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Difference between revisions of "Coexpression cluster:C2519"

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|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0007023!2.80e-30!115;UBERON:0001049!7.44e-23!57;UBERON:0005068!7.44e-23!57;UBERON:0006241!7.44e-23!57;UBERON:0007135!7.44e-23!57;UBERON:0002616!2.00e-19!59;UBERON:0000955!2.17e-18!69;UBERON:0006238!2.17e-18!69;UBERON:0003080!7.81e-18!42;UBERON:0001017!1.61e-17!82;UBERON:0002780!1.88e-17!41;UBERON:0001890!1.88e-17!41;UBERON:0006240!1.88e-17!41;UBERON:0005743!6.09e-17!86;UBERON:0000073!1.38e-16!94;UBERON:0001016!1.38e-16!94;UBERON:0003075!5.12e-16!86;UBERON:0007284!5.12e-16!86;UBERON:0002346!1.66e-15!90;UBERON:0002020!2.00e-14!34;UBERON:0003528!2.00e-14!34;UBERON:0001893!3.50e-14!34;UBERON:0002791!1.15e-13!33;UBERON:0001869!2.60e-13!32;UBERON:0002390!1.03e-12!102;UBERON:0003061!1.03e-12!102;UBERON:0002193!1.06e-12!112;UBERON:0002619!5.30e-12!22;UBERON:0001950!5.89e-11!20;UBERON:0003056!9.26e-11!61;UBERON:0000956!1.33e-09!25;UBERON:0000203!1.33e-09!25;UBERON:0002371!1.61e-08!80;UBERON:0000153!4.15e-08!129;UBERON:0007811!4.15e-08!129;UBERON:0000025!6.60e-08!194;UBERON:0001474!9.13e-08!86;UBERON:0000033!1.55e-07!123
 
|ontology_enrichment_uberon=UBERON:0007023!2.80e-30!115;UBERON:0001049!7.44e-23!57;UBERON:0005068!7.44e-23!57;UBERON:0006241!7.44e-23!57;UBERON:0007135!7.44e-23!57;UBERON:0002616!2.00e-19!59;UBERON:0000955!2.17e-18!69;UBERON:0006238!2.17e-18!69;UBERON:0003080!7.81e-18!42;UBERON:0001017!1.61e-17!82;UBERON:0002780!1.88e-17!41;UBERON:0001890!1.88e-17!41;UBERON:0006240!1.88e-17!41;UBERON:0005743!6.09e-17!86;UBERON:0000073!1.38e-16!94;UBERON:0001016!1.38e-16!94;UBERON:0003075!5.12e-16!86;UBERON:0007284!5.12e-16!86;UBERON:0002346!1.66e-15!90;UBERON:0002020!2.00e-14!34;UBERON:0003528!2.00e-14!34;UBERON:0001893!3.50e-14!34;UBERON:0002791!1.15e-13!33;UBERON:0001869!2.60e-13!32;UBERON:0002390!1.03e-12!102;UBERON:0003061!1.03e-12!102;UBERON:0002193!1.06e-12!112;UBERON:0002619!5.30e-12!22;UBERON:0001950!5.89e-11!20;UBERON:0003056!9.26e-11!61;UBERON:0000956!1.33e-09!25;UBERON:0000203!1.33e-09!25;UBERON:0002371!1.61e-08!80;UBERON:0000153!4.15e-08!129;UBERON:0007811!4.15e-08!129;UBERON:0000025!6.60e-08!194;UBERON:0001474!9.13e-08!86;UBERON:0000033!1.55e-07!123
 +
|tf_chipseq_enrich=ATF3#467;3:16.8473808945066:0.000340998682365564:0.00346435422058143!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512252409447469!CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0172982285482437!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817493779573956!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.00072687051965566!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997078061838762!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240491469049894!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160918889850368!ESR1#2099;3:23.0764524721159:0.000133910524496857:0.00175807432657791!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.019205956349166!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186117953347944!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248140654903433!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.0030754606463689!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466237814062163!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142397338412933!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434977647121437!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000826691015390015!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00796466612514825!SIX5#147912;3:12.8150365165942:0.000766447113693038:0.0060167596292083!SMARCC2#6601;3:70.6165308201732:4.74678670742709e-06:0.000147194078662998!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00684324139619552!SREBF1#6720;4:47.0058494404883:2.04523668136926e-07:1.10274896110235e-05!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000584588768220294!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00507967882022681!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.00976780280047915
 
