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Coexpression cluster:C232: Difference between revisions

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|ontology_enrichment_disease=DOID:162!1.13e-14!235;DOID:0050687!4.66e-14!143;DOID:14566!2.87e-13!239;DOID:305!1.30e-10!106;DOID:3095!9.91e-08!22;DOID:2994!9.91e-08!22
|ontology_enrichment_disease=DOID:162!1.13e-14!235;DOID:0050687!4.66e-14!143;DOID:14566!2.87e-13!239;DOID:305!1.30e-10!106;DOID:3095!9.91e-08!22;DOID:2994!9.91e-08!22
|ontology_enrichment_uberon=UBERON:0000073!1.87e-33!94;UBERON:0001016!1.87e-33!94;UBERON:0001017!2.75e-33!82;UBERON:0005743!1.10e-32!86;UBERON:0000955!7.24e-27!69;UBERON:0006238!7.24e-27!69;UBERON:0001049!2.92e-26!57;UBERON:0005068!2.92e-26!57;UBERON:0006241!2.92e-26!57;UBERON:0007135!2.92e-26!57;UBERON:0002346!4.79e-26!90;UBERON:0003075!5.68e-25!86;UBERON:0007284!5.68e-25!86;UBERON:0002616!1.63e-24!59;UBERON:0000924!1.60e-23!173;UBERON:0006601!1.60e-23!173;UBERON:0004121!1.91e-22!169;UBERON:0002780!3.24e-19!41;UBERON:0001890!3.24e-19!41;UBERON:0006240!3.24e-19!41;UBERON:0003056!6.76e-19!61;UBERON:0003080!4.00e-18!42;UBERON:0002020!3.11e-17!34;UBERON:0003528!3.11e-17!34;UBERON:0001893!5.54e-17!34;UBERON:0000033!7.09e-17!123;UBERON:0002791!1.43e-16!33;UBERON:0001869!4.10e-16!32;UBERON:0000153!1.83e-15!129;UBERON:0007811!1.83e-15!129;UBERON:0000956!6.86e-13!25;UBERON:0000203!6.86e-13!25;UBERON:0002619!2.16e-11!22;UBERON:0001950!2.15e-10!20;UBERON:0000064!9.59e-10!219;UBERON:0003076!2.08e-09!15;UBERON:0003057!2.08e-09!15;UBERON:0004732!7.93e-09!13;UBERON:0004733!2.95e-08!12;UBERON:0002028!2.95e-08!12;UBERON:0007277!2.95e-08!12;UBERON:0000119!3.38e-07!312;UBERON:0002680!8.43e-07!9;UBERON:0001895!8.43e-07!9;UBERON:0010092!8.43e-07!9
|ontology_enrichment_uberon=UBERON:0000073!1.87e-33!94;UBERON:0001016!1.87e-33!94;UBERON:0001017!2.75e-33!82;UBERON:0005743!1.10e-32!86;UBERON:0000955!7.24e-27!69;UBERON:0006238!7.24e-27!69;UBERON:0001049!2.92e-26!57;UBERON:0005068!2.92e-26!57;UBERON:0006241!2.92e-26!57;UBERON:0007135!2.92e-26!57;UBERON:0002346!4.79e-26!90;UBERON:0003075!5.68e-25!86;UBERON:0007284!5.68e-25!86;UBERON:0002616!1.63e-24!59;UBERON:0000924!1.60e-23!173;UBERON:0006601!1.60e-23!173;UBERON:0004121!1.91e-22!169;UBERON:0002780!3.24e-19!41;UBERON:0001890!3.24e-19!41;UBERON:0006240!3.24e-19!41;UBERON:0003056!6.76e-19!61;UBERON:0003080!4.00e-18!42;UBERON:0002020!3.11e-17!34;UBERON:0003528!3.11e-17!34;UBERON:0001893!5.54e-17!34;UBERON:0000033!7.09e-17!123;UBERON:0002791!1.43e-16!33;UBERON:0001869!4.10e-16!32;UBERON:0000153!1.83e-15!129;UBERON:0007811!1.83e-15!129;UBERON:0000956!6.86e-13!25;UBERON:0000203!6.86e-13!25;UBERON:0002619!2.16e-11!22;UBERON:0001950!2.15e-10!20;UBERON:0000064!9.59e-10!219;UBERON:0003076!2.08e-09!15;UBERON:0003057!2.08e-09!15;UBERON:0004732!7.93e-09!13;UBERON:0004733!2.95e-08!12;UBERON:0002028!2.95e-08!12;UBERON:0007277!2.95e-08!12;UBERON:0000119!3.38e-07!312;UBERON:0002680!8.43e-07!9;UBERON:0001895!8.43e-07!9;UBERON:0010092!8.43e-07!9
|tf_chipseq_enrich=TAF7#6879;20:3.74854734587669:1.22287687352815e-07:7.02895089677525e-06
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.559049,0.713637,0.999984,0.743352,0.679115,0.906518,0.944884,0.445708,0.999986,0.82551,0.553208,0.84445,0.683637,0.612346,0.844271,0.873293,0.927257,0.942565,0.990988,0.973499,0.157342,0.478274,0.739054,0.82395,0.983465,0.965377,0.047698,0.599131,0.510401,0.37101,0.0436287,0.999465,0.991908,0.258843,0.601255,0.997693,0.944934,0.8058,0.41747,0.0649473,0.322696,0.999808,0.997896,0.2945,0.00161626,0.280329,0.72685,0.797391,0.00452669,0.612383,0.505291,0.791375,0.959961,0.999871,0.990839,0.873739,0.821848,0.924314,0.987053,0.759664,0.99964,0.700505,0.628968,0.973462,0.721116,0.980148,0.850225,0.777875,0.964432,0.826633,0.521315,0.756594,0.749003,1,1,0.990923,0.875767,0.676051,0.757732,0.903762,0.0859519,0.871107,0.687707,0.797697,