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Coexpression cluster:C419: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0006955!immune response!0.00762103817707793!913;51561;27240$GO:0002376!immune system process!0.00762103817707793!913;51561;27240$GO:0044459!plasma membrane part!0.0223191625900676!913;55679;27240$GO:0042169!SH2 domain binding!0.0307081295662209!27240
|gostat_on_coexpression_clusters=GO:0006955!immune response!0.00762103817707793!913;51561;27240$GO:0002376!immune system process!0.00762103817707793!913;51561;27240$GO:0044459!plasma membrane part!0.0223191625900676!913;55679;27240$GO:0042169!SH2 domain binding!0.0307081295662209!27240
|id=C419
|id=C419
|ontology_enrichment_celltype=CL:0000542!1.02e-36!53;CL:0000051!1.02e-36!53;CL:0000838!6.50e-36!52;CL:0000738!1.64e-20!140;CL:0000988!7.79e-20!182;CL:0002087!1.60e-19!119;CL:0000084!4.99e-19!25;CL:0000827!4.99e-19!25;CL:0000037!1.34e-18!172;CL:0000566!1.34e-18!172;CL:0002031!1.37e-17!124;CL:0000945!3.93e-16!24;CL:0000826!3.93e-16!24;CL:0002032!1.43e-15!165;CL:0000837!1.43e-15!165;CL:0000791!1.89e-14!18;CL:0000789!1.89e-14!18;CL:0002420!1.89e-14!18;CL:0002419!1.89e-14!18;CL:0000790!1.89e-14!18;CL:0000625!1.30e-09!11;CL:0000236!1.44e-09!14
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000178!2.26e-09!15;UBERON:0000179!2.26e-09!15;UBERON:0000463!2.26e-09!15
|ontology_enrichment_uberon=UBERON:0002370!8.36e-34!4;UBERON:0005058!8.36e-34!4;UBERON:0009113!8.36e-34!4;UBERON:0003295!8.36e-34!4;UBERON:0005562!8.36e-34!4;UBERON:0003351!6.07e-23!6;UBERON:0004177!7.84e-20!7;UBERON:0005057!7.84e-20!7;UBERON:0000974!3.25e-14!10;UBERON:0003408!3.25e-14!10;UBERON:0001042!3.25e-14!10;UBERON:0009145!3.25e-14!10;UBERON:0006562!5.10e-13!11;UBERON:0009722!5.10e-13!11;UBERON:0007690!5.10e-13!11;UBERON:0008814!2.42e-08!18;UBERON:0001557!5.94e-08!19
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9,0.235899,0.856634,0.589412,0.275417,0.388597,0.808549,0.280868,0.602333,0.239412,0.436659,0.207178,0.952873,0.713261,0.271656,0.519108,0.364154,0.353396,0.67848,0.858815,0.814785,0.104486,0.909,0.885254,0.933201,0.469226,0.780122,0.495105,0.220266,0.83702,0.721551,0.344663,0.430169,0.70251,0.525428,0.795369,0.752683,0.321363,0.549551,0.991066,0.680398,0.136862,0.603481,0.66743,0.676146,0.99511,0.950862,0.346779,0.567231,0.336783,0.399855,0.466407,0.544633,0.35342,0.241869,0.460229,0.731799,0.956935,0.745998,0.312428,0.934918,0.637792,0.81918,0.791496,0.951948,0.377715,0.323001,0.565254,0.394929,0.456156,0.161823,0.119255,0.601392,0.760707,0.251627,0.65829,0.785594,0.998822,0.999997,0.842756,0.585585,0.600204,0.427526,0.235218,0.333257,0.553392,0.54974,0.466724,0.311908,0.607103,0.441745,0.871424,0.736281,0.264616,0.679611,0.308144,0.358135,0.621105,0.541825,0.779982,0.588104,0.865283,0.375583,0.881838,0.468581,0.933106,0.733534,0.51746,0.86054,0.575642,0.957949,0.781163,0.845668,0.731578,0.404168,0.817127,0.368474,0.996372,0.742084,0.449454,0.537548,0.391661,0.712554,0.375332,0.198288,0.740147,0.775411,0.82128,0.692953,0.342712,0.408493,0.754676,0.269337,0.503875,0.960091,0.617334,0.615623,0.808455,0.200445,0.549408,0.91397,0.66714,0.702262,0.568673,0.907719,0.583365,0.61707,0.187066,0.770193,0.532469,0.408073,0.181542,0.498153,0.492953,0.805247,0.743159,0.799346,0.678232,0.385