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Coexpression cluster:C2227: Difference between revisions

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|full_id=C2227_chronic_Hodgkin_CD34_CD133_acute_thymus_liposarcoma
|full_id=C2227_chronic_Hodgkin_CD34_CD133_acute_thymus_liposarcoma
|id=C2227
|id=C2227
|ontology_enrichment_celltype=CL:0000988!3.34e-14!182;CL:0000037!2.78e-13!172;CL:0000566!2.78e-13!172;CL:0002032!2.46e-12!165;CL:0000837!2.46e-12!165;CL:0000542!4.32e-08!53;CL:0000051!4.32e-08!53;CL:0000838!1.22e-07!52
|ontology_enrichment_celltype=CL:0000988!9.45e-18!177;CL:0000037!8.86e-17!168;CL:0000566!8.86e-17!168;CL:0002032!6.73e-16!161;CL:0000837!6.73e-16!161;CL:0002242!5.08e-09!55;CL:0000763!8.93e-09!108;CL:0000049!8.93e-09!108;CL:0000542!8.67e-08!53;CL:0000051!8.67e-08!53;CL:0000838!3.33e-07!52
|ontology_enrichment_disease=DOID:2531!1.32e-31!51;DOID:0060083!1.32e-31!51;DOID:1240!3.29e-28!39;DOID:8692!1.02e-22!31;DOID:0050686!4.11e-09!137;DOID:1036!2.45e-07!8
|ontology_enrichment_disease=DOID:2531!4.48e-46!51;DOID:0060083!4.48e-46!51;DOID:1240!2.29e-41!39;DOID:8692!1.24e-32!31;DOID:0050686!1.63e-15!137;DOID:1036!1.04e-10!8;DOID:162!2.49e-08!235;DOID:14566!3.97e-08!239;DOID:0060058!6.23e-07!10
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00511524376019119!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00267678798719124!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.000725829344336548!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.0099557226556318!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160650325476471!ELK4#2005;4:16.235681658468:1.43847748454449e-05:0.000342998059379776!EP300#2033;4:6.7739417262232:0.000474845982144264:0.0043361405551425!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00389858592177651!GATA1#2623;4:13.5603081438004:2.95627390049268e-05:0.000613208122926623!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000720208754607761!GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.75529154167856e-05!GTF2B#2959;4:31.9438299343242:9.59435337635006e-07:4.08156689316751e-05!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.000716834865008953!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000625681155115579!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185659534743639!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00306961668674484!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391093078938091!MAX#4149;4:6.45255550900712:0.000576761319564549:0.0048476078749398!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142187284675164!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088624118755769!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00767008398887342!NR2C2#7182;4:32.6146109052409:8.82887529809196e-07:3.81655176844961e-05!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00443339226654341!PBX3#5090;4:21.9145126867441:4.33289161192893e-06:0.000136138046648088!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188189092517096!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000825589127998626!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00794858008372017!SIX5#147912;4:17.086715355459:1.17257016123224e-05:0.00029723799774013!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000240879402439501!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00683285424905075!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249250554238258!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000583523080775696!STAT2#6773;4:65.2637711864407:5.50053512607993e-08:3.45858150531404e-06!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321467044621286!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243645510548501!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00119907058195633!THAP1#55145;4:31.3691446028513:1.03171810326891e-06:4.31178899509011e-05!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00507200131664044!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000680420627792207!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106668189295651!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00346130973230001!ZNF143#7702;4:13.5008765522279:3.00867915035614e-05:0.000620014683867492
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997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.458838,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.833813,0.758305,0.278645,0.0769795,0.155708,0.000219214,0.22995,0.652972,0.0760151,0.0629459,0.0300882,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.960445,0.974549,0.0388045,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.00640224,0.459091,0.54832,0.502211,0.296013,0.649813,0.537932,0.459994,0.523209,0.548059,0.25423,0.490559,0.45013,0.500698,0.472542,0.685908,0.747471,0.529642,0.509113,0.483077,0.590496,0.603763,0.541914,0.259354,0.938109,0.934991,0.290703,0.622694,0.722684,0.139104,0.360199,0.608176,0.657141,0.824761,0.365494,0.212703,0.56318,0.364079,0.680099,0.579886,0.421038,0.0108102,0.328518,0.545608,0.310552,0.865054,0.483764,0.528161,0.784052,0.209437,0.11765,0.748403,0.598945,0.630688,0.464001,0.871271,0.579004,0.870272,0.839946,0.860705,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,0.86719,0.721266,0.50338,0.620526,0.404625,0.759068,0.424691,0.357704,0.479581,0.62689,0.884725,0.642173,0.284496,0.512545,0.512178,0.563206,0.829402,0.684899,0.263302,0.552023,0.180735,0.775168,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.0782409,0.503881,0.454761,0.639483,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.0696091,0.0485429,0.385425,0.307816,0.461541,0.386339,0.382854,0.598787,0.478745,0.24434,0.319747,0.136743,0.197104,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.347466,0.387134,0.559969,0.358813,0.668972,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.215342,0.447581,0.42505,0.254628,0.713293,0.479347,0.416962,0.632833,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,6.25362e-05,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.00571761,0.244395,0.106889,0.128632,0.0845989,0.159153,0.00365225,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.0345639,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
}}
}}

