Personal tools

Coexpression cluster:C1453: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 6: Line 6:
|ontology_enrichment_disease=DOID:3119!2.90e-07!14
|ontology_enrichment_disease=DOID:3119!2.90e-07!14
|ontology_enrichment_uberon=UBERON:0007023!4.92e-15!115;UBERON:0001049!5.45e-12!57;UBERON:0005068!5.45e-12!57;UBERON:0006241!5.45e-12!57;UBERON:0007135!5.45e-12!57;UBERON:0005743!1.06e-11!86;UBERON:0001017!1.11e-11!82;UBERON:0000073!1.12e-10!94;UBERON:0001016!1.12e-10!94;UBERON:0002616!2.47e-10!59;UBERON:0003080!6.84e-09!42;UBERON:0003075!1.20e-08!86;UBERON:0007284!1.20e-08!86;UBERON:0000955!1.63e-08!69;UBERON:0006238!1.63e-08!69;UBERON:0002780!5.11e-08!41;UBERON:0001890!5.11e-08!41;UBERON:0006240!5.11e-08!41;UBERON:0002346!6.02e-08!90;UBERON:0001869!3.44e-07!32;UBERON:0001950!5.39e-07!20;UBERON:0002020!8.98e-07!34;UBERON:0003528!8.98e-07!34
|ontology_enrichment_uberon=UBERON:0007023!4.92e-15!115;UBERON:0001049!5.45e-12!57;UBERON:0005068!5.45e-12!57;UBERON:0006241!5.45e-12!57;UBERON:0007135!5.45e-12!57;UBERON:0005743!1.06e-11!86;UBERON:0001017!1.11e-11!82;UBERON:0000073!1.12e-10!94;UBERON:0001016!1.12e-10!94;UBERON:0002616!2.47e-10!59;UBERON:0003080!6.84e-09!42;UBERON:0003075!1.20e-08!86;UBERON:0007284!1.20e-08!86;UBERON:0000955!1.63e-08!69;UBERON:0006238!1.63e-08!69;UBERON:0002780!5.11e-08!41;UBERON:0001890!5.11e-08!41;UBERON:0006240!5.11e-08!41;UBERON:0002346!6.02e-08!90;UBERON:0001869!3.44e-07!32;UBERON:0001950!5.39e-07!20;UBERON:0002020!8.98e-07!34;UBERON:0003528!8.98e-07!34
|tfbs_overrepresentation=0.272825,0.113895,0.919872,0.093154,0.359621,0.492787,0.0841651,0.657264,0.0643695,0.0507505,0.259407,0.399944,0.341907,0.236085,0.275252,0.119969,0.262088,0.18676,0.102909,0.204438,0.341686,0.247578,0.157234,0.180791,0.0814159,0.384547,0.37494,0.173212,0.0392706,0.178021,0.3679,0.215086,0.0357376,0.373119,0.128625,0.161809,0.902769,0.0840902,0.226218,0.128959,0.183651,0.0486174,0.260466,0.334176,0.227213,0.0711697,0.074588,0.330075,0.210181,0.227712,0.284405,0.105423,0.135407,0.177342,0.358057,0.0753565,0.203364,0.380173,0.150513,0.199999,0.0579941,0.276509,0.205409,0.146128,0.10616,0.0984283,0.580456,0.116417,0.164736,0.3062,0.61426,0.130776,0.170145,0.224513,0.0148962,0.0339424,0.183676,0.0854797,0.0731115,0.0144524,0.182113,0.402334,0.0831938,0.216503,0.497782,0.440248,0.00809903,0.37437,0.847037,0.121557,0.164159,0.0967167,0.181667,0.0925031,0.163486,0.216824,0.827684,0.28366,0.17689,0.473112,0.111667,0.137451,0.263619,0.0727591,0.390176,0.080182,0.12949,0.561883,0.267635,0.466115,0.331856,0.0668385,0.276738,0.0350582,0.192196,0.0663658,0.0402636,0.1101,0.258716,0.160649,0.305628,0.383317,0.260612,0.0142872,0.194257,0.322526,0.173151,0.0293679,0.161604,0.251658,0.115605,0.144069,0.111159,0.045053,0.235761,0.204515,0.125521,0.10761,0.0649881,0.00789487,0.0450332,0.0311348,0.366262,0.28766,0.273522,0.133829,0.18788,0.161361,0.0763672,0.227065,0.361034,0.266711,0.328768,0.0524571,0.0835935,0.221281,0.14393,0.40461,0.100724,0.0663128,0.403582,0.181487,0.219679,0.273735,0.472167,0.215506,0.0784618,0.238515,0.0790799,0.526782,0.327089,0.256483,0.712672,0.10534,0.153476,0.172044,0.260974,0.330576,0.325054,0.069998,0.292457,0.229948,0.0540612,0.21779,0.142014,0.0270952,0.332561,0.0787371,0.158872,0.317,0.20281,0.339514,0.230757,0.405269,0.212647,0.0919303,0.150381,0.116937,0.130723,0.207318,0.170629,0.117148,0.0607132,0.117534,0.254283,0.451528,0.472314,0.280641,0.370039,0.324906,0.0896296,0.197823,0.22763,0.213053,0.527451,0.309534,0.301442,0.191696,0.122022,0.195373,0.263715,0.606181,0.287766,0.296123,0.142265,0.237192,0.258424,0.164555,0.117251,0.116204,0.814864,0.253782,0.0819301,0.147153,0.18264,0.177704,0.092224,0.45696,0.30027,0.383466,0.331647,0.57619,0.187116,0.15928,0.219