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Coexpression cluster:C3876: Difference between revisions

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|full_id=C3876_colon_liver_Hepatocyte_choriocarcinoma_chorionic_Renal_serous
|full_id=C3876_colon_liver_Hepatocyte_choriocarcinoma_chorionic_Renal_serous
|id=C3876
|id=C3876
|ontology_enrichment_celltype=CL:0000066!1.80e-47!254;CL:0000223!1.63e-17!59;CL:0000076!9.17e-13!62;CL:0002076!2.66e-12!43;CL:0002139!1.37e-11!24;CL:0000115!1.15e-10!35;CL:0002078!7.67e-10!44;CL:0000213!1.02e-09!57;CL:0000215!1.02e-09!57;CL:0000071!2.30e-08!18;CL:0002546!2.30e-08!18
|ontology_enrichment_celltype=CL:0000066!1.22e-49!253;CL:0000223!8.50e-18!58;CL:0002076!6.97e-13!42;CL:0000076!9.02e-13!63;CL:0002139!1.46e-12!24;CL:0000115!2.33e-12!36;CL:0002078!1.40e-11!45;CL:0000213!2.26e-11!58;CL:0000215!2.26e-11!58;CL:0000071!3.48e-09!18;CL:0002546!3.48e-09!18;CL:0002251!5.52e-07!20;CL:1000449!7.64e-07!15
|ontology_enrichment_disease=DOID:305!4.29e-20!106;DOID:0050687!3.49e-17!143;DOID:299!7.51e-07!25
|ontology_enrichment_disease=DOID:305!6.98e-19!106;DOID:0050687!1.22e-16!143
|ontology_enrichment_uberon=UBERON:0004119!1.94e-22!169;UBERON:0000925!1.94e-22!169;UBERON:0006595!1.94e-22!169;UBERON:0004921!3.09e-19!129;UBERON:0004185!3.09e-19!129;UBERON:0000477!7.96e-19!286;UBERON:0001007!1.98e-18!155;UBERON:0001555!1.98e-18!155;UBERON:0007026!1.98e-18!155;UBERON:0004111!3.24e-18!241;UBERON:0000077!8.08e-17!130;UBERON:0001041!2.09e-16!98;UBERON:0005177!1.99e-15!107;UBERON:0000064!4.94e-15!219;UBERON:0007023!9.23e-15!115;UBERON:0000025!4.89e-13!194;UBERON:0000062!1.64e-12!511;UBERON:0005911!2.52e-12!82;UBERON:0000481!3.09e-12!347;UBERON:0000468!1.61e-11!659;UBERON:0001004!1.96e-11!72;UBERON:0000483!2.17e-11!309;UBERON:0000922!3.06e-11!612;UBERON:0000119!6.77e-11!312;UBERON:0000466!1.18e-10!126;UBERON:0002050!1.84e-10!605;UBERON:0005423!1.84e-10!605;UBERON:0000923!3.05e-10!604;UBERON:0005291!3.05e-10!604;UBERON:0006598!3.05e-10!604;UBERON:0002532!3.05e-10!604;UBERON:0000467!4.83e-10!625;UBERON:0000480!5.75e-10!626;UBERON:0005172!6.28e-10!55;UBERON:0005173!6.28e-10!55;UBERON:0008947!8.59e-10!38;UBERON:0003258!8.59e-10!38;UBERON:0000065!1.07e-09!53;UBERON:0009569!1.52e-09!113;UBERON:0002365!3.27e-09!31;UBERON:0002330!3.27e-09!31;UBERON:0001048!1.23e-08!168;UBERON:0002530!1.28e-08!59;UBERON:0001986!2.30e-08!18;UBERON:0004638!2.30e-08!18;UBERON:0004852!2.30e-08!18;UBERON:0009497!2.19e-07!25;UBERON:0000015!2.19e-07!25;UBERON:0002423!2.19e-07!25;UBERON:0006235!2.19e-07!25;UBERON:0004161!2.19e-07!25;UBERON:0003929!2.30e-07!54;UBERON:0000487!2.83e-07!22;UBERON:0000924!4.44e-07!173;UBERON:0006601!4.44e-07!173;UBERON:0002417!4.47e-07!61;UBERON:0000916!4.47e-07!61;UBERON:0000072!5.13e-07!46;UBERON:0004121!5.37e-07!169;UBERON:0001049!5.85e-07!57;UBERON:0005068!5.85e-07!57;UBERON:0006241!5.85e-07!57;UBERON:0007135!5.85e-07!57
|ontology_enrichment_uberon=UBERON:0000477!1.10e-26!373;UBERON:0011216!1.57e-22!223;UBERON:0004119!4.95e-22!160;UBERON:0000925!4.95e-22!160;UBERON:0006595!4.95e-22!160;UBERON:0004921!1.14e-18!118;UBERON:0004111!1.73e-18!240;UBERON:0001007!3.20e-18!145;UBERON:0001555!3.20e-18!145;UBERON:0007026!3.20e-18!145;UBERON:0001041!8.84e-16!87;UBERON:0000064!2.87e-15!218;UBERON:0005177!5.65e-14!101;UBERON:0000062!3.65e-13!503;UBERON:0007023!6.77e-13!114;UBERON:0000481!7.11e-13!342;UBERON:0000025!1.47e-12!192;UBERON:0005911!2.62e-12!82;UBERON:0000468!4.57e-11!656;UBERON:0000483!9.70e-11!306;UBERON:0005172!2.25e-10!54;UBERON:0005173!2.25e-10!54;UBERON:0001004!3.08e-10!74;UBERON:0000119!3.17e-10!309;UBERON:0000467!6.04e-10!624;UBERON:0000480!7.16e-10!625;UBERON:0009569!9.99e-10!112;UBERON:0000466!2.72e-09!117;UBERON:0002365!3.09e-09!31;UBERON:0002330!3.09e-09!31;UBERON:0004638!3.48e-09!18;UBERON:0001986!3.48e-09!18;UBERON:0004852!3.48e-09!18;UBERON:0000922!3.72e-09!592;UBERON:0008947!7.79e-09!38;UBERON:0003258!7.79e-09!38;UBERON:0002530!8.34e-09!59;UBERON:0001008!1.01e-08!48;UBERON:0006554!1.43e-08!47;UBERON:0000065!2.33e-08!54;UBERON:0005423!3.34e-08!581;UBERON:0001048!3.74e-08!160;UBERON:0000487!4.92e-08!22;UBERON:0002417!9.36e-08!60;UBERON:0000916!9.36e-08!60;UBERON:0003929!2.00e-07!54;UBERON:0009497!3.53e-07!25;UBERON:0000015!3.53e-07!25;UBERON:0002423!3.53e-07!25;UBERON:0006235!3.53e-07!25;UBERON:0004161!3.53e-07!25;UBERON:0006555!3.85e-07!16;UBERON:0004819!3.85e-07!16;UBERON:0000353!5.66e-07!15;UBERON:0004211!7.64e-07!15;UBERON:0009773!7.64e-07!15;UBERON:0001231!7.64e-07!15;UBERON:0001285!7.64e-07!15;UBERON:0007684!7.64e-07!15;UBERON:0004208!7.64e-07!15
