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Coexpression cluster:C215: Difference between revisions

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{{Coexpression_clusters
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1,0.998397,0.152443,0.536954,0.50645,0.946887,0.4521,0.951275,0.936816,0.986499,0.99911,0.231419,0.736223,0.571579,0.999917,0.967884,0.819724,0.998297,0.962995,0.621709,0.434517,0.460925,0.556326,0.979044,0.608038,0.545606,0.530442,0.967803,0.705364,0.820334,0.709109,0.983102,0.717152,0.91507,0.923104,0.447611,0.638302,0.670329,0.405977,0.796157,0.994834,0.965212,0.445178,0.992926,0.665718,0.870992,0.996789,0.979457,0.843693,0.991126,0.920801,0.575583,0.9914,0.95155,0.00245495,0.533322,0.658163,0.807654,0.941891,0.981387,0.979971,0.609261,0.404733,0.995365,0.958304,0.996923,0.798761,0.623017,0.924751,0.0617038,0.701113,0.937777,0.913344,0.0825677,0.985749,0.594597,0.79255,0.708592,0.657781,0.993871,0.965173,0.294616,0.979184,0.792529,0.219068,0.128377,0.756445,0.657078,0.365012,0.676307,0.734305,0.808274,0.537396,0.924098,0.835371,0.762914,0.998931,0.888975,0.116965,0.0882922,0.102674,0.84915,0.515032,0.998971,0.999069,0.994706,0.996046,0.172464,0.467444,0.869573,0.998625,0.774838,0.997119,0.998493,0.987344,0.964176,0.96867,0.568133,0.986898,0.354279,0.626649,0.99892,0.686893,0.987026,0.0845006,0.904161,0.965619,0.998148,0.767808,0.976815,0.861069,0.96556,0.731871,0.71838,0.71953,0.889913,0.845603,0.615666,0.362642,0.976698,0.268185,0.995748,0.206719,0.730681,0.529925,0.857728,0.216102,0.782331,0.799385,0.195689,0.466717,0.468076,0.838665,0.824796,0.929973,0.645691,0.473086,0.63539,0.577288,0.964379,0.429378,0.986926,0.983556,0.281092,0.865711,0.82917,0.0849384,0.994115,0.98168,0.999711,0.963567,0.938847,0.645012,0.999144,0.835164,0.376665,0.968879,0.0755438,0.999581,0.985455,0.681351,0.537924,0.996508,0.929895,0.534619,0.993184,0.992363,0.999505,0.995913,0.895842,0.984037,0.234366,0.895623,0.133852,0.932692,0.970037,0.901543,0.873364,0.174756,0.435792,0.90684,0.976004,0.816698,0.84922,0.913655,0.829036,0.0159768,0.204887,0.916931,0.998772,0.995029,0.806924|tfbs_overrepresentation_for_novel_motifs=0.591198,0.217462,0.0485568,0.0660215,0.261182,0.571034,0.0267087,1.17132,0.269629,0.0104334,0.0101011,0.956761,0.00316677,0.255056,0.594848,0.185233,0.0993352,0.972045,0.00452573,0.0666692,0.11518,0.0366663,0.0127439,1.34645,0.509118,0.164784,0.156843,0.321243,0.614642,0.260275,0.117007,0.116374,0.9685,0.0900455,0.0169972,2.84474,0.000522363,0.0657646,0.230284,0.212334,0.182291,0.0351227,0.128457,3.28164,0.00222181,0.0677436,0.113055,0.127664,0.541328,0.0298962,0.0468335,0.121678,0.012355,0.156134,0.250153,0.259213,0.0796908,0.412452,0.00837553,0.0842605,0.424807,0.276579,0.104033,0.0874088,0.0314028,0.545508,0.839132,0.611811,0.359082,0.473124,0.00554441,0.0634387,2.99663e-05,0.248809,0.00831653,0.00579697,0.00117053,0.0805246,1.18449,0.999761,0.548241,0.611641,5.32696,0.963503,0.215209,5.24015e-08,0.100377,1.11539,0.201739,0.700455,0.382593,