Revision as of 12:12, 19 October 2012


Full id: C2227_chronic_Hodgkin_CD34_CD133_acute_thymus_liposarcoma



Phase1 CAGE Peaks

Hg19::chr12:58329689..58329704,-p4@ENST00000547492
Hg19::chr12:58329762..58329773,-p5@ENST00000547492
Hg19::chr12:58329776..58329791,-p3@ENST00000547492
Hg19::chr12:58329793..58329806,-p2@ENST00000547492


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><br>disease_data<br>

Disease
Ontology termp-valuen
hematologic cancer4.48e-4651
immune system cancer4.48e-4651
leukemia2.29e-4139
myeloid leukemia1.24e-3231
organ system cancer1.63e-15137
chronic leukemia1.04e-108
cancer2.49e-08235
disease of cellular proliferation3.97e-08239
lymphoma6.23e-0710


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
CCNT2#90546.336201576962630.0006203100587215640.00511524376019119
CEBPB#105147.971147625824820.0002476385788090830.00267678798719124
E2F4#1874412.66806031528443.88145892637771e-050.000725829344336548
E2F6#187645.017155731697390.00157802193473060.0099557226556318
ELF1#199744.258097958807540.003041525565781240.0160650325476471
ELK4#2005416.2356816584681.43847748454449e-050.000342998059379776
EP300#203346.77394172622320.0004748459821442640.0043361405551425
GABPB1#255347.067683836182170.0004006876864423170.00389858592177651
GATA1#2623413.56030814380042.95627390049268e-050.000613208122926623
GATA2#2624412.7449317335543.78864877853583e-050.000720208754607761
GATA3#2625427.2365163572061.81561517799785e-066.75529154167856e-05
GTF2B#2959431.94382993432429.59435337635006e-074.08156689316751e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.000716834865008953
HDAC2#3066413.41562023662633.0859005065161e-050.000625681155115579
HEY1#2346244.040111043105710.00375304636917980.0185659534743639
IRF1#365947.63716375356390.0002938853996185490.00306961668674484
JUND#372746.994663941871030.000417684217818580.00391093078938091
MAX#414946.452555509007120.0005767613195645490.0048476078749398
MXI1#460149.96157162875930.0001015224754950450.00142187284675164
MYC#460945.22228187160940.001344309395272740.0088624118755769
NFKB1#479045.488063424193840.001102199566301980.00767008398887342
NR2C2#7182432.61461090524098.82887529809196e-073.81655176844961e-05
PAX5#507946.669565531177830.0005052774169483260.00443339226654341
PBX3#5090421.91451268674414.33289161192893e-060.000136138046648088
POU2F2#545249.106124057742520.000145395665174930.00188189092517096
RFX5#5993412.04791082719514.74457429336527e-050.000825589127998626
SIN3A#2594245.408884726815140.001168172384885160.00794858008372017
SIX5#147912417.0867153554591.17257016123224e-050.00029723799774013
SMARCB1#6598418.25271578115749.00423392720929e-060.000240879402439501
SP1#666745.69838137814090.0009482606065333980.00683285424905075
SPI1#668848.204323508522730.000220661881527680.00249250554238258
SRF#6722413.79717826216782.75840773062708e-050.000583523080775696
STAT2#6773465.26377118644075.50053512607993e-083.45858150531404e-06
TAF1#687243.343046285745290.008005664898701650.0321467044621286
TBP#690843.706770687096390.005296377814784350.0243645510548501
TCF12#6938410.63446490218647.8163066689251e-050.00119907058195633
THAP1#55145431.36914460285131.03171810326891e-064.31178899509011e-05
USF1#739146.361499277207960.0006105011399140830.00507200131664044
USF2#7392412.99219738506963.50833029870167e-050.000680420627792207
YY1#752844.911170749853860.00171871838055440.0106668189295651
ZBTB7A#5134147.35190930787590.000342223540015990.00346130973230001
ZNF143#7702413.50087655222793.00867915035614e-050.000620014683867492



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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