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322334321592739!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320745459756867!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108738337609051!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00122842025436597!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276869470556912!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.002030696360455!SMARCC2#6601;3:94.1553744268976:1.19621075407887e-06:4.85357633819902e-05!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140247222644903
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322334321592739!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320745459756867!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108738337609051!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00122842025436597!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276869470556912!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.002030696360455!SMARCC2#6601;3:94.1553744268976:1.19621075407887e-06:4.85357633819902e-05!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140247222644903
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06475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.00100273,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.00896808,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.00176415,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.0538132,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00681584,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.00049486,0.0926491,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,1.70007e-06,0.000581378,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.0227848,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,1.80557e-07,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.000615006,0.034431,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.00238639,0.251466,0.0461822,0.11903,0.0838874,0.331451,0.00665699,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.00352872,0.103667,0.113069,0.025556,0.16791,0.09066,0.0125264,0.166967,0.188651,0.00340589,0.184948,0.156261,0.311847,0.511859,0.0590944,0.00309372,0.178389,0.218229,0.0290303,0.407281,0.252227,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.00202987,0.381071,0.580441,0.0863135,0.432035,0.722159,0.0886602,0.48809,0.0334527,0.443185,0.522904,6.58045e-05,0.0184337,0.227104,0.0380245,0.00310917,0.0867545,0.284625,0.0344717,0.0091887,0.375373,0.0465139,0.164197,0.128922,0.287881,0.574635,0.478174,0.336276,0.132529,0.258219,0.446557,0.243383,0.0186777,0.390974,0.0458848,0.683217,0.161598,0.164332,0.00422412,0.496032,0.00136122,0.0013757,0.0203982,0.0282154,3.25586e-05,0.0508568,0.000153842,0.0222555,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.0101316,0.163828,0.230581,0.120226,0.28424,0.0513026,0.314429,0.181415,0.282286,0.0674279,0.616388,0.0978616,0.516511,0.322213,0.0234043,0.00873429,0.61031,0.387276,0.522605,2.18573e-09,0.537348,0.222037,0.416621,0.10205,0.0252635,0.148994,3.41694e-05,0.204817,0.452428,0.138871,0.673493,0.166905,0.19783,0.0833851,0.316453,0.0289164,0.175199,0.332919,0.373557,0.523625,0.0164118,0.365487,0.534741,0.0889149,0.363192,0.236011,0.203486,0.273398,0.375787,0.0223007,0.351067,0.275347,0.019895,0.305885,0.241132,0.371414,0.30666,0.303709,0.15059,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.235208,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.0780405,0.275089,0.384593,0.47795,0.0105648,0.0656472,0.197805,0.608187,0.387069,0.332774,0.0406989,0.299887,0.266492,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.0233967,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.0254879,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.0273485,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.00161996,0.00591081,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.00229305,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.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}}
}}

