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Coexpression cluster:C1104: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!4.15e-24!82;UBERON:0000073!5.97e-24!94;UBERON:0001016!5.97e-24!94;UBERON:0005743!1.15e-23!86;UBERON:0000955!1.81e-21!69;UBERON:0006238!1.81e-21!69;UBERON:0007023!8.76e-21!115;UBERON:0003075!7.80e-18!86;UBERON:0007284!7.80e-18!86;UBERON:0002346!1.41e-17!90;UBERON:0001049!3.30e-17!57;UBERON:0005068!3.30e-17!57;UBERON:0006241!3.30e-17!57;UBERON:0007135!3.30e-17!57;UBERON:0002616!7.24e-17!59;UBERON:0003080!1.72e-14!42;UBERON:0002780!4.43e-14!41;UBERON:0001890!4.43e-14!41;UBERON:0006240!4.43e-14!41;UBERON:0003056!6.35e-14!61;UBERON:0000924!1.24e-13!173;UBERON:0006601!1.24e-13!173;UBERON:0004121!1.36e-13!169;UBERON:0000033!7.65e-13!123;UBERON:0000153!1.03e-12!129;UBERON:0007811!1.03e-12!129;UBERON:0001893!2.29e-11!34;UBERON:0002020!3.34e-11!34;UBERON:0003528!3.34e-11!34;UBERON:0002791!5.58e-11!33;UBERON:0001869!1.08e-10!32;UBERON:0000119!1.90e-09!312;UBERON:0000481!2.15e-09!347;UBERON:0000475!2.28e-09!365;UBERON:0000483!6.71e-09!309;UBERON:0000956!5.88e-08!25;UBERON:0000203!5.88e-08!25;UBERON:0000025!3.54e-07!194
|ontology_enrichment_uberon=UBERON:0001017!4.15e-24!82;UBERON:0000073!5.97e-24!94;UBERON:0001016!5.97e-24!94;UBERON:0005743!1.15e-23!86;UBERON:0000955!1.81e-21!69;UBERON:0006238!1.81e-21!69;UBERON:0007023!8.76e-21!115;UBERON:0003075!7.80e-18!86;UBERON:0007284!7.80e-18!86;UBERON:0002346!1.41e-17!90;UBERON:0001049!3.30e-17!57;UBERON:0005068!3.30e-17!57;UBERON:0006241!3.30e-17!57;UBERON:0007135!3.30e-17!57;UBERON:0002616!7.24e-17!59;UBERON:0003080!1.72e-14!42;UBERON:0002780!4.43e-14!41;UBERON:0001890!4.43e-14!41;UBERON:0006240!4.43e-14!41;UBERON:0003056!6.35e-14!61;UBERON:0000924!1.24e-13!173;UBERON:0006601!1.24e-13!173;UBERON:0004121!1.36e-13!169;UBERON:0000033!7.65e-13!123;UBERON:0000153!1.03e-12!129;UBERON:0007811!1.03e-12!129;UBERON:0001893!2.29e-11!34;UBERON:0002020!3.34e-11!34;UBERON:0003528!3.34e-11!34;UBERON:0002791!5.58e-11!33;UBERON:0001869!1.08e-10!32;UBERON:0000119!1.90e-09!312;UBERON:0000481!2.15e-09!347;UBERON:0000475!2.28e-09!365;UBERON:0000483!6.71e-09!309;UBERON:0000956!5.88e-08!25;UBERON:0000203!5.88e-08!25;UBERON:0000025!3.54e-07!194
|tf_chipseq_enrich=HMGN3#9324;4:4.67345584191462:0.00575188109993887:0.0259042997066199!SUZ12#23512;5:35.7969863650449:6.40694163759818e-08:3.95002702295819e-06!ZBTB7A#51341;4:4.20109103307194:0.0084941066128735:0.0324238304291628!ZNF263#10127;4:4.69819522114896:0.0056412295360981:0.0254817858881774
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9,0.182257,0.507227,0.291561,0.0337354,0.146629,0.0189194,0.000342077,0.177111,0.167984,0.337564,0.394053,0.123448,0.17256,0.126216,0.0947479,0.0787488,0.0883646,0.0324422,0.353144,0.407665,0.11039,0.361507,0.0955186,0.0754745,0.632378,0.00294979,0.0896836,0.133679,0.718626,0.038021,0.235824,0.23812,0.506939,0.0654706,0.554729,0.305348,0.0883079,0.192275,0.123717,0.3044,0.494788,0.435034,0.388488,0.27954,0.326131,0.0263379,0.0086744,0.168686,0.35711,0.180717,0.375467,0.246637,0.311267,0.0501326,0.347601,0.297851,0.195385,0.214528,0.187498,0.106912,0.207535,0.0510601,0.283013,0.17144,0.0304669,0.0417384,0.280244,0.000519824,0.0525779,0.1168,0.216736,0.112879,0.138362,0.1674,0.205022,0.304414,0.0775871,0.1646,0.0414545,0.00042666,0.239252,0.112638,0.54926,0.25636,0.392755,0.366993,0.843094,0.12921,0.107541,0.688004,0.136306,0.362226,0.0104549,0.158567,0.446426,0.551931,9.453e-05,0.268889,0.0751905,0.000269589,4.10107e-06,0.417001,0.436925,0.234633,0.150144,0.235575,0.111506,0.209512,0.415762,0.167545,0.1033,0.238509,0.156356,0.450242,0.322099,0.0857464,0.282499,0.101873,0.121306,0.246526,0.0222954,0.356991,0.227948,0.44271,0.128341,0.463619,0.168391,0.545636,0.320047,0.397073,0.437057,0.00216175,0.06691,0.358,0.0753755,0.318