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Coexpression cluster:C544: Difference between revisions

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|ontology_enrichment_disease=DOID:1749!3.62e-08!14
|ontology_enrichment_disease=DOID:1749!3.62e-08!14
|ontology_enrichment_uberon=UBERON:0000062!2.49e-14!511;UBERON:0001004!1.13e-13!72;UBERON:0000064!2.96e-12!219;UBERON:0000065!4.04e-11!53;UBERON:0004119!4.23e-10!169;UBERON:0000925!4.23e-10!169;UBERON:0006595!4.23e-10!169;UBERON:0000922!2.18e-09!612;UBERON:0002050!5.70e-09!605;UBERON:0005423!5.70e-09!605;UBERON:0000923!1.00e-08!604;UBERON:0005291!1.00e-08!604;UBERON:0006598!1.00e-08!604;UBERON:0002532!1.00e-08!604;UBERON:0000480!1.05e-08!626;UBERON:0000467!1.40e-08!625;UBERON:0005631!3.09e-08!14;UBERON:0000158!3.09e-08!14;UBERON:0001557!5.20e-08!19;UBERON:0000468!5.35e-08!659;UBERON:0000072!5.97e-08!46;UBERON:0001737!1.12e-07!9;UBERON:0000924!1.84e-07!173;UBERON:0006601!1.84e-07!173;UBERON:0000077!1.94e-07!130;UBERON:0004121!2.20e-07!169;UBERON:0000161!2.38e-07!35;UBERON:0000153!2.41e-07!129;UBERON:0007811!2.41e-07!129;UBERON:0008947!2.73e-07!38;UBERON:0003258!2.73e-07!38;UBERON:0000166!7.65e-07!21
|ontology_enrichment_uberon=UBERON:0000062!2.49e-14!511;UBERON:0001004!1.13e-13!72;UBERON:0000064!2.96e-12!219;UBERON:0000065!4.04e-11!53;UBERON:0004119!4.23e-10!169;UBERON:0000925!4.23e-10!169;UBERON:0006595!4.23e-10!169;UBERON:0000922!2.18e-09!612;UBERON:0002050!5.70e-09!605;UBERON:0005423!5.70e-09!605;UBERON:0000923!1.00e-08!604;UBERON:0005291!1.00e-08!604;UBERON:0006598!1.00e-08!604;UBERON:0002532!1.00e-08!604;UBERON:0000480!1.05e-08!626;UBERON:0000467!1.40e-08!625;UBERON:0005631!3.09e-08!14;UBERON:0000158!3.09e-08!14;UBERON:0001557!5.20e-08!19;UBERON:0000468!5.35e-08!659;UBERON:0000072!5.97e-08!46;UBERON:0001737!1.12e-07!9;UBERON:0000924!1.84e-07!173;UBERON:0006601!1.84e-07!173;UBERON:0000077!1.94e-07!130;UBERON:0004121!2.20e-07!169;UBERON:0000161!2.38e-07!35;UBERON:0000153!2.41e-07!129;UBERON:0007811!2.41e-07!129;UBERON:0008947!2.73e-07!38;UBERON:0003258!2.73e-07!38;UBERON:0000166!7.65e-07!21
|tfbs_overrepresentation=0.063297,0.0468604,0.031218,0.241984,7.27229e-06,3.17106e-14,0.0263249,0.0873763,0.171812,0.137198,0.572952,0.0161936,0.332123,0.00773284,0.000368464,0.00604592,0.0116251,0.117226,0.264861,0.137947,4.38356e-06,0.048284,0.0855959,0.00271407,0.213853,2.83235e-09,0.0462936,0.416622,4.07604e-06,0.107461,0.00222784,0.496503,0.0979725,1.68806e-10,0.00740596,0.393536,0.0179578,0.220321,0.516474,0.323747,0.437251,0.131693,0.0113475,0.684122,0.000113149,0.188753,0.197184,0.678579,0.487539,0.519116,0.612542,0.270683,0.337835,0.106716,0.357473,0.199071,0.474907,0.0488055,0.0116821,0.00403688,0.155722,5.51453e-06,0.478718,4.83286e-07,0.272384,0.000245014,1.08083e-05,0.00553834,0.0932583,0.000712005,0.000119677,0.327735,0.0166351,0.51345,0.000878895,0.0932062,0.113743,0.00223961,0.193549,0.0404083,0.434241,3.21037e-06,0.218157,0.499075,0.310166,0.00685493,0.313986,0.0024838,0.000138618,0.307337,0.398342,0.250391,2.8748e-05,0.240442,0.00182578,8.28911e-06,0.131519,0.0705029,0.423945,0.273536,0.00490396,3.68137e-06,0.579799,0.0198852,0.166823,0.00185511,0.0596624,0.208477,4.05728e-07,0.00981974,0.000187135,0.177989,0.234094,0.0961704,0.453781,0.176809,0.109917,0.281434,2.92813e-07,0.391156,0.644223,0.397639,0.0557273,0.398438,0.45772,2.48525e-06,0.102162,0.0809874,0.0900273,1.82971e-08,0.0481983,0.0728056,0.000396976,0.122444,1.43372e-06,0.477054,0.316158,0.275722,0.173362,0.0222073,0.00781578,0.00121918,0.0423346,0.617516,5.31751e-07,4.46414e-06,0.445