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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:26, 17 September 2013


Full id: C572_Urothelial_Prostate_Keratinocyte_Corneal_Mammary_Bronchial_Gingival



Phase1 CAGE Peaks

Hg19::chr2:20401847..20401864,-p@chr2:20401847..20401864
-
Hg19::chr2:20402086..20402095,-p@chr2:20402086..20402095
-
Hg19::chr2:20402138..20402149,-p@chr2:20402138..20402149
-
Hg19::chr2:20402306..20402318,-p@chr2:20402306..20402318
-
Hg19::chr2:20402607..20402620,-p@chr2:20402607..20402620
-
Hg19::chr2:20402634..20402650,-p@chr2:20402634..20402650
-
Hg19::chr2:20402663..20402684,-p@chr2:20402663..20402684
-
Hg19::chr2:20403746..20403774,+p@chr2:20403746..20403774
+
Hg19::chr2:20404043..20404055,-p@chr2:20404043..20404055
-
Hg19::chr2:20405127..20405142,-p@chr2:20405127..20405142
-
Hg19::chr2:20424816..20424834,-p1@SDC1
Hg19::chr2:20424844..20424863,-p2@SDC1
Hg19::chr2:20424884..20424897,-p3@SDC1
Hg19::chr2:20425105..20425154,-p7@SDC1
Hg19::chr2:20425158..20425206,-p6@SDC1
Hg19::chr2:20425208..20425273,-p5@SDC1


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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.32e-22160
endoderm3.32e-22160
presumptive endoderm3.32e-22160
digestive system6.58e-16145
digestive tract6.58e-16145
primitive gut6.58e-16145
urinary system structure1.11e-1347
subdivision of digestive tract2.34e-13118
renal system4.35e-1348
organism subdivision5.49e-13264
respiratory system3.87e-1274
surface structure2.89e-1199
endo-epithelium3.38e-1182
trunk region element3.55e-11101
orifice1.27e-1036
foregut7.31e-1087
epithelial bud1.82e-0937
trunk1.31e-08199
subdivision of trunk1.32e-08112
respiratory tract1.52e-0854
epithelial fold7.68e-0847
extraembryonic membrane1.19e-0714
membranous layer1.19e-0714
respiratory primordium1.66e-0738
endoderm of foregut1.66e-0738
immaterial anatomical entity2.21e-07117
thoracic cavity element2.34e-0734
thoracic cavity2.34e-0734
reproductive structure3.25e-0759
reproductive system3.25e-0759
oral opening5.34e-0722
embryonic uterus5.86e-0722
thoracic segment organ6.53e-0735
tracheobronchial tree7.10e-0715
lower respiratory tract7.10e-0715
multi-tissue structure8.34e-07342
female organism9.67e-0741
Disease
Ontology termp-valuen
carcinoma1.24e-11106
cell type cancer5.50e-09143


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)
MA0003.10.357653
MA0004.10.238283
MA0006.10.124371
MA0007.10.223897
MA0009.10.644692
MA0014.11.60737
MA0017.10.150184
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.10.644989
MA0046.10.634468
MA0048.10.957021
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.10.324189
MA0056.10
MA0057.10.615711
MA0058.10.167587
MA0059.10.166682
MA0060.10.0584466
MA0061.10.395503
MA0063.10
MA0066.10.321498
MA0067.10.948938
MA0068.11.2688
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.115.4255
MA0074.10.316991
MA0076.10.178863
MA0077.10.608956
MA0078.10.402443
MA0081.10.499456
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.369952
MA0089.10
MA0090.10.554239
MA0091.10.240316
MA0092.10.211423
MA0093.10.12631
MA0095.10
MA0098.10
MA0100.10.885358
MA0101.10.802624
MA0103.11.80818
MA0105.11.1728
MA0106.10.355999
MA0107.10.285979
MA0108.20.492699
MA0109.10
MA0111.10.199239
MA0113.10.370073
MA0114.10.278245
MA0115.10.874839
MA0116.11.51473
MA0117.10.680135
MA0119.10.471628
MA0122.11.67968
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.327047
MA0139.11.01536
MA0140.10.286995
MA0141.10.496178
MA0142.10.4668
MA0143.10.370225
MA0144.10.0738381
MA0145.10.23881
MA0146.10.922313
MA0147.10.617362
MA0148.10.257816
MA0149.10.279141
MA0062.20.0439512
MA0035.20.286421
MA0039.24.52087
MA0138.20.403517
MA0002.22.74818
MA0137.20.138998
MA0104.20.462925
MA0047.20.345656
MA0112.24.48098
MA0065.20.246686
MA0150.10.185024
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.321153
MA0155.10.837529
MA0156.10.140505
MA0157.10.442323
MA0158.10
MA0159.10.0884959
MA0160.10.743405
MA0161.10
MA0162.10.191058
MA0163.16.98598
MA0164.10.380804
MA0080.20.126365
MA0018.20.357181
MA0099.20.292649
MA0079.21.68108
MA0102.21.16862
MA0258.11.85944
MA0259.10.0929051
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
CTCFL#14069056.170773237179490.0009075479105462130.00660741695570136
HDAC2#306665.030857588734850.0007124528029200750.00572500256091172
RAD21#588563.883137710796120.002758119301476020.015123390650856
RXRA#625667.527981427174987.91408951389162e-050.00121229040003128
SMC3#912665.641849816849820.0003851015947973980.00377932958645419
ZNF143#770265.062828707085460.0006887958915479560.00555327729792936



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.

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