595,0.140173,0.0140511,0.312917,0.0842616,0.00767371,0.15977,0.201434,0.134947,0.304849,0.316782,0.212636,0.325012,0.00997262,0.0145573,0.291345,0.0235357,0.491263,0.00135759,0.255995,0.184894,0.0695172,0.244347,0.243363,0.382464,0.361244,0.207462,0.51104,0.487422,0.29768,0.217499,0.500934,0.225368,0.244195,0.0586175,0.348776,0.198885,0.608664,0.347052,0.386025,0.0172108,0.0833624,0.327304,0.217315,6.36565e-05,0.132491,0.48467,0.367752,0.436987,0.000434789,0.12497,0.0277275,0.0821811,0.35171,0.279549,0.0984834,0.284421,0.71736,0.0239625,0.1643,0.344864,0.458949,0.547863,0.741039,0.659829,0.726427,0.750889,0.401507,0.330231,0.648881,0.34295,0.673541,0.147712,0.910041,0.732853,6.39138e-07,0.684866,0.790371,0.0816012,0.39645,0.00859285,0.00445635,0.0101712,0.451787,0.00812386,7.42134e-07,0.680172,0.184591,0.226936,0.0031923,8.26469e-05,0.54891,0.341975,0.425103,0.547149,0.863925,0.000989971,6.32648e-05,0.771117,0.154752,0.74852,0.478352,0.00995888,0.685599,9.59122e-05,0.748102,0.337191,0.000147015,0.0977429,0.797881,0.000146833,0.664234,0.0722516,0.779967,0.0111832,0.106142,0.135789,0.411785,0.40673,0.415502,0.203449,8.44374e-05,0.371455,0.0191281,0.676266,0.327011,0.299176,0.0372357,0.210121,0.585578,0.272487,0.341296,0.0242779,0.258349,0.541728,0.130195,0.585566,0.373172,0.538803,8.32671e-05,0.187697,0.346345,0.816529,0.596462,0.00415477,0.017059,0.00197177,0.316667,0.0970096,0.000160481,0.536712,0.443364,0.133209,0.715255,0.765316,0.0385149,0.0545685,0.41419,0.7547,0.294507,0.124237,0.346938,0.40211,0.183851,0.588416,0.198404,0.362009,0.611179,0.664218,0.516101,0.706724,0.0919405,0.0353589,0.321679,0.0224116,0.466416,0.411899,0.525367,0.300829,0.161827,0.635414,0.528332,7.38818e-06,3.23966e-06,0.474724,0.661532,0.574524,0.570287,0.000258522,0.315643,0.0268574,0.490466,0.676249,0.418017,0.22688,0.440345,0.0873023,0.400622,0.391073,0.179706,0.170712,0.575489,0.762263,0.183236,0.00379836,0.775603,0.333846,0.171531,0.0938213,0.173588,0.67786,0.00098624,0.646027,0.620377,0.402066,0.000449178,0.0289699,0.610982,0.826815,0.202705,0.0103815,0.415214,0.364157,0.172412,1.45514e-05,0.415017,0.0769041,0.387804,0.502902,0.385339,0.159832,0.512288,0.338978,0.390233,0.339879,0.438999,0.103879,8.2258e-05,0.208523,0.0680722,0.4924,0.304359,0.497662,0.418843,0.749185,0.369586,0.394729,0.116157,0.444932,0.622992,0.00200857,0.436618,0.00197061,0.382758,0.264429,0.0960556,0.0744027,0.204325,0.265849,0.370442,0.451398,0.533438,0.0189729,0.279598,0.420279,0.00478497,0.000356668,0.150111,0.420451,0.514853,0.244241,0.307495,0.124582,0.3382,0.454846,0.350305,0.0875262,0.147486,0.117583,0.103076,0.166405,0.40865,0.634608,0.324846,0.0366694,0.215261,0.235004,0.133496,0.433115,0.331422,0.440492,0.397558,0.266168,0.504119,0.57634,0.371725,0.334024,0.500457,0.316975,0.435107,0.26559,0.378345,0.0836911,0.0136648,0.502341,0.507413,0.412407,0.10934,0.418893,3.5931e-05,0.0903341,7.01182e-05,0.249956,0.447581,0.141745,0.35808,0.0969253,0.000480118,0.400859,0.473667,0.327684,0.279523,0.499937,0.444635,0.356463,0.364875,0.211724,0.409573,0.579867,0.180313,0.436872,0.181464,0.000218398,0.0291553,0.120636,0.121001,0.0568736,0.172653,0.0924531,0.120918,0.593272,0.158598,0.425328,0.384398,0.462521,0.387627,0.179489,0.214126,0.143317,0.261663,0.14273,0.227254,0.147968,0.168955,0.274981,0.236422,0.0999117,0.149301,0.196723,0.0836477,0.287028,0.413461,0.00155586,0.545381,0.630108,0.299959,0.509613,0.498355,0.406059,0.452427,0.56256,0.494497,0.366448,0.540845,0.511559,0.280842,0.335456,0.416632,0.404559,0.545676,0.467154,0.0143467,0.249647,0.43669,0.446356,0.248584,0.397145,0.390152,0.537963,0.182951,0.488863,0.342785,0.447064,0.20487,0.603936,0.449548,0.41929,0.209566,0.189123,0.588995,0.355645,0.332105,0.0389799,0.158122,0.521096,0.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}}
}}