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09692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.0593965,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.0204239,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.0922008,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,1.32358e-05,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.787798,0.189107,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.0360207,0.758305,0.278645,0.365775,0.155708,0.248017,0.22995,0.285695,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.00605585,1.37583e-08,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.0756617,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.000422824,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,8.03044e-09,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.00231398,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,6.31811e-05,0.0780061,0.315336,0.230477,0.279823,0.0487563,8.82193e-05,0.140541,0.0478217,0.158752,0.170854,0.0575231,0.174063,0.000106434,0.459091,0.54832,0.502211,0.296013,0.649813,0.537932,0.459994,0.170061,0.548059,0.25423,0.490559,0.45013,0.500698,0.472542,0.685908,0.747471,0.529642,0.818701,0.483077,0.590496,0.603763,0.541914,0.627201,0.00233402,0.142078,0.290703,0.622694,0.722684,0.478691,0.360199,0.608176,0.657141,0.824761,0.0768516,0.212703,0.56318,0.364079,0.680099,0.579886,0.421038,0.569409,0.328518,0.545608,0.310552,0.324103,0.483764,0.261345,0.784052,0.209437,0.843495,0.401218,0.598945,0.169076,0.464001,0.152018,0.579004,0.150592,0.839946,0.586133,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.0215868,0.212239,0.294954,0.156999,0.35974,0.301684,0.39549,0.234254,0.357409,0.599068,0.721266,0.50338,0.620526,0.404625,0.759068,0.424691,0.357704,0.479581,0.62689,2.97623e-06,0.0854676,0.284496,0.512545,0.512178,0.201413,0.034169,0.684899,0.263302,0.552023,0.180735,0.775168,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.503881,0.454761,0.639483,0.142363,0.452129,0.301581,0.00371213,0.00938391,0.466529,0.545655,0.438176,0.349112,0.741477,0.385425,0.307816,0.461541,0.386339,0.382854,0.598787,0.478745,0.611661,0.319747,0.475047,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.70712,0.387134,0.559969,0.358813,0.303004,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.579645,0.447581,0.42505,0.254628,0.713293,0.479347,0.416962,0.632833,0.378333,0.738545,0.0384092,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.000403294,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.0617695,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.0078603,0.332769,0.262022,0.000341723,0.266687,0.184534,0.248707,0.0567862,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.00095279,0.327002,0.0452813,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.0371525,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.00817441,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.00393964,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.0805224,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
 
}}
 
}}

Revision as of 02:56, 5 September 2012


Full id: C2519_cerebellum_CD8_Natural_CD4_Mast_Basophils_Peripheral



Phase1 CAGE Peaks

  Short description
Hg19::chr1:144533782..144533805,+ p@chr1:144533782..144533805
+
Hg19::chr4:2420335..2420354,- p2@ZFYVE28
Hg19::chr4:2420357..2420413,- p1@ZFYVE28
Hg19::chr4:2420416..2420440,- p4@ZFYVE28


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Uber Anatomy
Ontology termp-valuen
adult organism2.80e-30115
neural tube7.44e-2357
neural rod7.44e-2357
future spinal cord7.44e-2357
neural keel7.44e-2357
regional part of brain2.00e-1959
brain2.17e-1869
future brain2.17e-1869
anterior neural tube7.81e-1842
central nervous system1.61e-1782
regional part of forebrain1.88e-1741
forebrain1.88e-1741
future forebrain1.88e-1741
regional part of nervous system1.38e-1694
nervous system1.38e-1694
neural plate5.12e-1686
presumptive neural plate5.12e-1686
neurectoderm1.66e-1590
gray matter2.00e-1434
brain grey matter2.00e-1434
telencephalon3.50e-1434
regional part of telencephalon1.15e-1333
cerebral hemisphere2.60e-1332
hematopoietic system1.03e-12102
blood island1.03e-12102
hemolymphoid system1.06e-12112
regional part of cerebral cortex5.30e-1222
neocortex5.89e-1120
pre-chordal neural plate9.26e-1161
cerebral cortex1.33e-0925
pallium1.33e-0925
bone marrow1.61e-0880
anterior region of body4.15e-08129
craniocervical region4.15e-08129
tube6.60e-08194
bone element9.13e-0886
head1.55e-07123


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#467316.84738089450660.0003409986823655640.00346435422058143
CCNT2#90546.336201576962630.0006203100587215640.00512252409447469
CHD2#110637.758017125587640.003351522464536340.0172982285482437
CTCF#1066445.360256373075030.001211145381643620.00817493779573956
E2F4#1874412.66806031528443.88145892637771e-050.00072687051965566
E2F6#187645.017155731697390.00157802193473060.00997078061838762
EBF1#187936.679850134926750.005184294118278910.0240491469049894
ELF1#199744.258097958807540.003041525565781240.0160918889850368
ESR1#2099323.07645247211590.0001339105244968570.00175807432657791
ETS1#211337.296570691651750.00400857377511390.019205956349166
HEY1#2346244.040111043105710.00375304636917980.0186117953347944
HMGN3#932448.178547723350590.0002234570284440470.00248140654903433
IRF1#365947.63716375356390.0002938853996185490.0030754606463689
MAX#414934.839416631755340.01315737137836840.0466237814062163
MXI1#460149.96157162875930.0001015224754950450.00142397338412933
PAX5#507935.002174148383370.01196533174786410.0434977647121437
RFX5#5993412.04791082719514.74457429336527e-050.000826691015390015
SIN3A#2594245.408884726815140.001168172384885160.00796466612514825
SIX5#147912312.81503651659420.0007664471136930380.0060167596292083
SMARCC2#6601370.61653082017324.74678670742709e-060.000147194078662998
SP1#666745.69838137814090.0009482606065333980.00684324139619552
SREBF1#6720447.00584944048832.04523668136926e-071.10274896110235e-05
SRF#6722413.79717826216782.75840773062708e-050.000584588768220294
USF1#739146.361499277207960.0006105011399140830.00507967882022681
ZNF143#7702310.12565741417090.001534861610688180.00976780280047915



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.