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Coexpression cluster:C4538: Difference between revisions

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|full_id=C4538_breast_placenta_malignant_choriocarcinoma_Sebocyte_glassy_lung
|full_id=C4538_breast_placenta_malignant_choriocarcinoma_Sebocyte_glassy_lung
|id=C4538
|id=C4538
|ontology_enrichment_celltype=CL:0000066!7.20e-38!254;CL:0002076!7.26e-15!43;CL:0002159!3.74e-13!13;CL:0000223!2.63e-10!59;CL:0002077!5.48e-09!33;CL:0000076!9.57e-09!62;CL:0000240!1.68e-08!6;CL:0000311!1.68e-08!6;CL:0000079!1.68e-08!6;CL:0000237!1.68e-08!6;CL:0000036!1.68e-08!6;CL:0000357!1.68e-08!6;CL:0000114!1.68e-08!6;CL:0002368!1.74e-08!13;CL:0000362!2.37e-08!8;CL:0000312!2.25e-07!5;CL:0002251!9.66e-07!21
|ontology_enrichment_celltype=CL:0000066!2.88e-34!253;CL:0002076!4.46e-19!42;CL:0000223!7.59e-14!58;CL:0002159!1.57e-13!14;CL:0002368!7.38e-10!13;CL:0000240!2.09e-09!6;CL:0000311!2.09e-09!6;CL:0000079!2.09e-09!6;CL:0000237!2.09e-09!6;CL:0000036!2.09e-09!6;CL:0000357!2.09e-09!6;CL:0000114!2.09e-09!6;CL:0002251!7.00e-09!20;CL:0000312!3.31e-08!5;CL:0000362!5.43e-08!9;CL:0000076!1.91e-07!63;CL:0000622!2.71e-07!5;CL:0000150!8.54e-07!9
|ontology_enrichment_disease=DOID:305!1.01e-22!106;DOID:0050687!1.07e-16!143;DOID:1749!1.41e-12!14;DOID:162!6.87e-07!235
|ontology_enrichment_disease=DOID:305!1.04e-25!106;DOID:0050687!5.82e-20!143;DOID:1749!6.73e-15!14;DOID:162!2.43e-08!235;DOID:14566!7.85e-08!239
|ontology_enrichment_uberon=UBERON:0001004!1.23e-24!72;UBERON:0000065!8.39e-18!53;UBERON:0004119!6.08e-15!169;UBERON:0000925!6.08e-15!169;UBERON:0006595!6.08e-15!169;UBERON:0000072!1.08e-14!46;UBERON:0008947!3.63e-14!38;UBERON:0003258!3.63e-14!38;UBERON:0000161!4.64e-12!35;UBERON:0000077!1.08e-11!130;UBERON:0000464!5.36e-11!104;UBERON:0000166!1.01e-10!21;UBERON:0005631!1.83e-10!14;UBERON:0000158!1.83e-10!14;UBERON:0001008!6.91e-10!45;UBERON:0005153!1.36e-09!37;UBERON:0001007!1.50e-09!155;UBERON:0001555!1.50e-09!155;UBERON:0007026!1.50e-09!155;UBERON:0001041!1.93e-09!98;UBERON:0006554!2.12e-09!44;UBERON:0004175!2.86e-09!25;UBERON:0000165!5.17e-09!28;UBERON:0000930!5.17e-09!28;UBERON:0001557!7.00e-09!19;UBERON:0004921!1.46e-08!129;UBERON:0004185!1.46e-08!129;UBERON:0001737!1.88e-08!9;UBERON:0005178!2.17e-08!34;UBERON:0002224!2.17e-08!34;UBERON:0005156!2.59e-08!59;UBERON:0000990!2.59e-08!59;UBERON:0005181!5.52e-08!35;UBERON:0003124!6.02e-08!7;UBERON:0003100!1.05e-07!41;UBERON:0005157!1.17e-07!51;UBERON:0000064!1.19e-07!219;UBERON:0003133!1.81e-07!48;UBERON:0000466!1.96e-07!126;UBERON:0001044!4.74e-07!6;UBERON:0003293!4.74e-07!6;UBERON:0003294!4.74e-07!6;UBERON:0010047!4.74e-07!6;UBERON:0000167!4.74e-07!6;UBERON:0000915!5.23e-07!52;UBERON:0005795!5.99e-07!22;UBERON:0003975!6.13e-07!22;UBERON:0004807!7.80e-07!28
|ontology_enrichment_uberon=UBERON:0001004!9.88e-23!74;UBERON:0004119!1.77e-15!160;UBERON:0000925!1.77e-15!160;UBERON:0006595!1.77e-15!160;UBERON:0000065!7.60e-15!54;UBERON:0000072!2.67e-13!47;UBERON:0000161!3.76e-13!36;UBERON:0008947!8.80e-13!38;UBERON:0003258!8.80e-13!38;UBERON:0000166!3.93e-12!22;UBERON:0001007!1.50e-10!145;UBERON:0001555!1.50e-10!145;UBERON:0007026!1.50e-10!145;UBERON:0000165!1.54e-10!29;UBERON:0000930!1.54e-10!29;UBERON:0001041!4.99e-10!87;UBERON:0003102!6.85e-10!99;UBERON:0001737!9.66e-10!9;UBERON:0004921!4.08e-09!118;UBERON:0004175!5.74e-09!25;UBERON:0005631!6.91e-09!14;UBERON:0000158!6.91e-09!14;UBERON:0005156!1.17e-08!59;UBERON:0000990!1.17e-08!59;UBERON:0001044!1.83e-08!6;UBERON:0003293!1.83e-08!6;UBERON:0003294!1.83e-08!6;UBERON:0010047!1.83e-08!6;UBERON:0000167!1.83e-08!6;UBERON:0005153!3.63e-08!37;UBERON:0001557!4.43e-08!19;UBERON:0001008!1.08e-07!48;UBERON:0000033!1.67e-07!56;UBERON:0000464!1.97e-07!95;UBERON:0003133!2.17e-07!48;UBERON:0003100!3.32e-07!41;UBERON:0006554!3.41e-07!47;UBERON:0005157!3.62e-07!47;UBERON:0005178!5.29e-07!34;UBERON:0002224!5.29e-07!34;UBERON:0005910!6.46e-07!6;UBERON:0000153!7.61e-07!62;UBERON:0007811!7.61e-07!62
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327304559108206!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168227821616514!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000678856249603644!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583507765483182!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000854160478492684!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157523525923085!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00473108704544811!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247678264187527
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327304559108206!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168227821616514!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000678856249603644!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583507765483182!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000854160478492684!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157523525923085!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00473108704544811!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247678264187527
