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Coexpression cluster:C4101: Difference between revisions

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|full_id=C4101_CD14_Eosinophils_mature_placenta_chorionic_immature_Smooth
|full_id=C4101_CD14_Eosinophils_mature_placenta_chorionic_immature_Smooth
|id=C4101
|id=C4101
|ontology_enrichment_celltype=CL:0002057!1.93e-09!42;CL:0000359!8.00e-09!32;CL:0002371!8.82e-09!591;CL:0000012!5.65e-08!682;CL:0000860!7.10e-08!45;CL:0000222!1.01e-07!119;CL:0000548!1.23e-07!679;CL:0000004!1.23e-07!679;CL:0000255!1.23e-07!679;CL:0002139!1.34e-07!24;CL:0000144!4.50e-07!625
|ontology_enrichment_celltype=CL:0000860!5.58e-11!42;CL:0002057!5.58e-11!42;CL:0002371!4.99e-10!588;CL:0000473!4.08e-09!48;CL:0000234!4.08e-09!48;CL:0000359!6.86e-09!32;CL:0000548!1.63e-08!679;CL:0000255!1.63e-08!679;CL:0000766!6.27e-08!72;CL:0000222!1.76e-07!121;CL:0002139!5.27e-07!24;CL:0000325!6.02e-07!87
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000055!5.74e-17!69;UBERON:0001981!2.36e-15!60;UBERON:0007500!2.36e-15!60;UBERON:0004537!2.36e-15!60;UBERON:0006965!2.36e-15!60;UBERON:0000926!1.01e-14!448;UBERON:0004120!1.01e-14!448;UBERON:0006603!1.01e-14!448;UBERON:0002049!1.84e-14!79;UBERON:0007798!1.84e-14!79;UBERON:0001637!5.33e-14!42;UBERON:0003509!5.33e-14!42;UBERON:0004572!5.33e-14!42;UBERON:0004872!1.01e-13!84;UBERON:0003081!1.38e-12!216;UBERON:0004573!5.67e-12!33;UBERON:0004571!5.67e-12!33;UBERON:0003914!6.10e-12!118;UBERON:0000467!3.20e-11!625;UBERON:0000480!4.45e-11!626;UBERON:0004535!6.14e-10!110;UBERON:0001009!1.23e-09!113;UBERON:0000468!3.61e-09!659;UBERON:0002204!6.51e-09!167;UBERON:0000923!4.40e-07!604;UBERON:0005291!4.40e-07!604;UBERON:0006598!4.40e-07!604;UBERON:0002532!4.40e-07!604;UBERON:0002050!5.15e-07!605;UBERON:0005423!5.15e-07!605;UBERON:0000947!8.44e-07!21;UBERON:0010191!8.44e-07!21
|ontology_enrichment_uberon=UBERON:0000055!1.34e-15!68;UBERON:0007500!7.47e-14!59;UBERON:0001981!7.47e-14!59;UBERON:0004537!7.47e-14!59;UBERON:0006965!7.47e-14!59;UBERON:0001637!2.28e-13!42;UBERON:0003509!2.28e-13!42;UBERON:0004572!2.28e-13!42;UBERON:0002049!5.03e-13!78;UBERON:0007798!5.03e-13!78;UBERON:0000926!2.09e-12!315;UBERON:0004120!2.09e-12!315;UBERON:0006603!2.09e-12!315;UBERON:0004872!3.67e-12!83;UBERON:0003081!4.55e-12!203;UBERON:0004573!4.06e-11!33;UBERON:0004571!4.06e-11!33;UBERON:0003914!2.42e-10!117;UBERON:0002204!4.05e-10!167;UBERON:0000467!3.86e-09!624;UBERON:0000480!5.28e-09!625;UBERON:0004535!1.76e-08!109;UBERON:0001009!3.56e-08!112;UBERON:0000468!1.12e-07!656
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129766323780271!BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00110006092710923!BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000284866679709357!BRCA1#672;3:20.1842306432238:0.000121570486027164:0.00164337302487587!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190392172797166!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00661342148794183!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032601248798389!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.032123527834925!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463291745627387!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00898924191094773!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.0024339509578189!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108880990002674!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128337146677055!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444821407182721!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157037142043125!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277346530791955!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155019146520529!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00643458749854418!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00544128896513076!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614772176833943!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190685523148445!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00422218009107216!ZBTB33#10009;3:31.6647250299812:3.14815888737575e-05:0.00063424106103132
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208866,2.54582e-08,0.00327141,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.0377931,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.00160873,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.0217163,0.0488949,0.174921,0.370421,0.0330727,5.99252e-06,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.190156,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.00836526,0.011488,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.00864322,0.131452,0.323837,3.73213e-05,0.051838,0.0993999,0.0500365,4.13072e-05,7.60655e-05,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.153605,0.655293,0.0255266,0.00514993,0.119215,0.192475,0.177967,0.0465298,0.057571,0.047591,0.392974,0.0608699,0.175319,0.0505407,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.0163112,4.67397e-05,0.00217769,0.0229515,0.218192,0.108277,0.0673484,6.67708e-06,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,1.57209e-05,0.0539144,0.114242,0.000143882,0.172425,0.104948,0.0266106,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.0257725,0.101607,0.327067,0.0159074,0.340936,0.151597,0.0626744,0.0195983,0.148574,0.034431,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.0282663,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.161789,0.0590944,0.247324,0.178389,0.218229,0.231073,0.0161946,0.0170505,0.0360851,0.0168763,0.131093,0.0434602,0.133616,0.103051,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.0189483,0.448797,0.197484,0.396996,0.36145,0.0966095,0.0129,0.580441,0.643768,0.432035,0.722159,0.390366,0.48809,0.153829,0.443185,0.522904,0.000322406,0.336835,0.227104,0.000951286,0.617852,0.38649,0.0450114,0.0344717,0.55194,0.729153,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.119142,0.032364,2.80434e-05,0.0889613,0.73485,0.029557,0.161598,0.013901,0.0868402,0.496032,0.000266268,0.37357,3.35117e-05,0.477353,0.00492096,0.160298,0.00415823,0.20342,0.200493,0.00171127,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.00465874,0.616388,0.0978616,0.516511,0.322213,0.656109,0.00873429,0.61031,0.0871388,0.522605,7.95705e-06,0.180745,0.222037,0.416621,0.0174635,0.462712,0.734551,0.057399,0.204817,0.452428,0.138871,0.000165333,0.166905,0.19783,0.0833851,0.316453,0.0289164,0.175199,0.332919,0.373557,0.523625,0.0980968,0.365487,0.00780726,0.39088,0.363192,0.236011,0.203486,0.273398,0.000131088,0.4466,0.351067,0.275347,0.637444,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.00258603,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.00446098,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.00081525,0.19104,0.163057,0.219428,0.00177656,0.0900729,0.0953646,0.166124,0.0348699,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.0015337,0.186804,0.123324,0.199468,0.0325925,0.000145586,3.04194e-07,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.00310436,0.00219731,0.00231953,0.20847,0.266544,0.113092,0.145701,0.00242972,0.162145,0.0284767,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.0363723,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.000142373,0.246105,0.173026,0.200432,0.139785,0.00149718,0.240478,0.00072309,0.13108,0.256963,0.222798,0.000975743,0.176789,0.000163687,0.202137,0.310405,0.00467879,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,3.28184e-06,0.000277451,0.00186843,0.187731,3.9263e-07,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.0056723,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,3.30228e-05,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.00335066,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.0342254,0.00084829,0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}}
}}

