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Coexpression cluster:C2638: Difference between revisions

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|full_id=C2638_breast_bronchogenic_Amniotic_liver_endometrioid_Hepatocyte_serous
|full_id=C2638_breast_bronchogenic_Amniotic_liver_endometrioid_Hepatocyte_serous
|id=C2638
|id=C2638
|ontology_enrichment_celltype=CL:0000066!9.59e-26!254;CL:0000223!1.48e-14!59;CL:0002076!1.72e-13!43;CL:0002321!1.16e-10!248;CL:0000220!2.76e-10!246;CL:0002251!1.09e-07!21
|ontology_enrichment_celltype=CL:0000066!2.60e-25!253;CL:0000223!3.12e-14!58;CL:0002076!5.61e-14!42;CL:0002321!4.62e-10!250;CL:0002251!5.33e-08!20;CL:0000076!8.15e-07!63
|ontology_enrichment_disease=DOID:1749!3.46e-07!14
|ontology_enrichment_disease=DOID:1749!4.39e-07!14
|ontology_enrichment_uberon=UBERON:0000468!9.05e-20!659;UBERON:0000475!2.35e-19!365;UBERON:0000481!3.28e-19!347;UBERON:0004119!1.12e-18!169;UBERON:0000925!1.12e-18!169;UBERON:0006595!1.12e-18!169;UBERON:0004111!3.90e-18!241;UBERON:0000477!1.88e-15!286;UBERON:0000467!2.79e-15!625;UBERON:0000922!3.41e-15!612;UBERON:0000480!6.09e-15!626;UBERON:0001007!8.54e-15!155;UBERON:0001555!8.54e-15!155;UBERON:0007026!8.54e-15!155;UBERON:0000483!2.19e-14!309;UBERON:0000119!6.38e-14!312;UBERON:0002050!3.73e-13!605;UBERON:0005423!3.73e-13!605;UBERON:0000923!7.04e-13!604;UBERON:0005291!7.04e-13!604;UBERON:0006598!7.04e-13!604;UBERON:0002532!7.04e-13!604;UBERON:0000064!1.98e-12!219;UBERON:0000466!1.04e-11!126;UBERON:0004921!2.65e-11!129;UBERON:0004185!2.65e-11!129;UBERON:0000062!5.07e-11!511;UBERON:0000077!6.86e-11!130;UBERON:0003104!7.03e-11!238;UBERON:0009142!7.03e-11!238;UBERON:0002100!7.60e-11!216;UBERON:0000025!2.68e-10!194;UBERON:0009569!3.08e-10!113;UBERON:0005177!3.11e-09!107;UBERON:0000464!4.35e-09!104;UBERON:0005911!6.08e-09!82;UBERON:0001004!6.17e-09!72;UBERON:0000161!2.62e-08!35;UBERON:0000166!6.28e-08!21;UBERON:0000033!6.32e-08!123;UBERON:0000153!1.11e-07!129;UBERON:0007811!1.11e-07!129;UBERON:0004121!1.21e-07!169;UBERON:0000915!1.86e-07!52;UBERON:0000924!1.87e-07!173;UBERON:0006601!1.87e-07!173;UBERON:0005256!2.00e-07!143;UBERON:0000165!2.73e-07!28;UBERON:0000930!2.73e-07!28;UBERON:0002365!3.43e-07!31;UBERON:0002330!3.43e-07!31;UBERON:0001041!4.31e-07!98;UBERON:0005178!4.65e-07!34;UBERON:0002224!4.65e-07!34;UBERON:0005631!4.70e-07!14;UBERON:0000158!4.70e-07!14;UBERON:0001444!5.35e-07!48
|ontology_enrichment_uberon=UBERON:0004119!1.11e-21!160;UBERON:0000925!1.11e-21!160;UBERON:0006595!1.11e-21!160;UBERON:0000477!7.59e-20!373;UBERON:0000481!1.33e-19!342;UBERON:0001007!1.16e-17!145;UBERON:0001555!1.16e-17!145;UBERON:0007026!1.16e-17!145;UBERON:0004111!2.33e-17!240;UBERON:0000468!9.57e-17!656;UBERON:0000475!7.16e-16!264;UBERON:0004921!5.36e-14!118;UBERON:0000483!8.91e-14!306;UBERON:0000119!4.06e-13!309;UBERON:0000467!4.10e-13!624;UBERON:0000480!7.55e-13!625;UBERON:0011216!2.22e-12!223;UBERON:0000922!2.38e-12!592;UBERON:0005423!2.15e-11!581;UBERON:0000064!4.07e-11!218;UBERON:0009569!1.28e-09!112;UBERON:0001004!1.38e-09!74;UBERON:0002050!1.40e-09!564;UBERON:0005911!1.96e-09!82;UBERON:0000062!2.47e-09!503;UBERON:0000025!3.17e-09!192;UBERON:0000161!3.63e-09!36;UBERON:0001041!5.53e-09!87;UBERON:0000923!1.12e-08!560;UBERON:0010316!1.12e-08!560;UBERON:0005291!1.12e-08!560;UBERON:0006598!1.12e-08!560;UBERON:0010317!1.12e-08!560;UBERON:0002532!1.12e-08!560;UBERON:0000466!1.71e-08!117;UBERON:0002100!2.80e-08!199;UBERON:0001008!4.17e-08!48;UBERON:0000166!4.33e-08!22;UBERON:0000033!8.50e-08!56;UBERON:0006554!8.72e-08!47;UBERON:0005177!8.86e-08!101;UBERON:0000153!1.68e-07!62;UBERON:0007811!1.68e-07!62;UBERON:0000165!2.62e-07!29;UBERON:0000930!2.62e-07!29;UBERON:0000915!2.67e-07!52;UBERON:0002365!5.36e-07!31;UBERON:0002330!5.36e-07!31;UBERON:0005178!8.79e-07!34;UBERON:0002224!8.79e-07!34