0.198363,0.393356,1.28149,0.00795653,0.671211,1.06471,0.146642,0.0563488,0.0729343,0.13813,0.386131,0.143659,0.678489,0.523315,0.00961865,0.0940006,0.47084,0.0256602,0.000823701,0.243289,0.862168,0.354944,0.0111586,0.345782,1.36479,6.70424e-05,0.115876,0.0728193,0.0555818,0.243272,0.199407,0.063723,0.583176,0.432294,0.276474,0.78774,0.127094,0.272261,0.0658543,0.577011,0.963892,1.40947,0.906777,0.392663,0.212098,0.111429,0.161185,0.35979,1.12806,0.748112,0.331642,0.494573,0.144753,0.0700482,0.0797928,0.852171,0.975366,0.0992824,0.100778,0.0161209,3.3524e-06,0.577571,0.000444856,0.512312,0.498621,0.416337,0.228882,0.17405,0.00299729,0.330738,0.187783,0.718083,2.74571,0.263335,0.301714,0.00527697,0.269602,0.00421678|tfbs_overrepresentation_jaspar=MA0003.1;0.000443641,MA0004.1;0.292819,MA0006.1;0.027879,MA0007.1;0.044566,MA0009.1;0.517127,MA0014.1;2.95732e-05,MA0017.1;0.359388,MA0019.1;1.39116,MA0024.1;0.117627,MA0025.1;0.259105,MA0027.1;1.6012,MA0028.1;0.172226,MA0029.1;0.400166,MA0030.1;0.772017,MA0031.1;0.306,MA0038.1;0.511884,MA0040.1;0.407817,MA0041.1;0.553037,MA0042.1;1.01404,MA0043.1;0.174193,MA0046.1;1.54245,MA0048.1;0.0140581,MA0050.1;0.131075,MA0051.1;2.58305,MA0052.1;2.59086,MA0055.1;0.00956919,MA0056.1;0,MA0057.1;0.00190511,MA0058.1;0.264486,MA0059.1;0.261771,MA0060.1;0.0255608,MA0061.1;0.113625,MA0063.1;0,MA0066.1;0.0273846,MA0067.1;0.395513,MA0068.1;0.148798,MA0069.1;0.165471,MA0070.1;0.933424,MA0071.1;0.221073,MA0072.1;0.922928,MA0073.1;7.65965e-05,MA0074.1;0.0262445,MA0076.1;0.299048,MA0077.1;0.463589,MA0078.1;0.194571,MA0081.1;0.139784,MA0083.1;1.60449,MA0084.1;1.35694,MA0087.1;0.470858,MA0088.1;0.000924625,MA0089.1;0,MA0090.1;0.530463,MA0091.1;0.297728,MA0092.1;0.109133,MA0093.1;0.264179,MA0095.1;0,MA0098.1;0,MA0100.1;0.296489,MA0101.1;0.15613,MA0103.1;0.0636,MA0105.1;7.81066e-05,MA0106.1;0.613607,MA0107.1;0.121051,MA0108.2;0.627577,MA0109.1;0,MA0111.1;0.0320901,MA0113.1;0.160472,MA0114.1;0.0574343,MA0115.1;0.336593,MA0116.1;0.0096387,MA0117.1;0.196603,MA0119.1;3.01402,MA0122.1;0.212824,MA0124.1;0.305891,MA0125.1;0.690351,MA0130.1;0,MA0131.1;0.806233,MA0132.1;0,MA0133.1;0,MA0135.1;0.561121,MA0136.1;0.528777,MA0139.1;0.0242189,MA0140.1;1.00904,MA0141.1;0.0596471,MA0142.1;0.269716,MA0143.1;1.45011,MA0144.1;1.46528,MA0145.1;0.000205966,MA0146.1;0.000534134,MA0147.1;0.0689055,MA0148.1;0.860451,MA0149.1;5.12865,MA0062.2;0.256593,MA0035.2;0.680551,MA0039.2;2.982e-09,MA0138.2;0.195748,MA0002.2;2.79566,MA0137.2;3.15679,MA0104.2;0.0251613,MA0047.2;0.582934,MA0112.2;0.0409959,MA0065.2;0.0193641,MA0150.1;1.03578,MA0151.1;0,MA0152.1;1.42545,MA0153.1;1.91916,MA0154.1;0.172834,MA0155.1;0.00216724,MA0156.1;0.493351,MA0157.1;1.3302,MA0158.1;0,MA0159.1;0.133693,MA0160.1;0.617337,MA0161.1;0,MA0162.1;7.64521e-07,MA0163.1;1.5854e-07,MA0164.1;0.17148,MA0080.2;0.26439,MA0018.2;0.0373716,MA0099.2;0.226802,MA0079.2;1.98724e-12,MA0102.2;0.582837,MA0258.1;0.0155231,MA0259.1;0.0120686,MA0442.1;0}}
|full_id=C215_chronic_acute_peripheral_Hepatocyte_osteosarcoma_NK_immature
|id=C215
}}