0.613319,0.906934,0.772735,0.994558,0.966214,0.542149,0.944589,0.607921,0.67597,0.705796,0.862452,0.7388,0.895065,0.962653,0.336276,0.995609,0.47728,0.998966,0.65275,0.987834,0.959808,0.886807,0.986817,0.344201,0.969423,0.964662,0.731812,0.804917,0.837772,0.99999,0.968072,0.447841,0.859165,0.717271,0.957944,0.963834,0.875478,0.855997,0.525684,0.812056,0.801014,0.430515,0.838643,0.992104,0.923989,0.831619,0.962674,0.91297,0.911978,0.985011,0.97988,0.601039,0.98582,0.979826,0.95401,0.882023,0.853773,0.89197,0.912818,0.409268,0.976188,0.8552,0.968218,0.508876,0.985748,0.822036,0.240063,0.670726,0.944609,0.999943,0.35126,0.996902,0.761202,0.993302,0.969665,0.993537,0.999028,0.526354,0.982769,0.942572,0.594839,0.945869,0.962731,0.824971,0.852706,0.905237,0.78104,0.995998,0.991103,0.23708,0.874878,0.992971,0.46284,0.886842,0.803987,0.9983,0.923068,0.996409,0.975305,0.886398,0.936329,0.99013,0.982034,0.998345,0.991883,0.818371,0.999789,1,0.425737,0.980537,0.973467,0.969475,0.907813,0.999624,0.963139,0.980536,0.992294,0.162415,0.934648,0.998996,0.998406,0.95199,0.725743,0.410426,0.566068,0.980027,0.668488,1,0.972282,0.991121,0.97367,0.694394,0.999808,0.999617,0.994214,0.999996,0.995871,1,0.764541,1,0.999911,0.999998,0.944825,0.666034,0.947277,0.589272,0.939277,0.932408,0.867185,0.858653,0.968289,0.815006,0.912584,0.871969,0.500998,0.9933,0.878003,0.778253,0.482699,0.67298,0.985931,0.880248,0.772017,0.511531,0.997394,0.999631,0.737772,0.999747,0.800199,0.999981,0.605411,0.795577,0.969983,0.982354,0.999932,0.784331,0.962971,0.764263,0.213782,0.986375,0.995328,0.999886,0.683983,0.960073,0.806755,0.999992,0.716763,0.988691,0.261461,0.78337,0.954385,0.902107,0.714115,0.609388,0.997355,0.981397,0.994901,0.986998,0.972226,0.43579,0.30985,0.944902,0.887737,0.915369,0.954954,0.651266,0.637986,0.917316,0.978529,0.659443,0.470415,0.938751,0.742941,0.323464,0.773923,0.850783,0.373738,0.967316,0.475319,0.763382,0.880154,0.975601,0.651,0.433961,0.96866,0.960597,0.995158,0.965803,0.905879,0.857763,0.649073,0.891635,0.629607,0.587387,0.780917,0.988645,0.951768,0.887317,0.845868,0.824335,0.966164,0.96985,0.713606,0.967648,0.72997,0.656282,0.686411,0.904374,0.807774,0.959775,0.844901,0.50209,0.926681,0.983952,0.418158,0.780768,0.948568,0.875041,0.803993,0.876198,0.740149,0.949921,0.853287,0.869695,0.975127,0.840473,0.748216,0.554262,0.694941,0.762139,0.764898,0.275921,0.572676,0.963725,0.969905,0.765577,0.735007,0.988914,0.922311,0.931178,0.829073,0.490209,0.863548,0.750078,0.0223445,0.966701,0.897648,0.837764,0.778585,0.514805,0.927682,0.884557,0.757651,0.515278,0.873862,0.229739,0.959318,0.774507,0.0730409,0.89752,0.976671,0.549858,0.404884,0.663808,0.612476,0.987317,0.835009,0.975107,0.855757,0.733349,0.623559,0.677006,0.71311,0.55002,0.680703,0.880341,0.987919,0.932583,0.984244,0.335842,0.769161,0.68692,0.997638,0.963923,0.958787,0.932119,0.918322,0.128891,0.782725,0.725662,0.421053,0.99028,0.540283,0.51098,0.601198,0.810159,0.232321,0.918441,0.414099,0.67925,0.978995,0.831774,0.809873,0.822329,0.65679,0.671654,0.320747,0.939757,0.885499,0.978529,0.755335,0.156319,0.0193143,0.995529,0.505667,0.735558,0.520579,0.989845,0.899253,0.67381,0.674988,0.845205,0.808262,0.570603,0.674722,0.952787,0.737043,0.953335,0.923754,0.905925,0.926531,0.821636,0.620328,0.740239,0.928889,0.387988,0.894241,0.752274,0.800664,0.93932,0.904688,0.600398,0.75563,0.298687,0.532909,0.947564,0.945942,0.973134,0.967307,0.991867,0.816364,0.94675,0.849833,0.940866,0.967155,0.974625,0.707499,0.981264,0.991182,0.59269,0.781042,0.870433,0.948005,0.300138,0.967445,0.640271,0.996971,0.456917,0.959617,0.887593,0.917132,0.987846,0.986561,0.902931,0.905467,0.834738,0.707351,0.412673,0.86436,0.695221,0.594302,0.851304,0.871183,0.545105,0.996225,0.97829,0.144681,0.883575,0.77685,0.618623,0.885298,0.884986,0.903512,0.270652,0.548984,0.542277,0.846607,0.994341
}}
}}

