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Coexpression cluster:C201: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.17e-10!106;DOID:0050687!5.85e-07!143
|ontology_enrichment_disease=DOID:305!1.17e-10!106;DOID:0050687!5.85e-07!143
|ontology_enrichment_uberon=UBERON:0007023!3.23e-26!115;UBERON:0004921!9.25e-13!129;UBERON:0004185!9.25e-13!129;UBERON:0001007!2.03e-10!155;UBERON:0001555!2.03e-10!155;UBERON:0007026!2.03e-10!155;UBERON:0004119!1.47e-09!169;UBERON:0000925!1.47e-09!169;UBERON:0006595!1.47e-09!169;UBERON:0000077!5.49e-09!130;UBERON:0001041!7.15e-08!98
|ontology_enrichment_uberon=UBERON:0007023!3.23e-26!115;UBERON:0004921!9.25e-13!129;UBERON:0004185!9.25e-13!129;UBERON:0001007!2.03e-10!155;UBERON:0001555!2.03e-10!155;UBERON:0007026!2.03e-10!155;UBERON:0004119!1.47e-09!169;UBERON:0000925!1.47e-09!169;UBERON:0006595!1.47e-09!169;UBERON:0000077!5.49e-09!130;UBERON:0001041!7.15e-08!98
|tf_chipseq_enrich=SUZ12#23512;12:7.42456013497228:7.74623847680728e-08:4.65482969090492e-06
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766,0.0970367,0.809955,0.955697,0.279774,0.816998,0.821763,0.910346,0.185299,0.999725,0.923024,0.656927,0.706675,0.451567,0.922036,0.533095,0.895316,0.92274,0.525259,0.981052,0.736771,0.994399,0.630007,0.750352,0.405681,0.995692,0.998807,0.625537,0.589274,0.726759,0.229371,0.245748,0.997236,0.562327,0.729744,0.932228,0.989527,0.896776,0.63959,0.603575,0.885214,0.89306,0.999078,0.978971,0.76241,0.536895,0.403309,0.513932,0.625479,0.495277,0.604679,0.607232,0.61549,0.974886,0.0911515,0.998178,0.895766,0.812603,0.665523,0.978917,0.968322,0.999163,0.475378,0.731939,1.71007e-27,0.816517,0.965926,0.111588,0.593398,0.812187,0.900799,0.624034,0.876656,0.965714,0.999972,1,0.869246,0.961372,0.954689,0.847796,0.600663,0.745399,0.934158,0.94712,0.625989,0.716823,0.822562,0.860183,0.992196,0.826246,0.0872976,0.896094,0.352954,0.776065,0.962199,0.127458,0.750065,0.799889,0.905159,0.795955,0.725061,0.8816,0.999891,0.988478,0.695021,0.998704,0.944589,0.999735,0.752493,0.999842,0.935766,0.825802,0.677763,0.986999,0.998451,0.942473,0.866593,0.482284,0.813151,0.922505,0.934135,0.522479,0.00261745,0.960915,0.979614,0.981408,0.970181,0.889603,0.808691,0.967345,0.90611,0.848309,0.960914,0.960322,0.916306,0.99441,0.504052,0.964947,0.652969,0.914726,0.941458,0.958816,0.34268,0.833903,0.502908,0.958307,0.725976,0.938719,0.992791,0.00547987,0.667328,0.912949,0.989823,0.142268,0.996899,0.085085,0.0254106,0.611332,0.990077,0.972405,0.999915,0.99971,0.629281,0.995625,0.730134,0.698712,0.54124,0.95451,0.69751,0.733099,0.896431,0.999181,0.999058,0.987565,0.998418,0.997205,0.996205,0.843369,0.297213,0.981028,0.986323,0.831104,0.645628,0.949804,0.0136311,0.99091,0.991535,0.947029,0.891611,0.51421,0.933355,0.986094,1,0.992415,0.97567,0.996108,0.976864,0.886933,0.981422,0.998164,0.997959,0.440486,0.