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Coexpression cluster:C159: Difference between revisions

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|tf_chipseq_enrich=GATA3#2625;14:3.49826815597141:4.82570150565378e-05:0.000838867242924392
|tf_chipseq_enrich=GATA3#2625;14:3.49826815597141:4.82570150565378e-05:0.000838867242924392
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0.921267,0.985519,0.857512,0.65159,0.999254,0.996564,0.762983,0.425181,0.609061,0.976651,0.993521,0.941251,0.879064,0.962975,0.993741,0.988322,0.682425,0.943684,0.911715,0.599657,0.976932,0.991481,0.979528,0.80299,0.961504,0.643447,0.438381,0.785741,0.782529,0.82807,0.701134,0.97999,0.889757,0.946521,0.922097,0.875343,0.963444,1,0.990763,0.575841,0.977716,0.845112,0.901619,0.942313,0.8716,0.920602,0.71566,0.53065,0.900872,0.999538,0.999281,0.941585,0.994296,0.489058,0.996289,0.9243,0.999865,0.884024,0.829946,0.993493,0.897898,0.401819,0.973964,0.503528,0.951671,0.798634,0.378984,0.955211,0.698479,1,1,0.99789,0.788007,0.919712,0.464697,0.601437,0.841336,0.707893,0.919625,0.942468,0.242202,0.985634,0.929173,0.983044,0.722034,0.752399,0.888911,0.498338,0.597683,0.934115,0.687358,0.991872,0.982197,0.802541,0.882209,0.751495,0.943372,0.999939,0.982743,0.954007,0.998706,0.745798,0.99865,0.535396,0.744521,0.389389,0.904789,0.88292,0.693516,0.999948,0.862061,0.933508,0.969881,0.659183,0.667188,0.997346,0.510549,0.943197,0.965119,0.889616,0.90275,0.906973,0.482169,0.998248,0.837848,0.958555,0.700558,0.810378,0.930523,0.759188,0.825142,0.973233,0.965521,0.350261,0.471496,0.734165,0.98298,0.90668,0.987216,0.609608,0.79562,0.859058,0.999877,0.99869,0.981182,0.813119,0.862771,0.985051,0.960248,0.99989,0.890645,0.976299,0.7167,0.99987,0.985634,0.999992,0.999459,0.736929,0.999581,0.883959,0.800989,0.59575,0.974924,0.993641,0.86857,0.981763,0.985816,0.999942,0.993881,0.997627,0.990208,0.981976,0.808164,0.566367,0.932198,0.980968,0.885355,0.929447,0.875721,0.991998,0.999996,0.992865,0.982974,0.979848,0.935812,0.999543,0.999846,1,0.999108,0.967184,0.99995,0.999611,0.99799,0.99958,0.998544,0.999741,0.86926,0.21043,0.997452,0.354328,0.976628,0.987155,0.999071,0.687052,0.522428,0.941277,0.681988,1,0.998969,0.999999,0.999934,0.45831,0.999998,0.999861,0.976669,1,0.915108,1,0.796653,1,0.999926,0.999998,0.717704,0.702237,0.919296,0.989163,0.957032,0.995469,0.595048,0.990881,0.984963,0.9138,0.969795,0.709954,0.963084,0.97704,0.988732,0.836852,0.84301,0.993159,0.257238,0.983091,0.441916,0.762053,1,0.997454,0.996296,0.979167,0.994936,0.999988,0.93223,0.998242,0.992052,0.982999,0.999951,0.998717,0.949029,0.820679,0.999651,0.998944,0.999999,0.999933,0.324683,0.996205,0.907343,0.999996,0.650237,0.997005,0.823973,0.96517,0.998779,0.992694,0.978739,0.950714,0.983578,0.982608,0.983568,0.994012,0.997128,0.668427,0.0725518,0.583541,0.609938,0.871036,0.861368,0.974293,0.896627,1,0.953012,0.933868,0.947778,0.999176,0.6621,0.960461,0.249911,0.895718,0.898325,0.996176,0.892514,0.969679,0.946311,0.999144,0.806042,0.507941,0.861942,0.999711,0.991421,0.999548,0.999525,0.999142,0.999994,0.956917,0.973895,0.903202,0.990564,0.996359,0.95959,0.99098,0.999963,0.900825,0.999996,0.99962,0.996568,0.999865,0.999967,0.937982,0.999765,0.993022,0.947489,