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Coexpression cluster:C453: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0008201!heparin binding!0.0154244672082892!7057$GO:0007596!blood coagulation!0.0154244672082892!7057$GO:0050817!coagulation!0.0154244672082892!7057$GO:0007599!hemostasis!0.0154244672082892!7057$GO:0005539!glycosaminoglycan binding!0.0154244672082892!7057$GO:0030247!polysaccharide binding!0.0154244672082892!7057$GO:0050878!regulation of body fluid levels!0.0154244672082892!7057$GO:0001871!pattern binding!0.0154244672082892!7057$GO:0042060!wound healing!0.0154244672082892!7057$GO:0004866!endopeptidase inhibitor activity!0.0256253813300793!7057$GO:0030414!protease inhibitor activity!0.0256253813300793!7057$GO:0051674!localization of cell!0.0298834334157541!7057$GO:0006928!cell motility!0.0298834334157541!7057$GO:0004857!enzyme inhibitor activity!0.0298834334157541!7057$GO:0009611!response to wounding!0.0298834334157541!7057$GO:0030246!carbohydrate binding!0.0316584245849523!7057$GO:0009605!response to external stimulus!0.039458100442579!7057$GO:0007399!nervous system development!0.042152360767691!7057$GO:0065008!regulation of biological quality!0.0484432557904829!7057$GO:0022610!biological adhesion!0.0484432557904829!7057$GO:0007155!cell adhesion!0.0484432557904829!7057
|gostat_on_coexpression_clusters=GO:0008201!heparin binding!0.0154244672082892!7057$GO:0007596!blood coagulation!0.0154244672082892!7057$GO:0050817!coagulation!0.0154244672082892!7057$GO:0007599!hemostasis!0.0154244672082892!7057$GO:0005539!glycosaminoglycan binding!0.0154244672082892!7057$GO:0030247!polysaccharide binding!0.0154244672082892!7057$GO:0050878!regulation of body fluid levels!0.0154244672082892!7057$GO:0001871!pattern binding!0.0154244672082892!7057$GO:0042060!wound healing!0.0154244672082892!7057$GO:0004866!endopeptidase inhibitor activity!0.0256253813300793!7057$GO:0030414!protease inhibitor activity!0.0256253813300793!7057$GO:0051674!localization of cell!0.0298834334157541!7057$GO:0006928!cell motility!0.0298834334157541!7057$GO:0004857!enzyme inhibitor activity!0.0298834334157541!7057$GO:0009611!response to wounding!0.0298834334157541!7057$GO:0030246!carbohydrate binding!0.0316584245849523!7057$GO:0009605!response to external stimulus!0.039458100442579!7057$GO:0007399!nervous system development!0.042152360767691!7057$GO:0065008!regulation of biological quality!0.0484432557904829!7057$GO:0022610!biological adhesion!0.0484432557904829!7057$GO:0007155!cell adhesion!0.0484432557904829!7057
|id=C453
|id=C453
|ontology_enrichment_celltype=CL:0000222!5.68e-16!119;CL:0000055!7.12e-16!180;CL:0002139!2.72e-12!24;CL:0000115!2.82e-12!35;CL:0000057!4.22e-12!75;CL:0000220!1.08e-11!246;CL:0002321!2.60e-11!248;CL:0002078!6.82e-11!44;CL:0000071!7.83e-10!18;CL:0002546!7.83e-10!18;CL:0002371!5.61e-09!591;CL:0000680!2.44e-08!57;CL:0000056!2.44e-08!57;CL:0000355!2.44e-08!57;CL:0000192!3.27e-08!42;CL:0000514!3.27e-08!42;CL:0000359!4.30e-08!32;CL:0000213!5.14e-08!57;CL:0000215!5.14e-08!57;CL:0000187!1.23e-07!54;CL:0000183!4.23e-07!59