717,0.662864,0.792351,0.860481,0.350929,0.984767,0.983148,0.254737,0.613929,0.675072,0.299151,0.318291,0.435795,0.503134,0.518028,0.0629515,0.621918,0.600579,0.945183,0.714067,0.936043,0.950875,0.82796,0.768652,0.154294,0.919935,0.534282,0.82225,0.210457,0.940166,0.975066,0.905384,0.970023,0.804396,0.846104,0.934379,0.999158,0.999706,0.610222,0.235398,0.881562,0.200733,0.931409,0.491809,0.619611,0.99258,0.756634,0.420154,0.378672,0.289457,0.377232,0.594439,0.962338,0.245988,0.0350507,0.94954,0.652967,0.954616,0.905985,0.980515,0.895721,0.411636,0.986148,0.915293,0.639661,0.988113,0.721563,0.961278,0.592322,0.779087,0.962334,0.90266,0.274584,0.10712,0.549294,0.161652,0.0923583,0.161401,0.967819,0.898166,0.393515,0.70443,0.924957,0.55457,0.357277,0.27558,0.761017,0.160782,0.641103,0.500302,0.490986,0.0859505,0.798392,0.929594,0.981052,0.644023,0.246788,0.230809,0.601295,0.241008,0.643994,0.942362,0.550492,0.144141,0.999967,0.736579,0.0168762,0.265224,0.803501,0.554186,0.993418,0.261723,0.278355,0.211729,0.697625,0.670738,0.181394,0.00945798,0.501695,0.952341,0.600801,0.785813,0.406097,0.51449,0.246768,0.605639,0.30107,0.272882,0.364505,0.87532,0.883937,0.543112,0.723807,0.326351,0.199962,0.266912,0.728045,0.997278,0.946117,0.647235,0.885097,0.337062,0.784755,0.795976,0.353409,0.921871,0.900912,0.540059,0.720396,0.811629,0.141087,0.0643224,0.827086,0.817456,0.874101,0.743803,0.562699,0.546331,0.930512,0.134347,0.580894,0.227631,0.253967,0.881224,0.474936,0.744367,0.891208,0.690231,0.119643,0.82851,0.7581,0.0462905,0.960719,0.938548,0.319675,0.903136,0.841097,0.788275,0.477338,0.731322,0.840913,0.239943,0.501272,0.90896,0.811496,0.449593,0.704777,0.758122,0.241732,0.75925,0.862182,0.119489,0.0411894,0.551473,0.426447,0.902196,0.731615,0.682862,0.844452,0.513106,0.79441,0.513375,0.864254,0.14619,0.429478,0.571485,0.137025,0.829888,0.808767,0.0902931,0.531134,0.232858,0.543265,0.653394,0.795365,0.609585,0.735272,0.511079,0.30989,0.845766,0.397524,0.597155,0.42745,0.845923,0.708553,0.61715,0.716288,0.616508,0.757144,0.875078,0.772038,0.269513,0.421365,0.348762,0.311318,0.109344,0.834897,0.670152,0.739926,0.273234,0.564431,0.600867,0.388154,0.857164,0.74851,0.0518412,0.518303,0.286689,0.431562,0.947374,0.796792,0.75185,0.907416,0.729384,0.858877,0.652975,0.804039,0.805986,0.451532,0.908608,0.911762,0.838467,0.57319,0.844498,0.346019,0.820172,0.667267,0.259141,0.869278,0.895652,0.448799,0.832951,0.700184,0.52404,0.377428,0.743656,0.675032,0.907085,0.866872,0.193978,0.460853,0.557662,0.835779,0.346765,0.739966,0.585498,0.151137,0.835662,0.594652,0.356456,0.357371,0.730393,0.47786,0.282947,0.357164,0.813105,0.697499,0.850323,0.495299,0.881006,0.81389,0.492504,0.562265,0.411605,0.646571,0.41022,0.586833,0.422486,0.469815,0.667954,0.603399,0.302951,0.425577,0.528129,0.258812,0.686493,0.27721,0.939505,0.137498,0.966954,0.705561,0.913106,0.421184,0.533045,0.873168,0.315813,0.903573,0.79088,0.279017,0.7037,0.677067,0.408547,0.551229,0.830948,0.752237,0.884486,0.608734,0.626459,0.137103,0.147797,0.62464,0.252077,0.816508,0.0525869,0.497482,0.200851,0.762864,0.602446,0.186184,0.215034,0.606542,0.844863,0.553496,0.512645,0.363635,0.444474,0.162614,0.920474,0.445744,0.919886,0.573425,0.145387,0.458123,0.745614,0.856835,0.676308,0.550393,0.291316
}}
}}

