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Coexpression cluster:C1694: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.343373863650849,0.39427933691332,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.237692141113291,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.157182883491893,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.590943521925605,0.771545605131671,0.809511724961312,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.722655400738442,0.327158097282158,0.840809017856645,0.305022922250855,0,0,0,0,0,0,0,0,0,0,0,0,0,0.287205473226075,0.826812629110424,0.795579631716107,0.21136343755771,0.389727590602526,0.332468362080336,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.914778446390301,0.164473294726456,0,0,0,0,0.187268914901325,0,0,0.152962663947244,0,0,0,0,0,0,0.0986009078228607,0,0,0,0,0,0,0,0,0,0,0.828830963264706,0.556331571484542,0,0,0,0,0,0,0,0,0,0.449961650245721,0.197713313938225,0.73770497787886,0.115102153805393,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.506925403549553,0.638640123387869,0,0,0.360122916322148,0,0.367410057325623,0.72954905160615,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0458873451077849,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.387014750515979,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.46224560579794,0.065666642656593,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.200838022744453,0.271979087934757,0,0,0,0,0,0,0,0,0,0,0,0,0.120782895346206,0,0,0,0,0,0.0584468268118252,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.197486100889927,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.214404368077712,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.198311194441065,0,0,0,0,0,0,0,0,0,0,0.213235139917941,0,0,0,0,0,0,0.210071535945973,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.201092823406828,0,0,0.0474795670351238,0,0,0,0,0,0,0,0,0.112508538720951,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0921546695012139,0.0872356535976564,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.163821185185472,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.132614371326254,1.25379711241259,0.255854471787867,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0806184284061465,0.102851129332916,0.105743346346567,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C1694_squamous_Prostate_Sebocyte_Gingival_Mallassezderived_clear_Urothelial|gostat_on_coexpression_clusters=GO:0032488!Cdc42 protein signal transduction!0.0219815772092478!55785$GO:0043088!regulation of Cdc42 GTPase activity!0.0219815772092478!55785$GO:0032489!regulation of Cdc42 protein signal transduction!0.0219815772092478!55785$GO:0032319!regulation of Rho GTPase activity!0.0219815772092478!55785$GO:0046847!filopodium formation!0.028616528426325!55785$GO:0030035!microspike biogenesis!0.028616528426325!55785$GO:0030027!lamellipodium!0.028616528426325!55785$GO:0022603!regulation of anatomical structure morphogenesis!0.028616528426325!55785$GO:0008360!regulation of cell shape!0.028616528426325!55785$GO:0022604!regulation of cell morphogenesis!0.028616528426325!55785$GO:0001726!ruffle!0.028616528426325!55785$GO:0030031!cell projection biogenesis!0.0304958262052178!55785$GO:0031252!leading edge!0.0405097317596002!55785$GO:0031267!small GTPase binding!0.0443909858229263!55785$GO:0051020!GTPase 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|full_id=C1694_squamous_Prostate_Sebocyte_Gingival_Mallassezderived_clear_Urothelial
|id=C1694
}}

Latest revision as of 11:50, 17 September 2013


Full id: C1694_squamous_Prostate_Sebocyte_Gingival_Mallassezderived_clear_Urothelial



Phase1 CAGE Peaks

Hg19::chr12:95510642..95510668,-p@chr12:95510642..95510668
-
Hg19::chr12:95510716..95510730,-p3@FGD6
Hg19::chr12:95510743..95510753,-p8@FGD6
Hg19::chr15:71389222..71389244,+p3@THSD4
Hg19::chr9:114908292..114908313,-p13@SUSD1


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:0032488Cdc42 protein signal transduction0.0219815772092478
GO:0043088regulation of Cdc42 GTPase activity0.0219815772092478
GO:0032489regulation of Cdc42 protein signal transduction0.0219815772092478
GO:0032319regulation of Rho GTPase activity0.0219815772092478
GO:0046847filopodium formation0.028616528426325
GO:0030035microspike biogenesis0.028616528426325
GO:0030027lamellipodium0.028616528426325
GO:0022603regulation of anatomical structure morphogenesis0.028616528426325
GO:0008360regulation of cell shape0.028616528426325
GO:0022604regulation of cell morphogenesis0.028616528426325
GO:0001726ruffle0.028616528426325
GO:0030031cell projection biogenesis0.0304958262052178
GO:0031252leading edge0.0405097317596002
GO:0031267small GTPase binding0.0443909858229263
GO:0051020GTPase binding0.0472640384308379



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 cell1.74e-34253
endo-epithelial cell2.85e-2342
general ecto-epithelial cell2.84e-2014
respiratory epithelial cell9.80e-1713
endodermal cell1.34e-1558
gingival epithelial cell3.00e-123
squamous epithelial cell3.15e-1263
epithelial cell of Malassez4.67e-123
epidermal cell2.01e-109
stratified squamous epithelial cell3.34e-106
keratin accumulating cell3.34e-106
stratified epithelial cell3.34e-106
keratinizing barrier epithelial cell3.34e-106
epithelial fate stem cell3.34e-106
stratified epithelial stem cell3.34e-106
surface ectodermal cell3.34e-106
ecto-epithelial cell5.41e-0934
transitional epithelial cell5.63e-094
urothelial cell5.63e-094
sebum secreting cell9.95e-092
epithelial cell of sweat gland9.95e-092
epithelial cell of skin gland9.95e-092
acinar cell of sebaceous gland9.95e-092
mammary gland epithelial cell1.04e-084
epithelial cell of alimentary canal7.77e-0820
keratinocyte2.22e-075
epithelial cell of tracheobronchial tree8.99e-079
epithelial cell of lower respiratory tract8.99e-079
Uber Anatomy
Ontology termp-valuen
gingival epithelium3.00e-123
epithelial bud4.44e-1137
endoderm-derived structure2.96e-10160
endoderm2.96e-10160
presumptive endoderm2.96e-10160
epithelial fold1.00e-0947
endo-epithelium1.16e-0982
mouth mucosa1.80e-0913
jaw skeleton3.86e-094
splanchnocranium3.86e-094
skin gland9.95e-092
epidermis gland9.95e-092
gland of integumental system9.95e-092
sebaceous gland9.95e-092
skin sebaceous gland9.95e-092
sweat gland9.95e-092
sweat gland placode9.95e-092
sebaceous gland placode9.95e-092
mammary gland1.04e-084
mammary bud1.04e-084
mammary ridge1.04e-084
mammary placode1.04e-084
respiratory system1.34e-0874
surface structure1.48e-0899
mucosa6.87e-0820
primary subdivision of cranial skeletal system2.22e-075
urothelium2.99e-075
respiratory system epithelium4.72e-0728
respiratory tract6.84e-0754
Disease
Ontology termp-valuen
squamous cell carcinoma1.37e-1814
carcinoma3.70e-11106
clear cell adenocarcinoma6.77e-082
cell type cancer6.07e-07143


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)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.12.92423
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.11.12656
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.11.65391
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.143081
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.21.66926
MA0079.23.83292e-05
MA0102.21.66336
MA0258.10.914277
MA0259.10.395396
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
MEF2A#4205311.24593854578640.001399366787411950.00910185388992442
RAD21#588536.21302033727380.007751055068811640.0318894008403238
RFX5#599337.228746496317060.00502918278958660.0234651010258057
STAT3#677448.415571997723390.0003771527211598630.00374175482523178



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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