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{{Coexpression_clusters
{
|full_id=C362_Small_Mallassezderived_Urothelial_Gingival_Prostate_Keratinocyte_Tracheal
 

Latest revision as of 11:21, 17 September 2013


Full id: C362_Small_Mallassezderived_Urothelial_Gingival_Prostate_Keratinocyte_Tracheal



Phase1 CAGE Peaks

Hg19::chr12:28124953..28124957,-p6@PTHLH
Hg19::chr12:28126393..28126427,-p@chr12:28126393..28126427
-
Hg19::chr14:51955483..51955495,+p23@FRMD6
Hg19::chr14:51955502..51955515,+p17@FRMD6
Hg19::chr14:51955524..51955550,+p9@FRMD6
Hg19::chr14:51955690..51955699,+p28@FRMD6
Hg19::chr14:51955719..51955733,+p15@FRMD6
Hg19::chr14:51955760..51955769,+p29@FRMD6
Hg19::chr14:51955771..51955826,+p6@FRMD6
Hg19::chr14:51955831..51955864,+p5@FRMD6
Hg19::chr14:51955873..51955899,+p12@FRMD6
Hg19::chr14:51955905..51955921,+p14@FRMD6
Hg19::chr14:51955948..51955957,+p34@FRMD6
Hg19::chr18:9617195..9617198,-p@chr18:9617195..9617198
-
Hg19::chr18:9649081..9649088,+p@chr18:9649081..9649088
+
Hg19::chr1:183213092..183213099,+p@chr1:183213092..183213099
+
Hg19::chr1:183213177..183213210,+p@chr1:183213177..183213210
+
Hg19::chr1:183213228..183213235,+p@chr1:183213228..183213235
+
Hg19::chr1:183213249..183213267,+p@chr1:183213249..183213267
+
Hg19::chr1:183213300..183213316,+p@chr1:183213300..183213316
+
Hg19::chr1:183213326..183213338,+p@chr1:183213326..183213338
+
Hg19::chr1:183213340..183213356,+p@chr1:183213340..183213356
+
Hg19::chr1:183213362..183213385,+p@chr1:183213362..183213385
+
Hg19::chr1:183213387..183213401,+p@chr1:183213387..183213401
+
Hg19::chr1:183213404..183213419,+p@chr1:183213404..183213419
+
Hg19::chr1:183213421..183213517,+p@chr1:183213421..183213517
+
Hg19::chr21:44957893..44957903,-p@chr21:44957893..44957903
-
Hg19::chr2:186298808..186298827,+p@chr2:186298808..186298827
+
Hg19::chr2:186298833..186298844,+p@chr2:186298833..186298844
+
Hg19::chr3:190252374..190252383,-p@chr3:190252374..190252383
-
Hg19::chr9:113802831..113802865,-p@chr9:113802831..113802865
-


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:0007595lactation0.038081176237861
GO:0046058cAMP metabolic process0.038081176237861
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.038081176237861
GO:0009187cyclic nucleotide metabolic process0.038081176237861
GO:0048609reproductive process in a multicellular organism0.038081176237861
GO:0032504multicellular organism reproduction0.038081176237861
GO:0007565female pregnancy0.038081176237861
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.038081176237861
GO:0019933cAMP-mediated signaling0.038081176237861
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0436693462621119
GO:0019935cyclic-nucleotide-mediated signaling0.0436693462621119
GO:0008544epidermis development0.0442043833252614
GO:0007398ectoderm development0.0442043833252614