0.948197,0.966588,0.712364,0.877882,0.994635,0.995613,0.0576863,0.998959,0.998413,0.649005,0.998447,0.793291,0.999791,0.665922,0.704524,0.989668,0.48647,0.956807,0.981782,0.997981,0.98102,0.993793,0.996452,0.88847,0.981134,0.936066,0.999999,0.535732,0.986717,0.995353,0.34587,0.293773,0.699985,0.971535,0.99187,0.999257,0.999099,0.991685,0.835186,0.884044,0.998049,0.997899,0.949471,0.719345,0.998057,0.999987,0.987228,0.675949,0.95895,0.62037,0.95837,0.990647,0.759799,0.916647,0.857417,0.816204,0.465039,0.824736,0.910907,0.984302,0.842883,0.977053,0.404597,0.652972,0.778094,0.949016,0.979399,0.798577,0.991925,0.530779,0.857445,0.999281,0.986936,0.994319,0.843012,0.998641,0.524962,0.860642,0.999417,0.93464,0.915725,0.999804,0.997646,0.935633,0.968886,0.19784,0.99637,0.999656,0.937827,0.994865,0.975368,0.968113,0.90742,0.972772,0.999657,0.541328,0.985163,0.749401,0.912394,0.981022,0.991781,0.971855,0.884215,0.997484,0.99998,0.756144,0.977885,0.955754,0.997477,0.915558,0.864909,0.865779,0.844568,0.947726,0.779219,0.595833,0.999907,0.922404,0.998273,0.0446941,0.999937,0.945948,0.812551,0.888473,0.910069,0.509759,0.909103,0.909471,0.917378,0.943968,0.735969,0.789794,0.805843,0.460758,0.854403,0.743399,0.896182,0.989194,0.96989,0.993733,0.681715,0.804237,0.964568,0.910149,0.423128,0.825519,0.999752,0.999976,0.836548,0.981139,0.965862,0.994104,0.987308,0.967562,0.997171,0.998162,0.999403,0.973051,0.988579,0.977806,0.951611,0.988324,0.999622,0.881907,0.999922,0.956624,0.59699,0.989071,0.952207,0.971837,0.97499,0.99509,0.969114,0.305451,0.41178,0.997977,0.678891,0.872474,0.939666,0.931448,0.971666,0.979128,0.56346,0.992898,0.998005,0.97604,0.998295,0.989785,0.932171
|tfbs_overrepresentation_for_novel_motifs=0.155999,0.972004,0.0154983,0.513334,0.462918,0.194436,0.0855783,1.1142,3.13533,0.0110917,0.149035,0.251513,0.166234,0.171842,0.325504,0.959637,0.146139,0.245802,0.76092,0.448433,0.143074,0.935892,0.182133,0.1317,0.0723555,0.05193,1.0066,2.68153,0.341547,0.347689,1.53935,0.703181,0.0960257,0.420878,0.141569,0.186979,1.05906e-05,0.333153,0.7391,0.00317584,0.21476,0.101397,0.69311,1.2212,0.501196,0.0596653,0.188689,0.134386,1.01011,0.342015,0.53156,0.839914,0.59556,0.248847,0.137436,0.319899,2.51356,0.135415,0.802778,1.50042,0.809603,0.0294748,0.261842,0.0305672,0.10204,0.760019,0.185747,0.446398,0.380431,0.321642,0.271527,0.211752,0.0158162,0.136422,0.0671578,0.0477149,0.168578,0.113518,0.375217,0.129323,0.413565,0.0303369,0.38491,0.282671,0.359577,0.00590746,0.434073,0.315683,0.60249,0.528525,0.24369,0.0996092,0.746165,0.34593,0.142496,0.0837906,0.283064,0.0649226,0.37089,0.164896,0.327273,0.7316,1.77926,0.971483,0.0947262,0.142814,0.583614,0.0244005,0.138049,0.0319197,0.389386,0.484802,1.3163,0.281988,1.14944,0.131954,5.23514e-05,0.0563827,0.0233104,1.89369,0.413017,1.24389,0.190013,0.11111,0.28607,0.275111,0.178632,0.0528408,0.468627,0.413571,0.0999075,0.977995,0.487988,0.40332,0.702519,0.206759,0.205191,0.934365,0.224637,0.939062,0.573256,1.73427,0.0271674,0.227892,0.45033,0.125975,0.216657,0.790532,0.850874,1.55323,0.293199,2.83254e-05,0.100072,0.0102553,0.191282,0.344156,0.557954,0.40127,0.938791,0.00147928,0.200767,0.637116,0.373958,0.286084,0.484787,0.383101,0.196115,0.0846123,0.0539948
}}
}}