471,0.0897781,0.201549,0.166211,0.00969157,0.584778,0.0011066,0.010533,0.0259825,0.158811,0.356162,0.769889,0.259776,5.09686e-05,0.000806568,0.433014,0.504808,0.00241396,0.272174,0.0054112,0.00174027,0.53793,0.0233514,0.00615775,2.03157e-11,0.000238381,0.867614,0.0404157,0.0123592,0.414284,0.211778,0.107172,0.671706,0.18585,0.624767,0.523049,0.145697,0.501404,0.0010471,0.51177,0.317605,0.20734,0.00163079,0.0956361,2.87786e-08,0.00135135,0.170995,0.0622179,0.000679056,0.0311767,0.369815,0.296967,0.327619,0.14144,0.0167716,0.297442,0.162609,0.298313,0.0103333,0.00188583,1.24058e-11,0.0151674,0.376459,0.671502,0.233607,0.464493,1.17974e-05,7.29928e-06,8.49961e-09,0.649864,0.0200116,0.0034173,0.308375,0.0247152,0.000282939,0.000422698,0.0733554,1.06389e-07,0.0711195,0.179441,0.0544325,0.399148,0.297675,0.295312,0.000140565,0.0225399,0.2151,0.00120503,0.435274,0.425557,0.0313675,0.097721,0.0824612,2.39533e-11,1.06467e-19,9.63866e-06,0.443992,0.388337,0.034203,0.00168908,0.382333,0.48873,0.128796,0.50603,0.0178812,2.40426e-12,1.57587e-19,0.116872,0.116997,0.259019,5.66693e-05,0.721312,0.335483,0.550394,0.303874,0.000141444,1.10654e-05,0.00124124,0.180475,0.380645,0.0841024,0.0024229,0.0356209,0.359143,0.0116975,0.00643724,0.81107,0.0546481,0.401444,0.197322,5.98359e-11,0.00067528,0.00629142,0.10068,0.00240971,6.45048e-22,1.34306e-05,0.149565,8.94023e-13,2.41291e-26,0.820605,4.92342e-05,1.68479e-14,0.00147035,4.87496e-05,2.92242e-09,1.68366e-09,0.000577594,7.60509e-09,3.75059e-09,1.92604e-05,0.000959727,2.80946e-06,2.70909e-10,1.47229e-08,2.92997e-10,0.691146,7.41955e-05,0.679034,1.25145e-18,0.483293,0.000597942,0.406724,9.38917e-15,0.0552037,2.61577e-29,6.14921e-14,6.36261e-17,3.16684e-05,0.00158664,4.01182e-06,2.73581e-12,2.89547e-09,1.53491e-11,9.7705e-06,8.90658e-08,0.000411611,0.0575698,2.94446e-10,2.71399e-06,0.563668,1.25806e-09,2.55062e-09,0.00020088,5.19866e-05,9.01554e-14,1.58181e-07,0.0494158,0.00147702,9.2086e-06,1.98382e-16,2.46148e-21,5.56241e-10,0.315936,9.23307e-08,0.756956,7.64552e-07,0.544574,4.83186e-06,0.687707,2.24701e-14,0.0137992,0.107268,1.09193e-24,1.63556e-09,0.228618,2.10679e-08,0.0815785,0.012432,9.69527e-21,1.11008e-08,0.325166,0.349565,0.322063,2.82439e-05,0.000811642,2.08517e-14,7.52831e-05,3.6548e-16,7.76924e-14,8.19744e-05,5.92822e-10,0.000617058,2.53006e-06,3.64385e-13,0.230146,0.0726637,6.35423e-09,2.14131e-08,3.97813e-19,0.000827094,1.22169e-06,1.42381e-06,1.34095e-19,0.00018637,5.47741e-14,0.000155091,0.281767,0.00028651,1.86516e-22,2.33866e-05,1.07959e-06,0.354545,5.48296e-10,1.01608e-11,9.46223e-23,9.2515e-08,3.33323e-08,1.424e-15,0.0344083,5.86727e-06,0.0606424,0.000326385,0.936678,2.41338e-05,0.00249389,2.99159e-25,0.0263704,0.60892,0.236808,1.12018e-10,2.07101e-17,0.559756,0.118013,1.14473e-14,0.000998581,5.11706e-06,3.34087e-26,0.343473,0.000302288,2.83331e-21,5.44392e-16,2.24714e-15,0.124968,1.59165e-25,7.8105e-08,4.88302e-08,0.0311085,6.74611e-18,5.58018e-07,2.32001e-10,0.0323606,0.144902,2.93974e-11,0.000166286,0.00637694,0.263323,0.904477,3.60858e-07,1.95226e-14,0.0574166,0.0246197,0.00382769,0.626717,0.0713667,0.128114,6.7119e-08,4.56761e-06,0.000222907,0.293891,0.608006,2.18412e-12,1.60256e-11,9.28206e-07,3.1595e-07,1.55002e-12,3.98415e-10,2.96671e-11,2.09547e-06,0.000403782,0.336232,0.277231,0.702373,0.368829,0.285365,2.85089e-09,0.761322,0.000386404,6.7492e-23,0.000172345,3.10352e-13,0.146362,5.43851e-23,0.22295,0.60689,0.535251,0.000211349,2.71244e-13,0.0370786,0.307527,0.290666,0.000165816,0.000286899,4.2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}}
}}