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0418,1.93377e-05,0.199971,0.0966069,0.127758,0.0164446,0.0012141,0.169234,0.0876426,0.0952322,0.0112557,0.00013661,0.107043,0.275244,0.00481323,0.0160457,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,1.1672e-06,0.123526,0.0906475,0.0558058,0.28262,0.166024,0.137332,0.0145999,0.0656973,0.211746,0.220538,9.12913e-05,7.69244e-05,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.00340073,0.170307,0.0217163,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.000234172,0.11002,0.00370214,0.0286025,0.190156,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.00335855,0.00203513,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,4.27652e-05,0.00502301,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.128564,0.000419898,0.112518,0.0226843,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.00452901,0.144075,0.0340203,0.0741807,0.0425274,0.153605,0.655293,0.00204117,0.0465945,0.000310064,0.0198413,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.000444106,0.0355833,0.125606,0.175094,0.911304,0.145116,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,4.46154e-06,0.00293103,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.00921075,0.0450031,0.0539144,0.114242,3.49213e-06,0.172425,5.76291e-06,0.00217546,3.25328e-05,0.00259914,0.0759837,0.286863,0.152372,0.00144552,0.0257725,0.101607,0.327067,0.172982,0.340936,0.000654973,0.0626744,0.191335,0.148574,0.504592,0.0128248,0.0718905,0.00435853,0.0602373,0.144304,0.15063,0.000166026,0.0126914,0.0154015,0.193653,0.137219,0.228144,0.251466,0.0050797,0.11903,0.0838874,0.00806892,1.88222e-07,0.112651,0.186638,0.01625,0.00464715,0.264079,0.249049,0.140533,0.0997756,0.0364628,0.103667,0.00664782,0.025556,0.000902392,0.09066,0.220462,0.166967,0.188651,0.0813902,0.00122372,0.156261,0.311847,0.511859,0.00178152,0.247324,0.178389,0.0020701,0.0290303,0.0020598,0.619906,0.0360851,0.412187,0.000416337,0.0434602,0.133616,0.0177337,0.0115948,0.00328135,0.0162067,0.231447,0.544776,0.43956,0.37006,0.00255501,0.022688,0.197484,0.396996,0.36145,0.406019,0.0841307,0.216033,0.643768,0.432035,0.722159,0.390366,0.48809,0.0334527,3.39738e-05,0.522904,0.616975,0.336835,0.227104,0.000951286,0.250246,0.0867545,0.0450114,0.00583062,0.04783,0.729153,0.0465139,0.164197,0.462688,0.287881,0.21103,6.0419e-05,0.336276,0.468444,0.258219,0.446557,0.032364,0.777351,0.0140783,0.149257,0.683217,0.161598,0.0527155,0.277094,6.5727e-07,0.0239796,0.0805771,0.78509,0.477353,0.452741,0.746954,0.000852086,0.20342,0.200493,0.20558,0.300504,0.0361545,0.425963,0.349197,0.0131573,0.000717871,0.141318,0.411941,0.0961477,0.00677445,0.354789,0.163828,0.230581,0.120226,0.0448825,1.93743e-08,0.0556238,0.181415,0.282286,0.446891,0.616388,0.408413,1.01409e-06,0.000699859,1.93712e-08,0.33942,0.61031,0.00162648,0.522605,0.802166,0.00120002,0.222037,0.416621,0.416292,0.00379537,0.734551,0.0019893,0.00169113,0.452428,0.0101228,0.00105709,0.166905,0.19783,0.0833851,0.00691922,0.00457272,0.0163316,0.332919,0.373557,0.170369,0.0164118,0.0111982,0.000145338,0.0140668,0.363192,0.00266072,0.203486,0.273398,1.0176e-05,0.0223007,0.351067,0.00438156,0.637444,0.305885,0.00285094,9.35975e-06,0.00623664,0.303709,0.0323359,0.0135408,0.508064,0.250964,0.0131557,0.457886,0.0344603,0.0262575,0.509064,0.196976,0.00136659,1.38286e-09,0.601877,0.000565784,0.459728,0.283463,0.563586,0.0272975,0.399569,0.273281,0.368095,0.275089,0.0133102,0.47795,0.359231,0.339729,0.197805,0.608187,0.000156135,0.332774,0.52832,0.299887,0.0814305,0.205413,0.17639,0.0779009,0.276869,4.41089e-06,0.0337138,0.18966,7.76854e-07,0.188263,6.55315e-05,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.000130607,0.00469907,0.166124,0.252184,0.378361,0.255516,0.20753,0.0224033,0.179412,0.193601,0.220904,0.000138062,7.52509e-05,0.310674,0.00206345,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,2.36575e-05,0.0855609,0.131118,0.20837,0.247588,6.79935e-06,0.0673329,0.20847,0.00394192,0.113092,0.145701,0.229428,0.162145,0.228955,1.24367e-09,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,3.99854e-06,0.00972162,0.154941,0.000318033,0.0986735,0.108462,3.68621e-05,0.21593,0.158479,0.220319,0.195218,0.124213,0.00361981,0.30793,0.180606,0.159884,0.257294,0.150733,0.0254879,0.123917,0.184317,0.00123184,6.66781e-05,0.258496,0.261744,0.203781,5.49812e-06,0.0232077,0.141867,0.0199603,1.26764e-05,0.115972,0.0273485,0.0030448,1.7611e-06,0.200432,1.42291e-08,8.12543e-05,4.75501e-07,1.03176e-06,0.13108,0.256963,0.222798,0.172134,0.176789,0.00485777,0.00162178,0.000591588,0.0437875,0.218161,0.0822373,9.03667e-05,0.106739,2.67472e-05,0.0537737,0.000648679,0.078016,0.0407233,0.0537355,0.0577193,0.261724,0.00186843,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.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}}
}}