Revision as of 13:37, 26 November 2012


Full id: C159_choriocarcinoma_pancreatic_placenta_chorionic_testicular_bronchioalveolar_seminal



Phase1 CAGE Peaks

Hg19::chr10:114437568..114437582,-p1@ENST00000443652
Hg19::chr10:134217889..134217902,+p12@PWWP2B
Hg19::chr10:79617081..79617125,-p@chr10:79617081..79617125
-
Hg19::chr10:79617136..79617150,-p@chr10:79617136..79617150
-
Hg19::chr10:79617159..79617171,-p@chr10:79617159..79617171
-
Hg19::chr10:79617174..79617179,-p@chr10:79617174..79617179
-
Hg19::chr10:79617215..79617226,-p@chr10:79617215..79617226
-
Hg19::chr10:8223647..8223685,-p@chr10:8223647..8223685
-
Hg19::chr11:18960954..18960967,-p1@MRGPRX1
Hg19::chr11:18961040..18961073,-p2@MRGPRX1
Hg19::chr11:6281059..6281104,+p1@CCKBR
Hg19::chr12:15082050..15082081,-p1@ERP27
Hg19::chr13:78505877..78505880,-p@chr13:78505877..78505880
-
Hg19::chr14:104638084..104638094,+p@chr14:104638084..104638094
+
Hg19::chr14:62585332..62585337,+p2@ENST00000554895
Hg19::chr14:62585350..62585362,+p1@ENST00000554895
Hg19::chr14:62585418..62585425,+p3@ENST00000554895
Hg19::chr14:96968802..96968817,+p2@PAPOLA
Hg19::chr15:52497258..52497274,-p@chr15:52497258..52497274
-
Hg19::chr15:52497278..52497279,-p@chr15:52497278..52497279
-
Hg19::chr15:59243695..59243703,-p@chr15:59243695..59243703
-
Hg19::chr15:91072855..91072876,+p8@CRTC3
Hg19::chr15:96607616..96607625,-p3@ENST00000558860
Hg19::chr15:96833987..96834012,-p@chr15:96833987..96834012
-
Hg19::chr15:96869511..96869525,+p16@NR2F2
Hg19::chr16:89971162..89971177,+p@chr16:89971162..89971177
+
Hg19::chr16:89971202..89971207,+p@chr16:89971202..89971207
+
Hg19::chr16:89971221..89971231,+p@chr16:89971221..89971231
+
Hg19::chr17:45928521..45928539,-p1@SP6
Hg19::chr17:63533845..63533851,-p@chr17:63533845..63533851
-
Hg19::chr17:63533919..63533920,-p@chr17:63533919..63533920
-
Hg19::chr17:63533962..63533988,-p@chr17:63533962..63533988
-
Hg19::chr17:63533993..63534003,-p@chr17:63533993..63534003
-
Hg19::chr19:24346270..24346279,-p2@LOC100101266
Hg19::chr19:39627378..39627388,+p@chr19:39627378..39627388
+
Hg19::chr19:48977067..48977088,+p@chr19:48977067..48977088
+
Hg19::chr19:51267068..51267083,+p@chr19:51267068..51267083
+
Hg19::chr19:54198538..54198542,+p1@MIR519B
Hg19::chr19:54231988..54231990,+p@chr19:54231988..54231990
+
Hg19::chr19:884972..884979,-p@chr19:884972..884979
-
Hg19::chr19:884982..884988,-p@chr19:884982..884988
-
Hg19::chr19:884994..885014,-p@chr19:884994..885014
-
Hg19::chr19:929006..929018,+p14@ARID3A
Hg19::chr19:929027..929051,+p4@ARID3A
Hg19::chr1:146989697..146989701,-p1@LOC100289211
Hg19::chr1:172648770..172648783,+p@chr1:172648770..172648783
+
Hg19::chr1:172648801..172648806,+p@chr1:172648801..172648806
+
Hg19::chr1:200877847..200877851,+p@chr1:200877847..200877851
+
Hg19::chr1:200877866..200877876,+p@chr1:200877866..200877876
+
Hg19::chr1:2021518..2021526,-p@chr1:2021518..2021526
-
Hg19::chr1:229087653..229087688,-p@chr1:229087653..229087688
-
Hg19::chr1:26686541..26686559,-p@chr1:26686541..26686559
-
Hg19::chr1:26686590..26686595,-p@chr1:26686590..26686595
-
Hg19::chr20:55563221..55563236,+p@chr20:55563221..55563236
+
Hg19::chr21:19117606..19117619,+p@chr21:19117606..19117619
+
Hg19::chr22:26106667..26106674,+p@chr22:26106667..26106674
+
Hg19::chr2:11251843..11251854,-p@chr2:11251843..11251854
-
Hg19::chr2:11251855..11251865,-p@chr2:11251855..11251865
-
Hg19::chr2:11251872..11251879,-p@chr2:11251872..11251879
-
Hg19::chr2:16067839..16067847,-p@chr2:16067839..16067847
-
Hg19::chr2:16067860..16067865,-p@chr2:16067860..16067865
-
Hg19::chr2:163101340..163101352,-p7@FAP
Hg19::chr2:16504272..16504306,+p@chr2:16504272..16504306
+
Hg19::chr2:16504345..16504381,+p@chr2:16504345..16504381
+
Hg19::chr2:172087828..172087839,-p20@TLK1
Hg19::chr2:192456035..192456041,+p@chr2:192456035..192456041
+
Hg19::chr2:242913327..242913332,+p1@ENST00000426962
Hg19::chr2:41605365..41605372,+p@chr2:41605365..41605372
+
Hg19::chr2:46656327..46656345,+p3@LOC388946
Hg19::chr2:46656347..46656363,+p2@LOC388946
Hg19::chr2:46669579..46669581,+p@chr2:46669579..46669581
+
Hg19::chr2:46682317..46682319,+p@chr2:46682317..46682319
+
Hg19::chr2:71277301..71277315,+p@chr2:71277301..71277315
+
Hg19::chr2:71277316..71277323,+p@chr2:71277316..71277323
+
Hg19::chr2:71277325..71277344,+p@chr2:71277325..71277344
+
Hg19::chr2:88803506..88803509,+p@chr2:88803506..88803509
+
Hg19::chr2:97535773..97535843,-p1@SEMA4C
Hg19::chr3:195581080..195581110,-p1@ENST00000444346
Hg19::chr3:87174378..87174403,-p@chr3:87174378..87174403
-
Hg19::chr4:106135812..106135817,+p@chr4:106135812..106135817
+
Hg19::chr4:176372622..176372659,-p@chr4:176372622..176372659
-
Hg19::chr4:183164566..183164573,+p14@ODZ3
Hg19::chr4:183164574..183164586,+p8@ODZ3
Hg19::chr4:189027159..189027178,-p4@TRIML2
Hg19::chr4:189064784..189064793,+p1@TRIML1
Hg19::chr4:8582132..8582151,+p3@GPR78
Hg19::chr5:16897687..16897692,-p@chr5:16897687..16897692
-
Hg19::chr5:172721751..172721762,-p2@ENST00000501670
Hg19::chr5:172721766..172721775,-p3@ENST00000501670
Hg19::chr5:39220845..39220852,-p@chr5:39220845..39220852
-
Hg19::chr5:70868039..70868044,+p@chr5:70868039..70868044
+
Hg19::chr6:148501038..148501057,-p@chr6:148501038..148501057
-
Hg19::chr6:25218773..25218788,-p10@CMAHP
Hg19::chr6:56258939..56258948,-p8@COL21A1
Hg19::chr6:56258957..56258965,-p10@COL21A1
Hg19::chr6:90213624..90213631,+p@chr6:90213624..90213631
+
Hg19::chr7:107643964..107643973,-p10@LAMB1
Hg19::chr7:12628967..12628976,+p6@SCIN
Hg19::chr7:134932245..134932256,-p@chr7:134932245..134932256
-
Hg19::chr7:2883766..2883775,-p7@GNA12
Hg19::chr8:135708824..135708829,-p24@ZFAT
Hg19::chr9:134585127..134585165,-p7@RAPGEF1
Hg19::chrX:49819025..49819038,+p@chrX:49819025..49819038
+
Hg19::chrX:49819043..49819049,+p@chrX:49819043..49819049
+
Hg19::chrX:49819053..49819064,+p@chrX:49819053..49819064
+
Hg19::chrX:56058051..56058060,-p@chrX:56058051..56058060
-
Hg19::chrX:62654223..62654277,-p@chrX:62654223..62654277
-
Hg19::chrX:62654282..62654291,-p@chrX:62654282..62654291
-
Hg19::chrX:7137573..7137574,+p19@STS