Revision as of 20:30, 8 August 2012


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
epithelial cell8.00e-16254
endo-epithelial cell2.38e-1443
endodermal cell1.21e-0959
respiratory epithelial cell2.72e-0913
general ecto-epithelial cell5.20e-0713
Uber Anatomy
Ontology termp-valuen
organ2.49e-14511
respiratory system1.13e-1372
organ part2.96e-12219
respiratory tract4.04e-1153
endoderm-derived structure4.23e-10169
endoderm4.23e-10169
presumptive endoderm4.23e-10169
embryo2.18e-09612
embryonic structure5.70e-09605
developing anatomical structure5.70e-09605
germ layer1.00e-08604
embryonic tissue1.00e-08604
presumptive structure1.00e-08604
epiblast (generic)1.00e-08604
anatomical group1.05e-08626
anatomical system1.40e-08625
extraembryonic membrane3.09e-0814
membranous layer3.09e-0814
upper respiratory tract5.20e-0819
multi-cellular organism5.35e-08659
segment of respiratory tract5.97e-0846
larynx1.12e-079
ectoderm1.84e-07173
presumptive ectoderm1.84e-07173
mixed endoderm/mesoderm-derived structure1.94e-07130
ectoderm-derived structure2.20e-07169
orifice2.38e-0735
anterior region of body2.41e-07129
craniocervical region2.41e-07129
respiratory primordium2.73e-0738
endoderm of foregut2.73e-0738
oral opening7.65e-0721
Disease
Ontology termp-valuen
squamous cell carcinoma3.62e-0814


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)

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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


No analysis results for this cluster

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.