Revision as of 16:02, 19 October 2012


Full id: C4538_breast_placenta_malignant_choriocarcinoma_Sebocyte_glassy_lung



Phase1 CAGE Peaks

Hg19::chr6:10419750..10419757,-p30@TFAP2A
Hg19::chr6:10419768..10419819,-p6@TFAP2A
Hg19::chr6:10419824..10419840,-p9@TFAP2A


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
respiratory system9.88e-2374
endoderm-derived structure1.77e-15160
endoderm1.77e-15160
presumptive endoderm1.77e-15160
respiratory tract7.60e-1554
segment of respiratory tract2.67e-1347
orifice3.76e-1336
respiratory primordium8.80e-1338
endoderm of foregut8.80e-1338
oral opening3.93e-1222
digestive system1.50e-10145
digestive tract1.50e-10145
primitive gut1.50e-10145
mouth1.54e-1029
stomodeum1.54e-1029
foregut4.99e-1087
surface structure6.85e-1099
larynx9.66e-109
subdivision of digestive tract4.08e-09118
internal genitalia5.74e-0925
extraembryonic membrane6.91e-0914
membranous layer6.91e-0914
reproductive structure1.17e-0859
reproductive system1.17e-0859
saliva-secreting gland1.83e-086
gland of oral region1.83e-086
gland of foregut1.83e-086
oral gland1.83e-086
oral cavity1.83e-086
epithelial bud3.63e-0837
upper respiratory tract4.43e-0819
renal system1.08e-0748
head1.67e-0756
anatomical space1.97e-0795
reproductive organ2.17e-0748
female organism3.32e-0741
urinary system structure3.41e-0747
epithelial fold3.62e-0747
thoracic cavity element5.29e-0734
thoracic cavity5.29e-0734
transitional epithelium6.46e-076
anterior region of body7.61e-0762
craniocervical region7.61e-0762
Disease
Ontology termp-valuen
carcinoma1.04e-25106
cell type cancer5.82e-20143
squamous cell carcinoma6.73e-1514
cancer2.43e-08235
disease of cellular proliferation7.85e-08239


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)

{{{tfbs_overrepresentation_jaspar}}}



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
E2F1#186934.907389214879320.008460985347239390.0327304559108206
EP300#203336.77394172622320.003216880500103790.0168227821616514
ESR1#2099330.76860329615453.43136389821584e-050.000678856249603644
FOXA1#3169311.08141974938550.000734755275698670.00583507765483182
GATA3#2625327.2365163572064.94721007899563e-050.000854160478492684
JUND#372736.994663941871030.002921845042734990.0157523525923085
NRF1#4899312.21027944771090.0005492172401020010.00473108704544811
SP1#666735.69838137814090.005403962701712170.0247678264187527



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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