Revision as of 14:02, 5 September 2012


Full id: C232_teratocarcinoma_HES3GFP_H9_iPS_testicular_neuroblastoma_cerebellum



Phase1 CAGE Peaks

Hg19::chr10:98161098..98161100,+p@chr10:98161098..98161100
+
Hg19::chr11:122684227..122684231,+p@chr11:122684227..122684231
+
Hg19::chr11:2022489..2022501,-p37@H19
Hg19::chr11:41327517..41327518,+p@chr11:41327517..41327518
+
Hg19::chr11:92850299..92850305,-p@chr11:92850299..92850305
-
Hg19::chr12:68284590..68284597,-p@chr12:68284590..68284597
-
Hg19::chr12:8034314..8034336,-p@chr12:8034314..8034336
-
Hg19::chr13:102603275..102603278,+p@chr13:102603275..102603278
+
Hg19::chr13:27914684..27914686,-p@chr13:27914684..27914686
-
Hg19::chr13:44925859..44925864,+p@chr13:44925859..44925864
+
Hg19::chr13:51747485..51747488,-p@chr13:51747485..51747488
-
Hg19::chr14:98103699..98103702,-p@chr14:98103699..98103702
-
Hg19::chr15:73150394..73150400,+p@chr15:73150394..73150400
+
Hg19::chr15:79787932..79787937,-p@chr15:79787932..79787937
-
Hg19::chr16:16064786..16064790,-p@chr16:16064786..16064790
-
Hg19::chr1:10875488..10875494,+p@chr1:10875488..10875494
+
Hg19::chr1:146544055..146544062,-p@chr1:146544055..146544062
-
Hg19::chr1:38619558..38619563,+p@chr1:38619558..38619563
+
Hg19::chr1:62661907..62661916,+p@chr1:62661907..62661916
+
Hg19::chr1:62675663..62675671,-p@chr1:62675663..62675671
-
Hg19::chr20:52685670..52685678,+p@chr20:52685670..52685678
+
Hg19::chr2:168243434..168243438,+p@chr2:168243434..168243438
+
Hg19::chr2:169769806..169769861,-p2@SPC25
Hg19::chr2:202835658..202835677,+p@chr2:202835658..202835677
+
Hg19::chr2:48919688..48919703,+p@chr2:48919688..48919703
+
Hg19::chr2:48919725..48919761,+p@chr2:48919725..48919761
+
Hg19::chr3:14658573..14658581,+p@chr3:14658573..14658581
+
Hg19::chr3:186700341..186700345,+p@chr3:186700341..186700345
+
Hg19::chr3:194646645..194646650,-p@chr3:194646645..194646650
-
Hg19::chr3:32455724..32455728,-p@chr3:32455724..32455728
-
Hg19::chr3:32904712..32904715,+p@chr3:32904712..32904715
+
Hg19::chr3:32937906..32937913,+p@chr3:32937906..32937913
+
Hg19::chr3:32938576..32938590,+p@chr3:32938576..32938590
+
Hg19::chr4:113572878..113572895,-p@chr4:113572878..113572895
-
Hg19::chr4:113628003..113628015,-p1@ENST00000505632
Hg19::chr5:116157646..116157650,+p@chr5:116157646..116157650
+
Hg19::chr5:118738398..118738400,+p@chr5:118738398..118738400
+
Hg19::chr5:120034108..120034114,-p@chr5:120034108..120034114
-
Hg19::chr5:122512045..122512049,+p@chr5:122512045..122512049
+
Hg19::chr5:147253888..147253894,-p@chr5:147253888..147253894
-
Hg19::chr5:81591218..81591231,+p@chr5:81591218..81591231
+
Hg19::chr6:10417667..10417676,-p54@TFAP2A
Hg19::chr7:148034419..148034425,+p@chr7:148034419..148034425
+
Hg19::chr7:21120890..21120893,+p@chr7:21120890..21120893