356475,0.783692,0.213467,0.616924,0.890981,0.985564,0.634197,0.986926,0.956125,0.980209,0.999942,0.780231,0.999971,0.997706,0.699497,0.998728,0.892123,0.484591,0.99987,0.99512,0.999835,0.012664,0.542857,1,0.987285,0.860903,0.939858,0.428008,0.111353,0.957752,0.962293,0.720706,0.94738,0.989772,0.778077,0.767207,0.513553,0.93987,0.634786,0.86036,0.177421,0.859652,0.993912,0.0201638,0.974187,0.905559,0.88158,0.996946,0.0994294,0.998412,0.324631,0.992857,0.585699,0.966629,0.998911,0.767193,0.960351,0.998498,0.998752,0.00431394,0.783668,0.998787,0.510265,0.999623,0.559426,0.584015,0.746212,0.378351,0.967574,0.725068,0.708432,0.90471,0.451003,0.840915,0.965814,0.9609,0.998593,0.844613,0.987369,0.781397,0.918255,0.997168,0.671836,0.589477,0.0105543,0.859437,0.969608,0.530791,0.728108,0.992053,0.999986,0.988536,0.995087,0.994788,0.654467,0.388669,0.880856,0.344728,0.634822,0.78996,0.902508,0.9836,0.964843,0.661624,0.723833,0.934506,0.678648,0.0578791,0.998469,0.99703,0.773225,0.97877,0.987542,0.99547,0.983664,0.756264,0.994236,0.973541,0.657678,0.996149,0.846104,0.564674,0.546402,0.989256,0.990684,0.984112,0.797062,0.999299,0.974434,0.285145,0.966915,0.888058,0.646326,0.174558,0.0147808,0.817682,0.960072,0.812777,0.866707,0.916727,0.112397,0.822431,0.858027,0.96258,0.986557,0.921805,0.933198,0.721401,0.952998,0.82306,0.898447,0.986364,0.873193,0.616821,0.0714511,0.903619,0.521871,0.932464,0.971589,0.897406,0.712007,0.655289,0.474906,0.256973,0.591252,0.928982,0.871933,0.0465789,0.969164,0.654805,0.69481,0.892178,0.443176,0.982375,0.671608,0.847728,0.986736,0.967059,0.628459,0.420232,0.83034,0.951334,0.992833,0.557785,0.286263,0.281835,0.764836,0.716003,0.923425,0.72538,0.820672,0.989384,0.968492,0.939491,0.815271,0.80949,0.484146,0.683766,0.902389,0.99716,0.693887,0.819197,0.660136,0.970556,0.990939,0.902144,0.987861,0.788226,0.692257,0.973452,0.64782,0.601283,0.6957,0.98818,0.861917,0.887833,0.438769,0.591677,0.829117,0.653209,0.425886,0.967248,0.876967,0.581932,0.852282,0.913103,0.93472,0.464612,0.673341,0.977486,0.688971,0.0852913,0.962822,0.428282,0.936259,0.942225,0.971394,0.977303,0.998699,0.408476,0.997745,0.807857,0.438009,0.775164,0.644705,0.643755,0.67455,0.774919,0.992357,0.573616,0.617749,0.810881,0.722209,0.66906,0.401082,0.76691,0.534168,0.97011,0.831702,0.348999,0.843226,0.882526,0.316814,0.00488947,0.70419,0.84604,0.920722,0.636078,0.901975,0.171191,0.909891,0.804081,0.996657,0.590856,0.997573,0.684507,0.983067,0.916604,0.914675,0.954484,0.772271,0.79384,0.834019,0.335033,0.85056,0.868667,0.554198,0.804738,0.931911,0.998336,0.645262,0.961234,0.998931,0.84226,0.931292,0.924446,0.993432,0.883734,0.65719,0.71433,0.528653,0.742637,0.955631,0.818479,0.872792,0.755176,0.697139,0.887039,0.7468,0.844712,0.970802,0.591738,0.238798,0.781451,0.244825,0.966497,0.677552,0.958836,0.796396,0.8679,0.956913
}}
}}