Revision as of 15:28, 19 October 2012


Full id: C3876_colon_liver_Hepatocyte_choriocarcinoma_chorionic_Renal_serous



Phase1 CAGE Peaks

Hg19::chr1:155100342..155100359,+p1@EFNA1
Hg19::chr1:155100366..155100377,+p2@EFNA1
Hg19::chr1:155100387..155100398,+p3@EFNA1


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
anatomical cluster1.10e-26373
organ system subdivision1.57e-22223
endoderm-derived structure4.95e-22160
endoderm4.95e-22160
presumptive endoderm4.95e-22160
subdivision of digestive tract1.14e-18118
anatomical conduit1.73e-18240
digestive system3.20e-18145
digestive tract3.20e-18145
primitive gut3.20e-18145
foregut8.84e-1687
organ part2.87e-15218
trunk region element5.65e-14101
organ3.65e-13503
adult organism6.77e-13114
multi-tissue structure7.11e-13342
tube1.47e-12192
endo-epithelium2.62e-1282
multi-cellular organism4.57e-11656
epithelium9.70e-11306
abdomen element2.25e-1054
abdominal segment element2.25e-1054
respiratory system3.08e-1074
cell layer3.17e-10309
anatomical system6.04e-10624
anatomical group7.16e-10625
subdivision of trunk9.99e-10112
immaterial anatomical entity2.72e-09117
exocrine gland3.09e-0931
exocrine system3.09e-0931
blood vessel endothelium3.48e-0918
endothelium3.48e-0918
cardiovascular system endothelium3.48e-0918
embryo3.72e-09592
respiratory primordium7.79e-0938
endoderm of foregut7.79e-0938
gland8.34e-0959
renal system1.01e-0848
urinary system structure1.43e-0847
respiratory tract2.33e-0854
developing anatomical structure3.34e-08581
primordium3.74e-08160
simple squamous epithelium4.92e-0822
abdominal segment of trunk9.36e-0860
abdomen9.36e-0860
gut epithelium2.00e-0754
epithelium of foregut-midgut junction3.53e-0725
anatomical boundary3.53e-0725
hepatobiliary system3.53e-0725
foregut-midgut junction3.53e-0725
septum transversum3.53e-0725
excretory tube3.85e-0716
kidney epithelium3.85e-0716
parenchyma5.66e-0715
nephron epithelium7.64e-0715
renal tubule7.64e-0715
nephron tubule7.64e-0715
nephron7.64e-0715
uriniferous tubule7.64e-0715
nephrogenic mesenchyme7.64e-0715
Disease
Ontology termp-valuen
carcinoma6.98e-19106
cell type cancer1.22e-16143


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
E2F6#187635.017155731697390.00791769806886330.0322334321592739
EGR1#195834.988179094810140.008056488137383440.0320745459756867
HMGN3#932438.178547723350590.001827766942164210.0108738337609051
HNF4A#3172323.13229036295378.07584663437677e-050.00122842025436597
SIN3A#2594235.408884726815140.006318961977991520.0276869470556912
SMARCB1#6598318.25271578115740.000164397760679890.002030696360455
SMARCC2#6601394.15537442689761.19621075407887e-064.85357633819902e-05
ZBTB7A#5134137.35190930787590.002516255860282270.0140247222644903



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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