protein!0.045211431643751!50604$GO:0045216!intercellular junction assembly and maintenance!0.045211431643751!84612$GO:0030054!cell junction!0.0494088084778299!6198;84612

Revision as of 15:23, 12 September 2012


Full id: C262_breast_MCF7_skeletal_Reticulocytes_mucinous_hepatoblastoma_Wilms



Phase1 CAGE Peaks

Hg19::chr10:19498407..19498415,+p@chr10:19498407..19498415
+
Hg19::chr10:19498455..19498482,+p@chr10:19498455..19498482
+
Hg19::chr10:19498507..19498511,+p@chr10:19498507..19498511
+
Hg19::chr10:19498541..19498551,+p@chr10:19498541..19498551
+
Hg19::chr10:19498568..19498573,+p@chr10:19498568..19498573
+
Hg19::chr10:19520550..19520559,+p@chr10:19520550..19520559
+
Hg19::chr10:19832379..19832382,+p@chr10:19832379..19832382
+
Hg19::chr10:8904309..8904317,+p@chr10:8904309..8904317
+
Hg19::chr10:9012087..9012100,+p1@ENST00000456526
Hg19::chr10:9012105..9012111,+p3@ENST00000456526
Hg19::chr10:9012128..9012139,+p2@ENST00000456526
Hg19::chr10:9238697..9238718,-p@chr10:9238697..9238718
-
Hg19::chr11:131766993..131767004,-p2@ENST00000419440
Hg19::chr11:131767210..131767232,-p1@ENST00000419440
Hg19::chr11:18283431..18283456,+p1@ST13P5
Hg19::chr11:85539944..85539950,+p@chr11:85539944..85539950
+
Hg19::chr12:116933204..116933236,-p@chr12:116933204..116933236
-
Hg19::chr13:23500751..23500764,+p@chr13:23500751..23500764
+
Hg19::chr13:23500789..23500796,+p@chr13:23500789..23500796
+
Hg19::chr13:23583578..23583586,+p@chr13:23583578..23583586
+
Hg19::chr13:23733194..23733206,+p@chr13:23733194..23733206
+
Hg19::chr17:38843592..38843605,+p@chr17:38843592..38843605
+
Hg19::chr17:57184136..57184156,-p4@TRIM37
Hg19::chr17:57970469..57970506,+p1@RPS6KB1
Hg19::chr1:207038965..207038969,+p1@IL20
Hg19::chr20:47538238..47538278,+p1@ARFGEF2
Hg19::chr20:47538312..47538323,+p3@ARFGEF2
Hg19::chr20:49348109..49348123,+p1@PARD6B
Hg19::chr20:57429114..57429123,+p66@GNAS
Hg19::chr20:57429157..57429163,+p59@GNAS
Hg19::chr21:41755024..41755027,+p2@DSCAM-AS1
Hg19::chr21:41755185..41755210,+p1@DSCAM-AS1
Hg19::chr21:41756567..41756583,-p@chr21:41756567..41756583
-
Hg19::chr2:11674163..11674179,+p9@GREB1
Hg19::chr2:11674213..11674225,+p11@GREB1
Hg19::chr2:11679852..11679866,+p18@GREB1
Hg19::chr2:11732328..11732334,+p@chr2:11732328..11732334
+
Hg19::chr2:11745301..11745305,+p@chr2:11745301..11745305
+
Hg19::chr2:132301072..132301097,+p@chr2:132301072..132301097
+
Hg19::chr2:132301109..132301133,+p@chr2:132301109..132301133
+
Hg19::chr2:237768815..237768844,+p@chr2:237768815..237768844
+
Hg19::chr3:129226494..129226510,+p@chr3:129226494..129226510
+
Hg19::chr3:129226514..129226531,+p@chr3:129226514..129226531
+
Hg19::chr3:63849694..63849740,-p2@THOC7
Hg19::chr3:63849743..63849781,-p3@THOC7
Hg19::chr3:64009102..64009184,-p1@PSMD6
Hg19::chr5:177505250..177505293,-p@chr5:177505250..177505293
-
Hg19::chr6:151937957..151937962,-p@chr6:151937957..151937962
-
Hg19::chr9:1470588..1470601,+p@chr9:1470588..1470601
+
Hg19::chr9:83986187..83986191,-p@chr9:83986187..83986191
-


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:0045517interleukin-20 receptor binding0.0181900678706479
GO:0031852mu-type opioid receptor binding0.0181900678706479
GO:0031628opioid receptor binding0.0181900678706479
GO:0045616regulation of keratinocyte differentiation0.0181900678706479
GO:0045606positive regulation of epidermal cell differentiation0.0181900678706479
GO:0045684positive regulation of epidermis development0.0181900678706479
GO:0045618positive regulation of keratinocyte differentiation0.0181900678706479
GO:0005737cytoplasm0.0181900678706479
GO:0042517positive regulation of tyrosine phosphorylation of Stat3 protein0.0218069442542464
GO:0045604regulation of epidermal cell differentiation0.0363149639583208
GO:0046427positive regulation of JAK-STAT cascade0.0363149639583208
GO:0042531positive regulation of tyrosine phosphorylation of STAT protein0.0363149639583208
GO:0045682regulation of epidermis development0.0363149639583208
GO:0017022myosin binding0.0363149639583208
GO:0006510ATP-dependent proteolysis0.0363149639583208
GO:0042516regulation of tyrosine phosphorylation of Stat3 protein0.0363149639583208
GO:0032940secretion by cell0.0363149639583208
GO:0042503tyrosine phosphorylation of Stat3 protein0.0363149639583208
GO:0042509regulation of tyrosine phosphorylation of STAT protein0.0447089513687611
GO:0007043intercellular junction assembly0.045211431643751
GO:0046425regulation of JAK-STAT cascade0.045211431643751
GO:0042383sarcolemma0.045211431643751
GO:0046903secretion0.045211431643751
GO:0050731positive regulation of peptidyl-tyrosine phosphorylation0.045211431643751
GO:0007260tyrosine phosphorylation of STAT protein0.045211431643751
GO:0045216intercellular junction assembly and maintenance0.045211431643751
GO:0030054cell junction0.0494088084778299



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
epithelial cell4.84e-07254
Uber Anatomy
Ontology termp-valuen
adult organism4.75e-12115
subdivision of digestive tract1.17e-09129
endodermal part of digestive tract1.17e-09129
digestive system1.55e-09155
digestive tract1.55e-09155
primitive gut1.55e-09155
endoderm-derived structure1.31e-08169
endoderm1.31e-08169
presumptive endoderm1.31e-08169
mixed endoderm/mesoderm-derived structure3.74e-08130
foregut3.70e-0798
endo-epithelium4.87e-0782
Disease
Ontology termp-valuen
cell type cancer2.11e-37143
carcinoma1.03e-31106
cancer8.90e-31235
disease of cellular proliferation4.30e-29239
adenocarcinoma9.49e-1225
organ system cancer1.44e-09137
disease of anatomical entity4.82e-0939


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
EP300#2033172.303140186915890.0005473400735351360.004725830848209
ESR1#209974.307604461461630.001118844382451370.00767242209184755
FOXA1#3169112.43791234486480.004365693571589590.0206938987393113
GATA3#262594.902572944297087.7121315201363e-050.00118920316526135
MYC#4609171.77557583634720.0094161518774730.0355253769934038



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

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