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00818022456919604!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199749267902884!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161049426366166!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000627020161478667!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186303726294391!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248299059407042!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00307823661124878!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00888484552163583!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129540833472911!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000438461016996911!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00684797327380318!SP2#6668;3:19.6151478703835:0.000217100426924534:0.00248697504525297!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322645533825539!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249262657650383
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55909e-05,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.164404,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.0178622,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.0159364,0.101893,0.142875,0.167635,0.171311,0.458838,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.267945,0.758305,0.278645,0.365775,0.0128057,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.0176801,0.499775,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.0896967,0.61565,0.0780061,0.0559668,0.230477,0.000372597,0.295555,0.502112,0.724669,0.0478217,9.5926e-06,0.170854,0.0575231,0.174063,0.163504,0.003653,0.54832,0.502211,0.296013,0.649813,0.537932,0.459994,0.523209,0.0465928,0.25423,0.490559,0.45013,0.0334811,0.472542,0.685908,0.0510811,0.174869,0.818701,0.483077,0.590496,0.603763,0.184287,0.627201,0.00784768,0.934991,0.290703,0.017476,0.366999,0.478691,0.360199,0.0690757,0.657141,0.519564,0.365494,0.212703,0.201391,0.0762097,0.0287777,0.579886,0.421038,0.569409,0.0610883,0.545608,0.310552,0.143396,0.0295909,0.829658,0.784052,0.209437,0.11765,0.0514874,0.598945,0.169076,0.464001,0.0572812,0.579004,0.150592,0.839946,0.0500888,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.116739,0.212239,0.294954,0.156999,0.35974,0.025886,0.39549,0.234254,0.357409,0.599068,0.721266,0.50338,0.620526,0.404625,0.0151906,0.424691,0.715362,0.479581,0.62689,0.00679433,0.642173,0.284496,0.512545,0.512178,0.563206,0.829402,0.0299859,0.263302,0.00919591,0.180735,0.775168,0.216102,0.00340007,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.503881,0.454761,0.639483,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.0458396,0.438176,0.349112,0.155207,0.385425,0.00631453,0.461541,0.386339,0.382854,0.598787,0.139139,0.611661,0.0576521,0.475047,0.557967,5.56654e-05,0.282281,0.612712,0.2536,0.246827,0.00166308,0.70712,0.387134,0.00990479,0.358813,0.668972,0.574252,0.493455,0.0685505,0.457747,0.0694762,0.476541,0.579645,0.447581,0.42505,0.254628,0.713293,0.479347,0.416962,0.000600154,0.378333,0.152547,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.0460393,0.0292096,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.0713545,0.112422,0.170886,0.267687,0.315656,0.0450921,0.0887542,0.267811,0.00865954,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.0227344,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.0429696,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.04166,0.00394881,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.035332,0.30702,0.202977,0.170837,0.0604859,0.28543,0.222656,0.00239762,0.127111,0.259989,0.0888526,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.0472356,0.081972,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.0387226,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
}}
}}