|ontology_enrichment_celltype=CL:0002139!2.52e-14!24;CL:0000057!4.47e-14!76;CL:0000222!3.89e-11!121;CL:0000071!6.47e-11!18;CL:0002546!6.47e-11!18;CL:0002371!6.47e-11!588;CL:0000115!2.77e-10!36;CL:0002078!6.51e-09!45;CL:0000548!1.44e-08!679;CL:0000255!1.44e-08!679;CL:1000413!2.17e-07!9;CL:0002334!4.17e-07!12;CL:0000213!5.66e-07!58;CL:0000215!5.66e-07!58;CL:0002620!8.78e-07!23;CL:0002321!9.95e-07!250
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!1.25e-20!659;UBERON:0000055!2.52e-20!69;UBERON:0004872!4.08e-20!84;UBERON:0002049!2.84e-19!79;UBERON:0007798!2.84e-19!79;UBERON:0001981!4.83e-19!60;UBERON:0007500!4.83e-19!60;UBERON:0004537!4.83e-19!60;UBERON:0006965!4.83e-19!60;UBERON:0000480!1.88e-18!626;UBERON:0000467!2.14e-18!625;UBERON:0003914!2.48e-17!118;UBERON:0001009!7.53e-15!113;UBERON:0004535!1.88e-14!110;UBERON:0000490!3.07e-14!138;UBERON:0001637!1.11e-13!42;UBERON:0003509!1.11e-13!42;UBERON:0004572!1.11e-13!42;UBERON:0000926!1.47e-13!448;UBERON:0004120!1.47e-13!448;UBERON:0006603!1.47e-13!448;UBERON:0002100!8.29e-13!216;UBERON:0005256!1.13e-10!143;UBERON:0004573!1.60e-10!33;UBERON:0004571!1.60e-10!33;UBERON:0000914!4.88e-10!83;UBERON:0002329!4.88e-10!83;UBERON:0003077!4.88e-10!83;UBERON:0003059!4.88e-10!83;UBERON:0007282!4.88e-10!83;UBERON:0009618!4.88e-10!83;UBERON:0007285!4.88e-10!83;UBERON:0000486!5.86e-10!82;UBERON:0000487!7.29e-10!22;UBERON:0001986!7.83e-10!18;UBERON:0004638!7.83e-10!18;UBERON:0004852!7.83e-10!18;UBERON:0002050!1.90e-09!605;UBERON:0005423!1.90e-09!605;UBERON:0000923!2.25e-09!604;UBERON:0005291!2.25e-09!604;UBERON:0006598!2.25e-09!604;UBERON:0002532!2.25e-09!604;UBERON:0000922!3.96e-09!612;UBERON:0000475!8.03e-09!365;UBERON:0006914!1.19e-08!25;UBERON:0003102!1.95e-08!95;UBERON:0004290!3.29e-08!70;UBERON:0003081!3.62e-08!216;UBERON:0002385!3.70e-08!63;UBERON:0001015!3.70e-08!63;UBERON:0000383!3.70e-08!63;UBERON:0001134!4.17e-08!61;UBERON:0002036!4.17e-08!61;UBERON:0003082!4.17e-08!61;UBERON:0000947!4.30e-08!21;UBERON:0010191!4.30e-08!21;UBERON:0000477!7.03e-08!286;UBERON:0003104!8.07e-08!238;UBERON:0009142!8.07e-08!238;UBERON:0004111!2.88e-07!241;UBERON:0000483!5.43e-07!309
|ontology_enrichment_uberon=UBERON:0000055!1.40e-16!68;UBERON:0004872!9.17e-16!83;UBERON:0007500!3.82e-15!59;UBERON:0001981!3.82e-15!59;UBERON:0004537!3.82e-15!59;UBERON:0006965!3.82e-15!59;UBERON:0002049!8.32e-15!78;UBERON:0007798!8.32e-15!78;UBERON:0001637!2.12e-12!42;UBERON:0003509!2.12e-12!42;UBERON:0004572!2.12e-12!42;UBERON:0003914!2.91e-11!117;UBERON:0000487!3.72e-11!22;UBERON:0004638!6.47e-11!18;UBERON:0001986!6.47e-11!18;UBERON:0004852!6.47e-11!18;UBERON:0001009!2.88e-10!112;UBERON:0004535!3.62e-10!109;UBERON:0006914!1.12e-09!25;UBERON:0004573!4.60e-09!33;UBERON:0004571!4.60e-09!33;UBERON:0000947!1.24e-08!21;UBERON:0010191!1.24e-08!21;UBERON:0004923!1.52e-08!66;UBERON:0000926!5.03e-08!315;UBERON:0004120!5.03e-08!315;UBERON:0006603!5.03e-08!315;UBERON:0000467!5.05e-08!624;UBERON:0000490!6.02e-08!148;UBERON:0000480!6.62e-08!625;UBERON:0000468!1.42e-07!656;UBERON:0003915!2.17e-07!9;UBERON:0004700!2.17e-07!9;UBERON:0001917!2.17e-07!9;UBERON:0003081!3.34e-07!203