Revision as of 15:45, 19 October 2012


Full id: C419_acute_chronic_thymus_xeroderma_Burkitt_Hodgkin_CD4



Phase1 CAGE Peaks

Hg19::chr10:103666778..103666783,+p@chr10:103666778..103666783
+
Hg19::chr1:158299745..158299756,-p@chr1:158299745..158299756
-
Hg19::chr1:158300194..158300203,-p@chr1:158300194..158300203
-
Hg19::chr1:158323920..158323926,+p23@CD1E
Hg19::chr1:158323949..158323968,+p14@CD1E
Hg19::chr1:158324295..158324300,+p@chr1:158324295..158324300
+
Hg19::chr1:158326285..158326296,+p15@CD1E
Hg19::chr1:158326571..158326578,+p@chr1:158326571..158326578
+
Hg19::chr1:158326653..158326662,+p@chr1:158326653..158326662
+
Hg19::chr1:158326841..158326852,+p@chr1:158326841..158326852
+
Hg19::chr1:158327034..158327044,+p@chr1:158327034..158327044
+
Hg19::chr2:128398152..128398168,-p15@LIMS2
Hg19::chr4:145580883..145580893,+p@chr4:145580883..145580893
+
Hg19::chr4:8204368..8204371,+p@chr4:8204368..8204371
+
Hg19::chr7:142498552..142498565,+p@chr7:142498552..142498565
+
Hg19::chr7:142498640..142498656,+p@chr7:142498640..142498656
+
Hg19::chr7:142498877..142498900,+p2@AJ568018
Hg19::chr7:142498934..142498946,+p3@L34740
Hg19::chr7:142499376..142499383,+p@chr7:142499376..142499383
+
Hg19::chr8:1897606..1897618,-p@chr8:1897606..1897618
-
Hg19::chr8:1900745..1900751,+p@chr8:1900745..1900751
+
Hg19::chr9:100732599..100732614,+p@chr9:100732599..100732614
+
Hg19::chr9:35650561..35650570,-p3@SIT1
Hg19::chr9:35650572..35650659,-p2@SIT1


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:0006955immune response0.00762103817707793
GO:0002376immune system process0.00762103817707793
GO:0044459plasma membrane part0.0223191625900676
GO:0042169SH2 domain binding0.0307081295662209



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><br>

Uber Anatomy
Ontology termp-valuen
thymus8.36e-344
hemolymphoid system gland8.36e-344
thymic region8.36e-344
pharyngeal gland8.36e-344
thymus primordium8.36e-344
pharyngeal epithelium6.07e-236
hemopoietic organ7.84e-207
immune organ7.84e-207
neck3.25e-1410
gland of gut3.25e-1410
chordate pharynx3.25e-1410
pharyngeal region of foregut3.25e-1410
pharynx5.10e-1311
entire pharyngeal arch endoderm5.10e-1311
early pharyngeal endoderm5.10e-1311
pharyngeal arch system2.42e-0818
upper respiratory tract5.94e-0819


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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C419&oldid=2250494"