044,0.254951,0.156377,0.21083,0.606625,0.220359,0.292806,0.336043,0.336985,0.186448,0.186558,0.293852,0.202983,0.362971,0.134325,0.521047,0.120009,0.319541,0.300061,0.239783,0.0678354,0.155564,0.15574,0.175654,0.222213,0.145331,0.479224,0.122578,0.444637,0.693924,0.165683,0.0746442,0.243403,0.827706,0.455691,0.194104,0.599514,0.231172,0.673858,0.418125,0.558337,0.319502,0.454695,0.693419,0.240636,0.522841,0.391592,0.552041,0.635008,0.191087,0.783515,0.569904,0.469955,0.152702,0.0879932,0.26889,0.825036,0.54264,0.0655271,0.593966,0.33041,0.6682,0.207878,0.552298,0.388991,0.671702,0.611777,0.711836,0.875797,0.191888,0.432462,0.604085,0.658531,0.734265,0.442844,0.138021,0.512499,0.146287,0.17768,0.397052,0.407902,0.842556,0.486953,0.530428,0.821632,0.498324,0.695401,0.512667,0.293093,0.499918,0.371535,0.685903,0.607959,0.249045,0.847056,0.331481,0.702368,0.857981,0.519866,0.474883,0.417024,0.336852,0.572701,0.78433,0.468536,0.860083,0.753048,0.76366,0.771595,0.112682,0.483867,0.0410066,0.29984,0.129605,0.140844,0.335439,0.837308,0.781913,0.520224,0.65524,0.651648,0.0764901,0.798903,0.69534,0.38945,0.527767,0.90708,0.0881806,0.143918,0.0963729,0.877625,0.531159,0.752145,0.155199,0.206047,0.726789,0.494769,0.547216,0.668888,0.47878,0.962938,0.673583,0.404165,0.198375,0.356202,0.288188,0.812902,0.0984804,0.73237,0.664325,0.766191,0.901955,0.557914,0.268648,0.269896,0.622411,0.610862,0.332296,0.708323,0.440842,0.282051,0.0909735,0.2554,0.451268,0.251408,0.187452,0.211561,0.501137,0.488193,0.569315,0.167061,0.518055,0.841145,0.753073,0.435461,0.030583,0.456149,0.589702,0.0941811,0.647111,0.660192,0.595103,0.713637,0.308376,0.369917,0.774751,0.878565,0.683229,0.46597,0.563445,0.799582,0.142358,0.263421,0.703388,0.770075,0.293756,0.42025,0.605969,0.0989935,0.343113,0.0154082,0.115576,0.438442,0.313394,0.57398,0.0721289,0.577344,0.724447,0.645462,0.151595,0.863295,0.176949,0.134669,0.108266,0.348016,0.149912,0.111821,0.267815,0.396879,0.365836,0.689622,0.68834,0.346776,0.211334,0.494962,0.0851816,0.163804,0.23696,0.251518,0.202355,0.471945,0.121642,0.617317,0.0354999,0.515499,0.481305,0.628382,0.0908048,0.310441,0.0252256,0.198185,0.0156868,0.165877,0.0482532,0.202749,0.0858038,0.00776602,0.23191,0.241631,0.376483,0.349839,0.572771,0.0974547,0.15892,0.128942,0.331179,0.210172,0.390637,0.554857,0.352924,0.246924,0.341783,0.0940377,0.359953,0.64718,0.239194,0.32067,0.334938,0.309827,0.167604,0.181395,0.0223847,0.395388,0.202628,0.474729,0.00960329,0.317242,0.262323,0.378417,0.0592343,0.245796,0.0870651,0.101982,0.374106,0.282907,0.153213,0.185351,0.29465,0.231794,0.173078,0.108497,0.485366,0.767403,0.255803,0.0289867,0.127078,0.0829767,0.0896897,0.153874,0.145835,0.297422,0.349099,0.106792,0.149864,0.109211,0.081783,0.0678906,0.076236,0.444489,0.31161,0.361651,0.0953991,0.319245,0.236827,0.0650516,0.575882,0.390908,0.0773818,0.115736,0.662745,0.229952,0.205891,0.207936,0.454529,0.0563868,0.796918,0.268235,0.0761868,0.167255,0.107028,0.267379,0.443026,0.387018,0.343977,0.244992,0.632847,0.417985,0.491614,0.146453,0.315229,0.157053,0.332022,0.557852,0.273582,0.262915,0.306556,0.26147,0.170005,0.523331,0.491788,0.092369,0.18076,0.692556,0.248113,0.148878,0.206465,0.240599,0.245625,0.205821,0.696152,0.100989,0.188919,0.0975693,0.119835,0.145322,0.178533,0.267392,0.0668831,0.142859,0.477403,0.504405,0.881177,0.387334,0.494914,0.224219,0.347904,0.324262,0.795569,0.111827,0.0929171,0.63152,0.118035,0.319902,0.510835,0.137556,0.397628,0.49748,0.0699003,0.235435,0.31953,0.954017,0.799035,0.370285,0.0878758,0.204831,0.130161,0.205669,0.0963721,0.182511,0.369139,0.145449,0.0892237,0.208284,0.135613,0.401189,0.283386,0.0739625,0.247651,0.0879809,0.104922,0.215434,0.177269,0.31512,0.198881,0.394164,0.111068,0