Revision as of 12:29, 5 September 2012


Full id: C1104_heart_maxillary_teratocarcinoma_left_neuroblastoma_small_medulloblastoma



Phase1 CAGE Peaks

Hg19::chr10:112402997..112403008,+p@chr10:112402997..112403008
+
Hg19::chr10:112404070..112404099,+p2@RBM20
Hg19::chr10:112404108..112404122,+p3@RBM20
Hg19::chr10:112404132..112404145,+p4@RBM20
Hg19::chr10:112404166..112404180,+p5@RBM20
Hg19::chr10:112523532..112523536,+p@chr10:112523532..112523536
+
Hg19::chr20:33565418..33565443,+p6@MYH7B


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>


Cell Type
Ontology termp-valuen
neural cell3.98e-0725
glial cell (sensu Vertebrata)9.61e-0715
glial cell9.61e-0715
glioblast9.61e-0715
glioblast (sensu Vertebrata)9.61e-0715
Uber Anatomy
Ontology termp-valuen
central nervous system4.15e-2482
regional part of nervous system5.97e-2494
nervous system5.97e-2494
brain1.81e-2169
future brain1.81e-2169
adult organism8.76e-21115
neural plate7.80e-1886
presumptive neural plate7.80e-1886
neurectoderm1.41e-1790
neural tube3.30e-1757
neural rod3.30e-1757
future spinal cord3.30e-1757
neural keel3.30e-1757
regional part of brain7.24e-1759
anterior neural tube1.72e-1442
regional part of forebrain4.43e-1441
forebrain4.43e-1441
future forebrain4.43e-1441
pre-chordal neural plate6.35e-1461
ectoderm1.24e-13173
presumptive ectoderm1.24e-13173
ectoderm-derived structure1.36e-13169
head7.65e-13123
anterior region of body1.03e-12129
craniocervical region1.03e-12129
telencephalon2.29e-1134
gray matter3.34e-1134
brain grey matter3.34e-1134
regional part of telencephalon5.58e-1133
cerebral hemisphere1.08e-1032
cell layer1.90e-09312
multi-tissue structure2.15e-09347
organism subdivision2.28e-09365
epithelium6.71e-09309
cerebral cortex5.88e-0825
pallium5.88e-0825
tube3.54e-07194


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
HMGN3#932444.673455841914620.005751881099938870.0259042997066199
SUZ12#23512535.79698636504496.40694163759818e-083.95002702295819e-06
ZBTB7A#5134144.201091033071940.00849410661287350.0324238304291628
ZNF263#1012744.698195221148960.00564122953609810.0254817858881774



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.