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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:08, 17 September 2013


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
breast1.10e-5910
chest2.16e-5411
thoracic segment of trunk1.77e-1252
Disease
Ontology termp-valuen
thoracic cancer6.94e-1474
breast cancer6.94e-1474
adenocarcinoma1.10e-2425
disease of anatomical entity2.93e-1639


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)
MA0003.10.0370832
MA0004.10.545783
MA0006.10.03122
MA0007.11.16253
MA0009.10.258013
MA0014.10.0160214
MA0017.10.131947
MA0019.10.270778
MA0024.10.553073
MA0025.10.356605
MA0027.11.73957
MA0028.10.107747
MA0029.10.200942
MA0030.10.564853
MA0031.10.916561
MA0038.11.7548
MA0040.10.591062
MA0041.10.0350654
MA0042.10.114241
MA0043.10.258233
MA0046.10.250449
MA0048.11.52146
MA0050.10.820941
MA0051.10.817537
MA0052.10.596967
MA0055.11.53493
MA0056.10
MA0057.10.0492017
MA0058.11.53623
MA0059.10.539955
MA0060.12.16218
MA0061.10.728455
MA0063.10
MA0066.10.481212
MA0067.10.506892
MA0068.10.077453
MA0069.10.69234
MA0070.11.25293
MA0071.10.0481729
MA0072.10.237075
MA0073.11.34716
MA0074.10.47071
MA0076.10.0693386
MA0077.10.231873
MA0078.10.33075
MA0081.10.159797
MA0083.11.33948
MA0084.10.671627
MA0087.11.23512
MA0088.10.0377312
MA0089.10
MA0090.10.0171525
MA0091.11.26222
MA0092.10.458222
MA0093.10.840018
MA0095.10
MA0098.10
MA0100.10.235688
MA0101.10.591093
MA0103.10.780549
MA0105.10.504797
MA0106.10.0771872
MA0107.10.339326
MA0108.20.909263
MA0109.10
MA0111.10.685974
MA0113.10.285402
MA0114.10.0396474
MA0115.10.442812
MA0116.10.106908
MA0117.10.284729
MA0119.10.751112
MA0122.10.303641
MA0124.10.40896
MA0125.10.342802
MA0130.10
MA0131.10.35376
MA0132.10
MA0133.10
MA0135.10.279516
MA0136.10.0638731
MA0139.10.0609175
MA0140.10.402184
MA0141.10.157498
MA0142.10.426077
MA0143.10.28561
MA0144.10.282741
MA0145.10.300962
MA0146.10.151892
MA0147.10.0466595
MA0148.11.36867
MA0149.10.0443634
MA0062.20.0686137
MA0035.20.0471158
MA0039.20.223055
MA0138.20.101316
MA0002.21.08384
MA0137.20.419832
MA0104.20.200644
MA0047.21.376
MA0112.20.122222
MA0065.20.0314043
MA0150.10.927598
MA0151.10
MA0152.10.414251
MA0153.10.329951
MA0154.11.44769
MA0155.10.000315107
MA0156.10.0410735
MA0157.10.77844
MA0158.10
MA0159.10.216188
MA0160.11.01437
MA0161.10
MA0162.10.235146
MA0163.10.031899
MA0164.10.300222
MA0080.20.0953696
MA0018.20.0777542
MA0099.20.41491
MA0079.20.00053258
MA0102.20.705393
MA0258.10.256546
MA0259.10.0519619
MA0442.10



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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