.4137,0.146194,0.491435,0.281527,0.35188,0.3889,0.192889,0.547162,0.316041,0.565635,0.280212,0.121421,0.346061,0.275075,0.754571,0.287361,0.138613,0.175356,0.116846,0.267784,0.278571,0.185281,0.286026,0.31159,0.349805,0.255609,0.0956849,0.439697,0.493192,0.223892,0.160738,0.193111,0.213489,0.212611,0.338443,0.319005,0.180695,0.45842,0.436073,0.261316,0.189596,0.448839,0.196587,0.213353,0.0504588,0.307626,0.173101,0.525576,0.306056,0.341713,0.156156,0.33569,0.288104,0.526446,0.761719,0.114697,0.433479,0.324956,0.388835,0.408751,0.648685,0.855529,0.070868,0.654476,0.245,0.0850317,0.249379,0.661446,0.60218,0.696439,0.648789,0.409327,0.792771,0.685907,0.603176,0.670776,0.696176,0.355968,0.636386,0.592254,0.0881515,0.616927,0.82397,0.340734,0.677416,0.922804,0.628346,0.737948,0.750579,0.326884,0.772379,0.405032,0.91547,0.402631,0.768239,0.853963,0.623606,0.488239,0.754734,0.476894,0.926642,0.149698,0.301433,0.711296,0.148546,0.819065,0.373476,0.198334,0.717449,0.449761,0.6937,0.427531,0.801496,0.26122,0.929695,0.899649,0.297082,0.765839,0.8738,0.746016,0.622334,0.607585,0.811787,0.37236,0.810134,0.935968,0.567049,0.36546,0.360788,0.368898,0.510705,0.447298,0.10163,0.0562917,0.619669,0.287839,0.262665,0.654187,0.0178814,0.175142,0.583703,0.300816,0.407994,0.225997,0.145043,0.0267168,0.529993,0.329919,0.484887,0.805032,0.852842,0.282589,0.766238,0.540605,0.881739,0.563634,0.561918,0.624569,0.185857,0.628517,0.455987,0.0908572,0.659669,0.659285,0.711322,0.929537,0.823122,0.367684,0.339006,0.258457,0.893393,0.305952,0.356524,0.159817,0.177234,0.730276,0.319704,0.555004,0.607569,0.773067,0.0899962,0.597394,0.198803,0.628973,0.594475,0.416321,0.365565,0.47205,0.610358,0.693748,0.214684,0.474879,0.868553,0.518205,0.424119,0.60488,0.519279,0.515179,0.745866,0.623664,0.757999,0.438945,0.619652,0.125881,0.754688,0.39196,0.758981,0.0101665,0.346355,0.354044,0.841498,0.520214,0.708106,0.486574,0.809543,0.366382,0.639482,0.471879,0.600697,0.474504,0.253554,0.727464,0.589415,0.564042,0.356483,0.846483,0.624316,0.55481,0.443148,0.509842,0.866311,0.368631,0.321667,0.149733,0.477082,0.368449,0.066291,0.343349,0.0230279,0.341084,0.138667,0.127016,0.298707,0.345583,0.299527,0.390707,0.372757,0.172033,0.181635,0.304651,0.440771,0.246146,0.445744,0.371991,0.694395,0.326635,0.349721,0.39301,0.091593,0.566617,0.524829,0.388491,0.357781,0.338712,0.231439,0.359148,0.0641227,0.177916,0.232711,0.327419,0.402268,0.479755,0.163801,0.245045,0.373321,0.433875,0.395243,0.130132,0.373481,0.462042,0.213394,0.270174,0.406219,0.298,0.40549,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.465261,0.362561,0.213995,0.285875,0.225945,0.18761,0.20516,0.00695219,0.385234,0.291842,0.392097,0.352327,0.232997,0.451856,0.521039,0.328594,0.294205,0.448388,0.278746,0.387086,0.232479,0.334662,0.0642414,0.139427,0.450171,0.454978,0.366035,0.381922,0.372037,0.263608,0.3488,0.43615,0.218495,0.398705,0.431643,0.316114,0.360691,0.26003,0.35537,0.423126,0.288449,0.244977,0.447896,0.395958,0.314638,0.322324,0.184473,0.363414,0.524458,0.482957,0.388728,0.157712,0.3633,0.202084,0.104337,0.104656,0.279419,0.0118501,0.0797883,0.104584,0.180857,0.454949,0.378002,0.340219,0.412672,0.343186,0.155969,0.186603,0.124175,0.0284786,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,0.36701,0.504058,0.147397,0.210178,0.263371,0.457065,0.446399,0.360168,0.403229,0.507716,0.442751,0.323763,0.486842,0.458912,0.246162,0.295506,0.369944,0.358783,0.491474,0.417013,0.544575,0.21822,0.388558,0.397562,0.21727,0.351946,0.345508,0.142644,0.486223,0.437432,0.302171,0.0925994,0.178399,0.189006,0.400541,0.372405,0.182559,0.164471,0.533328,0.313891,0.292462,0.132855,0.137165,0.132237,0.191837,0.395568,0.320916,0.289812,0.0859703,0.441686,0.369492,0.226443
}}
}}