+
Hg19::chr7:24436189..24436212,+p@chr7:24436189..24436212
+
Hg19::chr7:44263545..44263550,-p@chr7:44263545..44263550
-
Hg19::chr7:66858115..66858118,+p@chr7:66858115..66858118
+
Hg19::chr8:101973268..101973275,+p@chr8:101973268..101973275
+
Hg19::chr8:38389009..38389020,+p@chr8:38389009..38389020
+
Hg19::chr9:17536850..17536852,+p@chr9:17536850..17536852
+
Hg19::chr9:5868313..5868316,+p@chr9:5868313..5868316
+
Hg19::chr9:79633621..79633632,+p2@FOXB2
Hg19::chr9:93653244..93653250,-p@chr9:93653244..93653250
-
Hg19::chrX:136646431..136646476,+p@chrX:136646431..136646476
+
Hg19::chrX:136648279..136648295,+p1@ZIC3
Hg19::chrX:136648297..136648319,+p3@ZIC3
Hg19::chrX:136648554..136648576,+p4@ZIC3
Hg19::chrX:136650899..136650918,+p7@ZIC3
Hg19::chrX:36968877..36968881,-p@chrX:36968877..36968881
-
Hg19::chrX:97828862..97828879,+p@chrX:97828862..97828879
+
Hg19::chrX:99848620..99848641,+p5@TNMD


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
neural cell3.33e-0825
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.87e-3394
nervous system1.87e-3394
central nervous system2.75e-3382
brain7.24e-2769
future brain7.24e-2769
neural tube2.92e-2657
neural rod2.92e-2657
future spinal cord2.92e-2657
neural keel2.92e-2657
neurectoderm4.79e-2690
neural plate5.68e-2586
presumptive neural plate5.68e-2586
regional part of brain1.63e-2459
ectoderm1.60e-23173
presumptive ectoderm1.60e-23173
ectoderm-derived structure1.91e-22169
regional part of forebrain3.24e-1941
forebrain3.24e-1941
future forebrain3.24e-1941
pre-chordal neural plate6.76e-1961
anterior neural tube4.00e-1842
gray matter3.11e-1734
brain grey matter3.11e-1734
telencephalon5.54e-1734
head7.09e-17123
regional part of telencephalon1.43e-1633
cerebral hemisphere4.10e-1632
anterior region of body1.83e-15129
craniocervical region1.83e-15129
cerebral cortex6.86e-1325
pallium6.86e-1325
regional part of cerebral cortex2.16e-1122
neocortex2.15e-1020
organ part9.59e-10219
posterior neural tube2.08e-0915
chordal neural plate2.08e-0915
segmental subdivision of nervous system7.93e-0913
segmental subdivision of hindbrain2.95e-0812
hindbrain2.95e-0812
presumptive hindbrain2.95e-0812
cell layer3.38e-07312
regional part of metencephalon8.43e-079
metencephalon8.43e-079
future metencephalon8.43e-079
Disease
Ontology termp-valuen
cancer1.13e-14235
cell type cancer4.66e-14143
disease of cellular proliferation2.87e-13239
carcinoma1.30e-10106
germ cell and embryonal cancer9.91e-0822
germ cell cancer9.91e-0822


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
TAF7#6879203.748547345876691.22287687352815e-077.02895089677525e-06



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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