Revision as of 14:15, 19 October 2012


Full id: C2638_breast_bronchogenic_Amniotic_liver_endometrioid_Hepatocyte_serous



Phase1 CAGE Peaks

Hg19::chr22:19950047..19950056,+p9@COMT
Hg19::chr22:19950060..19950096,+p3@COMT
Hg19::chr22:19950097..19950117,+p5@COMT
Hg19::chr22:19950126..19950137,+p14@COMT


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>


Cell Type
Ontology termp-valuen
epithelial cell2.60e-25253
endodermal cell3.12e-1458
endo-epithelial cell5.61e-1442
embryonic cell4.62e-10250
epithelial cell of alimentary canal5.33e-0820
squamous epithelial cell8.15e-0763
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.11e-21160
endoderm1.11e-21160
presumptive endoderm1.11e-21160
anatomical cluster7.59e-20373
multi-tissue structure1.33e-19342
digestive system1.16e-17145
digestive tract1.16e-17145
primitive gut1.16e-17145
anatomical conduit2.33e-17240
multi-cellular organism9.57e-17656
organism subdivision7.16e-16264
subdivision of digestive tract5.36e-14118
epithelium8.91e-14306
cell layer4.06e-13309
anatomical system4.10e-13624
anatomical group7.55e-13625
organ system subdivision2.22e-12223
embryo2.38e-12592
developing anatomical structure2.15e-11581
organ part4.07e-11218
subdivision of trunk1.28e-09112
respiratory system1.38e-0974
embryonic structure1.40e-09564
endo-epithelium1.96e-0982
organ2.47e-09503
tube3.17e-09192
orifice3.63e-0936
foregut5.53e-0987
germ layer1.12e-08560
germ layer / neural crest1.12e-08560
embryonic tissue1.12e-08560
presumptive structure1.12e-08560
germ layer / neural crest derived structure1.12e-08560
epiblast (generic)1.12e-08560
immaterial anatomical entity1.71e-08117
trunk2.80e-08199
renal system4.17e-0848
oral opening4.33e-0822
head8.50e-0856
urinary system structure8.72e-0847
trunk region element8.86e-08101
anterior region of body1.68e-0762
craniocervical region1.68e-0762
mouth2.62e-0729
stomodeum2.62e-0729
thoracic segment of trunk2.67e-0752
exocrine gland5.36e-0731
exocrine system5.36e-0731
thoracic cavity element8.79e-0734
thoracic cavity8.79e-0734
Disease
Ontology termp-valuen
squamous cell carcinoma4.39e-0714


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
CTCF#1066445.360256373075030.001211145381643620.00818022456919604
EBF1#187948.9064668465690.00015887907472010.00199749267902884
ELF1#199744.258097958807540.003041525565781240.0161049426366166
HDAC2#3066413.41562023662633.0859005065161e-050.000627020161478667
HEY1#2346244.040111043105710.00375304636917980.0186303726294391
HMGN3#932448.178547723350590.0002234570284440470.00248299059407042
IRF1#365947.63716375356390.0002938853996185490.00307823661124878
MYC#460945.22228187160940.001344309395272740.00888484552163583
RAD21#5885410.35503389545638.6948481184721e-050.00129540833472911
SMC3#9126415.04493284493281.95092670935632e-050.000438461016996911
SP1#666745.69838137814090.0009482606065333980.00684797327380318
SP2#6668319.61514787038350.0002171004269245340.00248697504525297
TAF1#687243.343046285745290.008005664898701650.0322645533825539
ZNF263#1012748.221841637010680.0002187871180958320.00249262657650383



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.