Revision as of 15:41, 19 October 2012


Full id: C4101_CD14_Eosinophils_mature_placenta_chorionic_immature_Smooth



Phase1 CAGE Peaks

Hg19::chr22:38598042..38598052,+p4@MAFF
Hg19::chr22:38598057..38598071,+p3@MAFF
Hg19::chr22:38598086..38598105,+p1@MAFF


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><br>



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
ATF3#467322.46317452600878.81932387510763e-050.00129766323780271
BATF#10538324.35780179230366.91705216281876e-050.00110006092710923
BHLHE40#8553344.87181354697741.10603738662898e-050.000284866679709357
BRCA1#672320.18423064322380.0001215704860271640.00164337302487587
CCNT2#90536.336201576962630.003930750035764890.0190392172797166
CHD2#1106310.34402283411690.0009033701102746880.00661342148794183
E2F1#186934.907389214879320.008460985347239390.032601248798389
EGR1#195834.988179094810140.008056488137383440.032123527834925
ELF1#199734.258097958807540.01295179875054610.0463291745627387
FOS#235338.99795530889440.001372499272417130.00898924191094773
FOSL2#2355316.93020060456170.0002060162053171620.0024339509578189
HMGN3#932438.178547723350590.001827766942164210.0108880990002674
IRF1#365937.63716375356390.002244692747297240.0128337146677055
JUN#3725312.51282919233630.0005103313992726250.00444821407182721
JUND#372736.994663941871030.002921845042734990.0157037142043125
SIN3A#2594235.408884726815140.006318961977991520.0277346530791955
STAT1#6772320.70658749719920.0001125992441046670.00155019146520529
STAT3#6774310.51946499715420.0008589184530415310.00643458749854418
TAF7#6879311.43306940492390.0006690181981945830.00544128896513076
TCF7L2#6934310.77017656313730.0008003181298398380.00614772176833943
USF1#739136.361499277207960.00388404057290560.0190685523148445
USF2#7392312.99219738506960.0004558979393427810.00422218009107216
ZBTB33#10009331.66472502998123.14815888737575e-050.00063424106103132



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.