Revision as of 14:05, 5 September 2012


Full id: C201_colon_small_adenocarcinoma_duodenum_temporal_signet_gall



Phase1 CAGE Peaks

Hg19::chr11:1074870..1074883,+p1@MUC2
Hg19::chr11:1088694..1088705,+p@chr11:1088694..1088705
+
Hg19::chr11:1088789..1088796,+p@chr11:1088789..1088796
+
Hg19::chr11:1092201..1092208,+p@chr11:1092201..1092208
+
Hg19::chr11:1092226..1092243,+p@chr11:1092226..1092243
+
Hg19::chr11:1092262..1092271,+p@chr11:1092262..1092271
+
Hg19::chr11:1092292..1092322,+p6@MUC2
Hg19::chr11:1092326..1092337,+p12@MUC2
Hg19::chr11:1092353..1092368,+p9@MUC2
Hg19::chr11:1092380..1092383,+p19@MUC2
Hg19::chr11:1092389..1092394,+p14@MUC2
Hg19::chr11:1092424..1092439,-p@chr11:1092424..1092439
-
Hg19::chr11:1092657..1092728,+p2@MUC2
Hg19::chr11:1092822..1092856,+p7@MUC2
Hg19::chr11:1093018..1093037,+p5@MUC2
Hg19::chr11:1093152..1093171,+p11@MUC2
Hg19::chr11:1093183..1093189,+p13@MUC2
Hg19::chr11:1093323..1093345,+p3@MUC2
Hg19::chr11:1093354..1093373,-p@chr11:1093354..1093373
-
Hg19::chr11:1093438..1093450,+p10@MUC2
Hg19::chr11:1093458..1093487,+p8@MUC2
Hg19::chr11:1093499..1093543,+p4@MUC2
Hg19::chr11:1093649..1093652,+p20@MUC2
Hg19::chr11:1093831..1093850,+p15@MUC2
Hg19::chr11:114430570..114430581,-p2@FAM55A
Hg19::chr11:114466397..114466426,-p2@FAM55D
Hg19::chr11:2448612..2448615,-p@chr11:2448612..2448615
-
Hg19::chr11:60260248..60260251,+p1@MS4A12
Hg19::chr11:6251405..6251412,-p@chr11:6251405..6251412
-
Hg19::chr11:64660916..64660922,-p1@ENST00000413053
p1@uc009ypx.2
Hg19::chr11:69294647..69294668,-p1@ENST00000542064
Hg19::chr12:12223888..12223897,+p6@BCL2L14
Hg19::chr12:3842242..3842262,-p9@EFCAB4B
Hg19::chr13:28552810..28552817,-p@chr13:28552810..28552817
-
Hg19::chr13:28552848..28552849,-p@chr13:28552848..28552849
-
Hg19::chr15:45734062..45734081,-p1@ENST00000559553
Hg19::chr15:78384901..78384904,+p3@SH2D7
Hg19::chr16:1275258..1275289,-p1@TPSG1
Hg19::chr16:2034649..2034664,+p11@GFER
Hg19::chr16:23765964..23765976,+p4@CHP2
Hg19::chr16:23766398..23766403,+p6@CHP2
Hg19::chr16:27344604..27344606,+p@chr16:27344604..27344606
+
Hg19::chr16:29748234..29748245,-p@chr16:29748234..29748245
-
Hg19::chr16:66878311..66878325,+p1@CA7
Hg19::chr16:67463701..67463709,+p@chr16:67463701..67463709
+
Hg19::chr16:67493110..67493128,-p6@ATP6V0D1
Hg19::chr17:1013514..1013520,-p@chr17:1013514..1013520
-
Hg19::chr17:74639830..74639844,-p2@ST6GALNAC1
Hg19::chr18:8974567..8974578,+p@chr18:8974567..8974578
+
Hg19::chr18:8974610..8974620,+p@chr18:8974610..8974620
+
Hg19::chr19:39303576..39303591,-p1@LGALS4
Hg19::chr1:160851193..160851215,-p3@ITLN1
Hg19::chr1:19614537..19614565,+p@chr1:19614537..19614565
+
Hg19::chr1:38201159..38201166,-p@chr1:38201159..38201166
-
Hg19::chr1:86934584..86934598,+p2@CLCA1
Hg19::chr22:43567750..43567759,-p6@TTLL12
Hg19::chr2:200329672..200329678,-p50@SATB2
Hg19::chr2:200333534..200333558,+p1@ENST00000446911
Hg19::chr2:242716231..242716254,+p1@GAL3ST2
Hg19::chr2:85108164..85108218,-p1@C2orf89
Hg19::chr3:108476254..108476257,-p1@RETNLB
Hg19::chr3:112123245..112123271,-p@chr3:112123245..112123271
-
Hg19::chr4:2038275..2038288,+p@chr4:2038275..2038288
+
Hg19::chr4:2038291..2038303,+p@chr4:2038291..2038303
+
Hg19::chr5:149546334..149546364,+p1@CDX1
Hg19::chr5:179394236..179394243,-p@chr5:179394236..179394243
-
Hg19::chr6:168479679..168479688,-p6@FRMD1
Hg19::chr6:168479694..168479708,-p3@FRMD1
Hg19::chr6:31836976..31837017,-p2@SLC44A4
Hg19::chr6:36178216..36178249,+p15@BRPF3
Hg19::chr7:100612647..100612650,+p8@MUC12
Hg19::chr7:100612686..100612700,+p3@MUC12
Hg19::chr7:107443661..107443675,-p1@SLC26A3
Hg19::chr7:129007938..129007947,+p14@AHCYL2
Hg19::chr7:129007975..129007990,+p4@AHCYL2
Hg19::chr7:75452673..75452691,-p3@CCL24
Hg19::chr8:86253920..86253944,-p2@CA1
Hg19::chr9:124926856..124926884,+p2@MORN5
Hg19::chr9:33240157..33240173,+p1@SPINK4
Hg19::chrX:100129320..100129329,-p3@NOX1
Hg19::chrX:100129340..100129353,-p2@NOX1


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

Uber Anatomy
Ontology termp-valuen
adult organism3.23e-26115
subdivision of digestive tract9.25e-13129
endodermal part of digestive tract9.25e-13129
digestive system2.03e-10155
digestive tract2.03e-10155
primitive gut2.03e-10155
endoderm-derived structure1.47e-09169
endoderm1.47e-09169
presumptive endoderm1.47e-09169
mixed endoderm/mesoderm-derived structure5.49e-09130
foregut7.15e-0898
Disease
Ontology termp-valuen
carcinoma1.17e-10106
cell type cancer5.85e-07143


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
SUZ12#23512127.424560134972287.74623847680728e-084.65482969090492e-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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