|tf_chipseq_enrich=ESR1#2099;8:11.1885830167834:2.63298906687883e-07:1.35728896917946e-05!GATA3#2625;12:14.8562816493851:2.7254465311872e-12:3.64926808039308e-10!POLR2A#5430;21:2.0498416685327:1.30673372631837e-06:5.18715179182685e-05
|tf_chipseq_enrich=ESR1#2099;8:11.1885830167834:2.63298906687883e-07:1.35728896917946e-05!GATA3#2625;12:14.8562816493851:2.7254465311872e-12:3.64926808039308e-10!POLR2A#5430;21:2.0498416685327:1.30673372631837e-06:5.18715179182685e-05
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8964,0.000967846,0.0796581,0.281443,6.62735e-12,0.905651,0.0347636,0.753219,2.77894e-09,0.825084,3.89215e-06,0.276871,0.283946,0.32592,0.820595,0.704578,1.8586e-08,0.00734746,0.366036,0.619736,1.44011e-11,0.00910617,0.912469,0.995241,0.000895499,0.102243,9.16925e-24,0.00216578,0.839122,6.52803e-11,2.58366e-06,0.725918,0.79288,2.88673e-07,1.51674e-08,0.345603,0.268637,0.227239,0.252306,0.067773,0.745672,0.0262981,2.96567e-13,0.000648597,0.966398,0.0258471,0.956936,0.542462,0.00344529,2.60312e-12,0.981414,0.616383,2.5628e-22,0.57461,0.89165,0.19169,0.997106,0.31744,0.034863,0.145825,0.339703,0.680436,0.362739,0.107833,0.00513671,0.00069332,0.881391,0.862566,0.451189,0.440456,0.75054,0.00390883,0.000855828,0.949833,0.114493,0.673238,0.388092,0.670883,0.495016,0.933911,0.451511,0.000500912,0.518598,0.805723,0.648527,0.118969,0.571705,0.019555,1.29545e-05,0.999802,0.987321,9.62147e-21,0.535947,2.32086e-19,0.000126997,0.437733,0.00637336,2.59939e-05,2.9895e-07,0.110589,0.687061,0.999948,0.662929,0.000554394,0.918278,0.605805,0.000227579,0.762395,0.997035,0.352624,0.300632,0.974285,0.369059,0.412841,0.487048,0.418772,0.844103,0.91979,0.233331,0.626303,0.0147145,1,1,0.241666,0.835538,1.71618e-09,0.400288,2.81767e-07,0.31035,0.522361,0.815318,3.11363e-05,0.290134,0.575294,0.413957,0.847456,6.07647e-11,0.245537,0.280191,0.286576,6.59755e-05,2.26146e-10,0.0360498,0.750395,0.556505,0.84079,0.0702459,0.311881,0.439833,0.916195,0.702487,0.796107,0.835659,0.544221,0.786175,0.751623,0.0364921,0.00789235,6.8546e-18,0.789313,0.692573,0.994205,0.71125,0.421379,0.506852,0.365935,0.00635499,0.336377,0.528269,0.709262,0.745646,0.0225127,0.000891477,0.850285,0.356849,0.711047,0.0677783,0.474033,0.793679,0.585442,0.583744,0.0192867,0.755547,0.166565,0.894457,0.620483,0.670632,0.537364,0.887448,2.1173e-05,0.220176,0.0158946,0.740234,0.501889,0.000400819,0.738067,0.453187,0.463428,2.76918e-05,0.353939,0.29492,0.9948,0.0744918,0.875513,0.763289,0.835595,0.573847,0.978412,0.99917,0.236251,0.979688,0.643161,0.27808,0.283289,0.98115,0.965945,0.275256,0.189893,0.00087766,0.516887,0.419152,3.92796e-09,0.385564