Latest revision as of 10:58, 17 September 2013


Full id: C215_chronic_acute_peripheral_Hepatocyte_osteosarcoma_NK_immature



Phase1 CAGE Peaks

Hg19::chr10:22607676..22607682,+p21@COMMD3
Hg19::chr10:22607725..22607736,+p18@COMMD3
Hg19::chr10:34307354..34307364,+p@chr10:34307354..34307364
+
Hg19::chr12:10084960..10084974,-p1@CLEC2A
Hg19::chr12:10084999..10085009,-p2@CLEC2A
Hg19::chr12:10095845..10095862,-p2@uc001qwo.1
Hg19::chr12:10151709..10151754,-p1@CLEC1B
Hg19::chr12:10151773..10151784,-p3@CLEC1B
Hg19::chr12:10205100..10205121,+p3@AB590792
Hg19::chr12:10205127..10205138,+p5@AB590792
Hg19::chr12:43611998..43612001,+p@chr12:43611998..43612001
+
Hg19::chr12:43612012..43612028,+p@chr12:43612012..43612028
+
Hg19::chr13:73126300..73126304,-p@chr13:73126300..73126304
-
Hg19::chr15:88484080..88484087,-p20@NTRK3
Hg19::chr19:33960599..33960608,-p@chr19:33960599..33960608
-
Hg19::chr19:46663654..46663668,+p@chr19:46663654..46663668
+
Hg19::chr21:20985006..20985010,+p@chr21:20985006..20985010
+
Hg19::chr21:22483836..22483880,+p@chr21:22483836..22483880
+
Hg19::chr21:22550109..22550126,+p@chr21:22550109..22550126
+
Hg19::chr21:22550139..22550141,+p@chr21:22550139..22550141
+
Hg19::chr21:22550147..22550151,+p@chr21:22550147..22550151
+
Hg19::chr21:22550165..22550181,+p@chr21:22550165..22550181
+
Hg19::chr21:47809029..47809044,+p@chr21:47809029..47809044
+
Hg19::chr22:49886217..49886230,-p@chr22:49886217..49886230
-
Hg19::chr22:49886244..49886251,-p@chr22:49886244..49886251
-
Hg19::chr2:164580742..164580760,-p@chr2:164580742..164580760
-
Hg19::chr2:219849008..219849011,-p13@FEV
Hg19::chr2:219849012..219849065,-p1@FEV
Hg19::chr2:219849078..219849085,-p10@FEV
Hg19::chr2:219849175..219849187,-p4@FEV
Hg19::chr2:219849306..219849309,+p@chr2:219849306..219849309
+
Hg19::chr3:126207173..126207218,-p@chr3:126207173..126207218
-
Hg19::chr4:117273886..117273928,+p@chr4:117273886..117273928
+
Hg19::chr4:134283870..134283873,+p@chr4:134283870..134283873
+
Hg19::chr4:42154250..42154256,-p12@BEND4
Hg19::chr4:42154592..42154600,-p15@BEND4
Hg19::chr4:90799994..90800011,+p@chr4:90799994..90800011
+
Hg19::chr5:120355553..120355565,-p@chr5:120355553..120355565
-
Hg19::chr5:155210..155224,+p@chr5:155210..155224
+
Hg19::chr5:155367..155409,+p@chr5:155367..155409
+
Hg19::chr5:155432..155458,+p@chr5:155432..155458
+
Hg19::chr5:86090158..86090169,+p@chr5:86090158..86090169
+