Revision as of 17:18, 8 August 2012


Full id: C1453_argyrophil_hepatocellular_Intestinal_small_liver_hepatoblastoma_gastrointestinal



Phase1 CAGE Peaks

Hg19::chr19:36611472..36611485,+p@chr19:36611472..36611485
+
Hg19::chr1:117008831..117008843,+p@chr1:117008831..117008843
+
Hg19::chr1:117008851..117008867,+p@chr1:117008851..117008867
+
Hg19::chr1:21996297..21996310,-p9@RAP1GAP
Hg19::chr1:235814345..235814362,-p9@GNG4
Hg19::chr9:139693833..139693853,+p10@KIAA1984


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:0009966regulation of signal transduction0.0232625119888189
GO:0008277regulation of G-protein coupled receptor protein signaling pathway0.0304795437772065
GO:0005834heterotrimeric G-protein complex0.0304795437772065
GO:0019897extrinsic to plasma membrane0.0308855156143789



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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism4.92e-15115
neural tube5.45e-1257
neural rod5.45e-1257
future spinal cord5.45e-1257
neural keel5.45e-1257
central nervous system1.11e-1182
regional part of nervous system1.12e-1094
nervous system1.12e-1094
regional part of brain2.47e-1059
anterior neural tube6.84e-0942
neural plate1.20e-0886
presumptive neural plate1.20e-0886
brain1.63e-0869
future brain1.63e-0869
regional part of forebrain5.11e-0841
forebrain5.11e-0841
future forebrain5.11e-0841
neurectoderm6.02e-0890
cerebral hemisphere3.44e-0732
neocortex5.39e-0720
gray matter8.98e-0734
brain grey matter8.98e-0734
Disease
Ontology termp-valuen
gastrointestinal system cancer2.90e-0714


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


No analysis results for this cluster

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.