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

GO IDGO nameFDR corrected p-value
GO:0004773steryl-sulfatase activity0.0374720357941834
GO:0045654positive regulation of megakaryocyte differentiation0.0374720357941834
GO:0043257laminin-8 complex0.0374720357941834
GO:0005607laminin-2 complex0.0374720357941834
GO:0009956radial pattern formation0.0374720357941834
GO:00469351-phosphatidylinositol-3-kinase regulator activity0.0374720357941834
GO:0015054gastrin receptor activity0.0408677544635792
GO:0001672regulation of chromatin assembly or disassembly0.0408677544635792
GO:0045652regulation of megakaryocyte differentiation0.0408677544635792
GO:0045010actin nucleation0.0408677544635792
GO:0043259laminin-10 complex0.0408677544635792
GO:0051128regulation of cellular component organization and biogenesis0.0449426208413752
GO:0048731system development0.0449426208413752
GO:0004951cholecystokinin receptor activity0.0449426208413752
GO:0030219megakaryocyte differentiation0.0449426208413752



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
germ line cell4.35e-377
germ cell4.35e-377
epithelial cell of pancreas1.96e-084
Uber Anatomy
Ontology termp-valuen
placenta2.11e-084
allantois2.11e-084


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
GATA3#2625143.498268155971414.82570150565378e-050.000838867242924392



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

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