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 cell2.04e-4342
epithelial cell7.51e-30253
endodermal cell8.22e-3058
epithelial cell of alimentary canal9.03e-2520
respiratory epithelial cell1.78e-2313
general ecto-epithelial cell1.84e-2114
squamous epithelial cell1.35e-1863
transitional epithelial cell1.14e-164
urothelial cell1.14e-164
gingival epithelial cell2.40e-133
epithelial cell of Malassez3.18e-133
bronchial epithelial cell2.04e-123
acinar cell2.46e-125
ecto-epithelial cell9.64e-1234
embryonic cell1.48e-11250
epithelial cell of tracheobronchial tree9.06e-119
epithelial cell of lower respiratory tract9.06e-119
protein secreting cell2.71e-106
mammary gland epithelial cell2.61e-094
sebum secreting cell7.57e-092
epithelial cell of sweat gland7.57e-092
epithelial cell of skin gland7.57e-092
acinar cell of sebaceous gland7.57e-092
corneal epithelial cell2.31e-082
epidermal cell3.09e-079
glandular epithelial cell7.06e-079
Uber Anatomy
Ontology termp-valuen
urothelium6.08e-205
mouth mucosa9.20e-1813
transitional epithelium1.43e-166
mucosa of oral region1.75e-144
respiratory system mucosa1.75e-144
respiratory system3.28e-1474
mucosa6.25e-1420
surface structure1.59e-1399
gingival epithelium2.40e-133
endoderm-derived structure3.01e-13160
endoderm3.01e-13160
presumptive endoderm3.01e-13160
orifice1.05e-1236
lower respiratory tract epithelium2.04e-123
epithelium of bronchus2.04e-123
oral opening2.38e-1222
head5.50e-1256
mouth3.35e-1129
stomodeum3.35e-1129
anterior region of body1.69e-1062
craniocervical region1.69e-1062
jaw skeleton5.10e-104
splanchnocranium5.10e-104
mammary gland2.61e-094
mammary bud2.61e-094
mammary ridge2.61e-094
mammary placode2.61e-094
skin gland7.57e-092
epidermis gland7.57e-092
gland of integumental system7.57e-092
sebaceous gland7.57e-092
skin sebaceous gland7.57e-092
sweat gland7.57e-092
sweat gland placode7.57e-092
sebaceous gland placode7.57e-092
subdivision of head1.42e-0849
epithelium of mucosa2.54e-088
primary subdivision of cranial skeletal system4.35e-085
epithelial fold1.10e-0747
bronchus1.29e-075
epithelial bud6.31e-0737
protuberance8.53e-076
pharyngeal arch8.53e-076
embryonic head8.53e-076
Disease
Ontology termp-valuen
squamous cell carcinoma1.39e-3414


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)
MA0003.16.61269e-10
MA0004.10.0905471
MA0006.10.0304162
MA0007.10.0818413
MA0009.10.406485
MA0014.10.0037669
MA0017.10.662194
MA0019.12.98687
MA0024.10.322368
MA0025.10.520106
MA0027.11.94566
MA0028.10.0349277
MA0029.14.34882
MA0030.10.328486
MA0031.11.39833
MA0038.10.145356
MA0040.10.342075
MA0041.11.11479
MA0042.10.59843
MA0043.10.406746
MA0046.10.397506
MA0048.10.000811211
MA0050.10.287124
MA0051.10.439954
MA0052.10.345132
MA0055.10.000115659
MA0056.10
MA0057.10.0051656
MA0058.10.0506385
MA0059.10.0501787
MA0060.10.00790927
MA0061.10.0287117
MA0063.10
MA0066.10.145606
MA0067.10.685278
MA0068.10.00249893
MA0069.10.394339
MA0070.10.385179
MA0071.10.123343
MA0072.10.381514
MA0073.12.50725e-15
MA0074.10.142444
MA0076.10.0564857
MA0077.10.37525
MA0078.11.11907
MA0081.10.418953
MA0083.10.412707
MA0084.10.860109
MA0087.10.379524
MA0088.10.000107744
MA0089.10
MA0090.10.223118
MA0091.10.0917987
MA0092.10.258792
MA0093.10.0312422
MA0095.10
MA0098.10
MA0100.10.153602
MA0101.10.130624
MA0103.10.027975
MA0105.10.000470504
MA0106.111.8045
MA0107.10.185157
MA0108.20.276987
MA0109.10
MA0111.10.0675805
MA0113.10.180801
MA0114.10.585362
MA0115.10.615724
MA0116.10.921368
MA0117.10.437859
MA0119.10.0446378
MA0122.10.459779
MA0124.10.578498
MA0125.11.2591
MA0130.10
MA0131.10.217579
MA0132.10
MA0133.10
MA0135.10.431776
MA0136.10.149526
MA0139.10.00413026
MA0140.10.121887
MA0141.10.0495619
MA0142.10.255934
MA0143.10.180914
MA0144.10.157126
MA0145.10.0014943
MA0146.19.21829e-06
MA0147.10.0166023
MA0148.11.66975
MA0149.10.116654
MA0062.20.00468224
MA0035.20.385357
MA0039.28.00021e-11
MA0138.20.20609
MA0002.20.0354968
MA0137.20.145957
MA0104.20.00782014
MA0047.22.89304
MA0112.20.000130987
MA0065.20.183559
MA0150.10.817476
MA0151.10
MA0152.10.125496
MA0153.10.489927
MA0154.10.411721
MA0155.10.000960937
MA0156.10.0375332
MA0157.10.236372
MA0158.10
MA0159.10.0167225
MA0160.10.110614
MA0161.10
MA0162.11.23482e-06
MA0163.12.62704e-05
MA0164.14.86115
MA0080.20.0312659
MA0018.20.171273
MA0099.20.125694
MA0079.20
MA0102.20.895427
MA0258.10.144068
MA0259.10.0182322
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
STAT3#6774134.411388547193712.03318712616835e-067.42981211581164e-05



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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