,0.634967,0.220099,0.716158,0.0194487,0.734317,0.467306,0.952623,0.980794,0.918711,0.999917,0.0757125,0.956445,0.747596,0.00477534,0.181586,0.999835,1,4.22093e-28,0.782028,0.921021,0.481118,0.000241716,0.964428,0.997226,0.999931,0.918078,0.731612,0.478358,0.917069,0.998105,1.66959e-07,0.950503,0.49318,0.374732,0.807409,1.0201e-05,0.999802,0.973657,0.999941,0.999782,0.370538,0.882013,0.981092,0.032748,0.948047,0.856518,0.999987,0.991419,0.995877,0.999958,0.99998,0.811338,5.49254e-05,0.0288406,1.98956e-05,0.886289,0.98293,0.957149,8.59946e-05,0.000312099,0.672831,0.979626,0.523516,4.25759e-08,0.830526,0.730741,0.853717,5.65947e-05,0.000999778,0.940686,0.937235,0.769609,0.0999697,0.925543,0.999112,0.978712,0.995153,0.0697468,0.999602,0.0880734,0.992114,0.292064,0.789346,0.997491,0.996491,0.841377,0.00751673,7.58005e-12,0.989492,0.987384,0.987181,1.08657e-05,0.816819,4.78105e-15,0.997492,0.011984,0.801412,0.471915,0.767221,0.706473,1.07235e-16,0.948638,0.856501,0.632746,0.97883,0.964418,0.918258,0.973627,0.963463,0.00021608,6.2255e-05,0.903874,0.0619437,0.807479,0.958043,0.00303458,0.938488,0.931268,6.68687e-11,0.00836298,0.931828,0.742979,0.993415,0.972217,0.762234,2.45094e-06,0.687296,0.98878,0.964408,3.54032e-06,0.994578,0.477879,0.461735,0.942298,0.990957,0.75004,0.989056,7.85729e-09,0.983807,0.000382708,9.26379e-06,0.90376,0.965477,0.000176052,0.285955,0.0241316,0.961763,0.192201,0.801367,0.682529,0.482592,0.795909,0.995957,9.45702e-13,0.744972,0.028744,8.32692e-18,0.448301,0.907191,0.814577,0.222365,5.20699e-06,1.95274e-05,0.783374,0.0182328,0.0277044,9.49353e-13,0.788748,0.375064,7.03216e-08,0.245475,0.499526,0.520481,0.736118,0.00162693,0.969384,0.00178676,7.35052e-05,0.149824,0.765441,6.28926e-17,0.839676,0.842777,0.0043662,1.1564e-06,0.0104658,0.802831,0.0677188,0.251441,5.25938e-05,0.215723,0.512442,0.621398,5.61314e-10,7.52441e-07,0.0953677,0.481038,0.643239,3.61611e-08,6.72528e-09,0.550147,0.400215,0.819936,0.0285593,0.00213045,0.320982,0.852102,0.726744,0.851435,0.392661,0.250143,0.394374,0.325066,1.01986e-16,0.899263,0.808159,0.389498,7.92567e-10,0.609011,0.00769253,4.70703e-13,0.362585,0.532351,0.717852,0.276095,6.86731e-06,8.98207e-07,0.646516,0.136968,5.211e-12,0.721289,0.887109,0.0014886,0.833863,0.253266,0.0648942,4.17315e-06,0.423381,0.643772,4.64361e-14,3.21246e-09,0.828673,0.00813002,0.674364,0.0222119,0.877651,0.595037,0.556258,1.95057e-06,0.000604983,0.227118,0.00552112,0.219218,0.866966,0.712864,1.15795e-09,0.88674,0.551411,0.74975,0.759888,1.35236e-05,0.00162022,0.291523,0.910958,6.5277e-08,0.467046,0.0866244,0.562972,0.332379,6.51534e-05,0.699274,0.448806,1.45017e-12,4.33965e-06,0.94083,0.0261288,0.00213951,0.78233,0.85791,5.18054e-06,0.129112,5.88908e-10,0.385017,0.614572,0.38369,1.52533e-14,0.0911975,4.74766e-18,0.636002,0.571625,0.281669,0.398417,0.497652,5.22457e-13,4.69743e-14,0.813022,0.257794,0.708054,0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}}
}}

