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{{Coexpression_clusters
{
|full_id=C544_nasal_Keratinocyte_Esophageal_Urothelial_Placental_Corneal_Prostate
|

Latest revision as of 11:25, 17 September 2013


Full id: C544_nasal_Keratinocyte_Esophageal_Urothelial_Placental_Corneal_Prostate



Phase1 CAGE Peaks

Hg19::chr17:39775781..39775811,-p@chr17:39775781..39775811
-
Hg19::chr17:39775857..39775872,-p@chr17:39775857..39775872
-
Hg19::chr17:39776987..39777014,-p@chr17:39776987..39777014
-
Hg19::chr17:39777017..39777027,+p@chr17:39777017..39777027
+
Hg19::chr17:39777054..39777079,-p5@KRT17
Hg19::chr17:39777082..39777104,-p6@KRT17
Hg19::chr17:39777267..39777358,-p1@EF608070
Hg19::chr17:39777878..39777913,+p@chr17:39777878..39777913
+
Hg19::chr17:39777922..39777964,-p@chr17:39777922..39777964
-
Hg19::chr17:39777995..39778013,-p@chr17:39777995..39778013
-
Hg19::chr17:39779227..39779270,-p3@KRT17
Hg19::chr17:39780328..39780347,+p@chr17:39780328..39780347
+
Hg19::chr17:39780497..39780517,+p@chr17:39780497..39780517
+
Hg19::chr17:39780530..39780549,-p2@KRT17
Hg19::chr17:39780624..39780631,-p8@KRT17
Hg19::chr17:39780634..39780644,-p4@KRT17
Hg19::chr17:39780819..39780835,-p1@KRT17


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:0005200structural constituent of cytoskeleton0.0347344872247733
GO:0008544epidermis development0.0347344872247733
GO:0007398ectoderm development0.0347344872247733
GO:0045111intermediate filament cytoskeleton0.0347344872247733
GO:0005882intermediate filament0.0347344872247733
GO:0009888tissue development0.0374082577809176



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 cell2.05e-3242
epithelial cell5.99e-32253
endodermal cell4.49e-2358
respiratory epithelial cell4.67e-2213
general ecto-epithelial cell5.84e-1614
epithelial cell of alimentary canal4.21e-1420
epithelial cell of tracheobronchial tree2.93e-139
epithelial cell of lower respiratory tract2.93e-139
transitional epithelial cell1.89e-104
urothelial cell1.89e-104
extraembryonic cell3.24e-1019
bronchial epithelial cell6.40e-093
duct epithelial cell1.70e-083
branched duct epithelial cell1.70e-083
tracheal epithelial cell1.70e-083
tracheoblast1.70e-083
placental epithelial cell2.11e-083
acinar cell3.55e-085
ecto-epithelial cell6.86e-0834
epithelial cell of Malassez1.09e-073
gingival epithelial cell1.12e-073
stratified squamous epithelial cell5.89e-076
keratin accumulating cell5.89e-076
stratified epithelial cell5.89e-076
keratinizing barrier epithelial cell5.89e-076
epithelial fate stem cell5.89e-076
stratified epithelial stem cell5.89e-076
surface ectodermal cell5.89e-076
epidermal cell7.41e-079
protein secreting cell8.51e-076
Uber Anatomy
Ontology termp-valuen
respiratory system1.30e-2574
respiratory tract1.35e-2254
endoderm-derived structure2.78e-22160
endoderm2.78e-22160
presumptive endoderm2.78e-22160
larynx5.76e-199
segment of respiratory tract4.10e-1847
upper respiratory tract6.48e-1719
respiratory primordium1.35e-1538
endoderm of foregut1.35e-1538
extraembryonic membrane1.22e-1414
membranous layer1.22e-1414
digestive system1.38e-12145
digestive tract1.38e-12145
primitive gut1.38e-12145
foregut3.86e-1287
urothelium4.27e-125
organ part1.37e-11218
subdivision of digestive tract2.10e-10118
transitional epithelium5.26e-106
tracheobronchial tree2.33e-0915
lower respiratory tract2.33e-0915
surface structure3.02e-0999
lower respiratory tract epithelium6.40e-093
epithelium of bronchus6.40e-093
oral opening2.04e-0822
chorion2.49e-087
amnion6.21e-087
orifice6.47e-0836
mouth mucosa9.92e-0813
gingival epithelium1.12e-073
extraembryonic structure1.18e-0724
organ segment1.88e-0798
mouth2.81e-0729
stomodeum2.81e-0729
tongue3.05e-073
gustatory system3.05e-073
future tongue3.05e-073
embryonic structure4.03e-07564
somatic layer of lateral plate mesoderm6.81e-078
head9.29e-0756
Disease
Ontology termp-valuen
squamous cell carcinoma5.60e-0914
carcinoma5.89e-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)
MA0003.10.805327
MA0004.10.221943
MA0006.11.20202
MA0007.10.208008
MA0009.10.621697
MA0014.10.154351
MA0017.10.425352
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.236024
MA0042.10.211928
MA0043.10.621991
MA0046.10.611559
MA0048.11.21321
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.11.42965
MA0056.10
MA0057.10.0616251
MA0058.10.153757
MA0059.10.15289
MA0060.10.422819
MA0061.10.155208
MA0063.10
MA0066.10.818531
MA0067.10.924196
MA0068.10.502018
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.10.0421727
MA0074.10.298586
MA0076.10.164578
MA0077.10.586275
MA0078.10.995054
MA0081.10.465308
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.755104
MA0089.10
MA0090.10.174619
MA0091.10.636604
MA0092.10.195947
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.116395
MA0103.10.706501
MA0105.11.06659
MA0106.10.894258
MA0107.10.0748038
MA0108.21.18798
MA0109.10
MA0111.11.63732
MA0113.10.350573
MA0114.11.90309
MA0115.10.850405
MA0116.13.92052
MA0117.10.656858
MA0119.10.862312
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.14.12693
MA0140.11.36176
MA0141.10.902543
MA0142.10.445733
MA0143.10.350722
MA0144.10.0651126
MA0145.11.49496
MA0146.10.441966
MA0147.10.0784275
MA0148.10.676348
MA0149.10.261654
MA0062.20.0377014
MA0035.20.268747
MA0039.20.0350337
MA0138.20.997372
MA0002.20.393994
MA0137.20.126444
MA0104.20.0505812
MA0047.20.87164
MA0112.21.42266
MA0065.21.52581
MA0150.10.170499
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.11.04686
MA0155.11.03039
MA0156.10.12788
MA0157.10.421609
MA0158.10
MA0159.10.571105
MA0160.10.252705
MA0161.10
MA0162.10.00317087
MA0163.10.745463
MA0164.10.948242
MA0080.20.11444
MA0018.20.337929
MA0099.20.754549
MA0079.20.000331013
MA0102.21.14323
MA0258.11.74426
MA0259.10.28219
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
CTCF#1066482.522473587329420.007107635535135630.0296309415477419
GATA2#262453.748509333398230.008250394534376350.0325131293779991
STAT3#677463.712752351936790.003618063751379640.0183119437911479



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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