Revision as of 16:01, 19 October 2012


Full id: C453_hepatic_Ewing_neurofibroma_spindle_tridermal_Olfactory_bone



Phase1 CAGE Peaks

Hg19::chr15:33025921..33025938,+p@chr15:33025921..33025938
+
Hg19::chr15:39882081..39882094,+p@chr15:39882081..39882094
+
Hg19::chr15:39882095..39882106,+p@chr15:39882095..39882106
+
Hg19::chr15:39883408..39883415,+p37@THBS1
Hg19::chr15:39888563..39888574,+p@chr15:39888563..39888574
+
Hg19::chr15:39888595..39888609,+p@chr15:39888595..39888609
+
Hg19::chr15:39888702..39888705,+p@chr15:39888702..39888705
+
Hg19::chr15:39888716..39888727,+p@chr15:39888716..39888727
+
Hg19::chr15:39888784..39888798,+p@chr15:39888784..39888798
+
Hg19::chr15:39888826..39888850,+p@chr15:39888826..39888850
+
Hg19::chr15:39888934..39888945,+p@chr15:39888934..39888945
+
Hg19::chr15:39889064..39889095,+p@chr15:39889064..39889095
+
Hg19::chr15:39889119..39889166,+p@chr15:39889119..39889166
+
Hg19::chr15:39889167..39889181,+p@chr15:39889167..39889181
+
Hg19::chr15:39889186..39889187,+p@chr15:39889186..39889187
+
Hg19::chr15:39889193..39889209,+p@chr15:39889193..39889209
+
Hg19::chr15:39889224..39889239,+p@chr15:39889224..39889239
+
Hg19::chr15:39889243..39889260,+p@chr15:39889243..39889260
+
Hg19::chr15:39889273..39889278,+p@chr15:39889273..39889278
+
Hg19::chr15:39889279..39889395,+p2@BC015134
Hg19::chr15:39889397..39889411,+p4@BC015134
Hg19::chr15:39889413..39889446,+p3@BC015134


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:0008201heparin binding0.0154244672082892
GO:0007596blood coagulation0.0154244672082892
GO:0050817coagulation0.0154244672082892
GO:0007599hemostasis0.0154244672082892
GO:0005539glycosaminoglycan binding0.0154244672082892
GO:0030247polysaccharide binding0.0154244672082892
GO:0050878regulation of body fluid levels0.0154244672082892
GO:0001871pattern binding0.0154244672082892
GO:0042060wound healing0.0154244672082892
GO:0004866endopeptidase inhibitor activity0.0256253813300793
GO:0030414protease inhibitor activity0.0256253813300793
GO:0051674localization of cell0.0298834334157541
GO:0006928cell motility0.0298834334157541
GO:0004857enzyme inhibitor activity0.0298834334157541
GO:0009611response to wounding0.0298834334157541
GO:0030246carbohydrate binding0.0316584245849523
GO:0009605response to external stimulus0.039458100442579
GO:0007399nervous system development0.042152360767691
GO:0065008regulation of biological quality0.0484432557904829
GO:0022610biological adhesion0.0484432557904829
GO:0007155cell adhesion0.0484432557904829



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>


Uber Anatomy
Ontology termp-valuen
vessel1.40e-1668
splanchnic layer of lateral plate mesoderm9.17e-1683
epithelial tube open at both ends3.82e-1559
blood vessel3.82e-1559
blood vasculature3.82e-1559
vascular cord3.82e-1559
vasculature8.32e-1578
vascular system8.32e-1578
artery2.12e-1242
arterial blood vessel2.12e-1242
arterial system2.12e-1242
epithelial tube2.91e-11117
simple squamous epithelium3.72e-1122
blood vessel endothelium6.47e-1118
endothelium6.47e-1118
cardiovascular system endothelium6.47e-1118
circulatory system2.88e-10112
cardiovascular system3.62e-10109
squamous epithelium1.12e-0925
systemic artery4.60e-0933
systemic arterial system4.60e-0933
aorta1.24e-0821
aortic system1.24e-0821
organ component layer1.52e-0866
mesoderm5.03e-08315
mesoderm-derived structure5.03e-08315
presumptive mesoderm5.03e-08315
anatomical system5.05e-08624
unilaminar epithelium6.02e-08148
anatomical group6.62e-08625
multi-cellular organism1.42e-07656
endothelial tube2.17e-079
arterial system endothelium2.17e-079
endothelium of artery2.17e-079
lateral plate mesoderm3.34e-07203


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
ESR1#2099811.18858301678342.63298906687883e-071.35728896917946e-05
GATA3#26251214.85628164938512.7254465311872e-123.64926808039308e-10
POLR2A#5430212.04984166853271.30673372631837e-065.18715179182685e-05



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.