Hg19::chr5:86090206..86090212,+p@chr5:86090206..86090212
+
Hg19::chr5:86213307..86213310,+p@chr5:86213307..86213310
+
Hg19::chr6:135668066..135668095,-p@chr6:135668066..135668095
-
Hg19::chr6:21065386..21065400,+p5@CDKAL1
Hg19::chr6:23916407..23916457,+p@chr6:23916407..23916457
+
Hg19::chr6:67780097..67780102,+p@chr6:67780097..67780102
+
Hg19::chr7:10000571..10000582,+p1@ENST00000451755
Hg19::chr7:10000610..10000618,+p2@ENST00000451755
Hg19::chr7:10000640..10000645,+p4@ENST00000451755
Hg19::chr8:108334188..108334201,-p11@ANGPT1
Hg19::chr8:108334209..108334228,-p8@ANGPT1
Hg19::chr8:108336622..108336625,+p@chr8:108336622..108336625
+
Hg19::chr8:114449751..114449769,-p7@CSMD3
Hg19::chr8:114725643..114725660,-p@chr8:114725643..114725660
-
Hg19::chr8:114747320..114747347,-p@chr8:114747320..114747347
-
Hg19::chr8:114747363..114747380,-p@chr8:114747363..114747380
-
Hg19::chr8:115089397..115089400,+p@chr8:115089397..115089400
+
Hg19::chr8:116673894..116673913,-p12@TRPS1
Hg19::chr8:130648181..130648190,-p@chr8:130648181..130648190
-
Hg19::chr8:2163693..2163732,-p@chr8:2163693..2163732
-
Hg19::chr8:2163883..2163896,-p@chr8:2163883..2163896
-
Hg19::chr8:2163929..2163941,-p@chr8:2163929..2163941
-
Hg19::chr8:41292975..41292985,+p2@ENST00000521725
Hg19::chr8:41292988..41293000,+p1@ENST00000521725
Hg19::chr8:76077242..76077244,+p@chr8:76077242..76077244
+
Hg19::chr9:133407203..133407218,+p@chr9:133407203..133407218
+
Hg19::chr9:133407256..133407273,+p@chr9:133407256..133407273
+


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><br>disease_data<br>

Disease
Ontology termp-valuen
chronic leukemia5.22e-268
myeloid leukemia7.41e-0831


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)
MA0003.10.000443641
MA0004.10.292819
MA0006.10.027879
MA0007.10.044566
MA0009.10.517127
MA0014.12.95732e-05
MA0017.10.359388
MA0019.11.39116
MA0024.10.117627
MA0025.10.259105
MA0027.11.6012
MA0028.10.172226
MA0029.10.400166
MA0030.10.772017
MA0031.10.306
MA0038.10.511884
MA0040.10.407817
MA0041.10.553037
MA0042.11.01404
MA0043.10.174193
MA0046.11.54245
MA0048.10.0140581
MA0050.10.131075
MA0051.12.58305
MA0052.12.59086
MA0055.10.00956919
MA0056.10
MA0057.10.00190511
MA0058.10.264486
MA0059.10.261771
MA0060.10.0255608
MA0061.10.113625
MA0063.10
MA0066.10.0273846
MA0067.10.395513
MA0068.10.148798
MA0069.10.165471
MA0070.10.933424
MA0071.10.221073
MA0072.10.922928
MA0073.17.65965e-05
MA0074.10.0262445
MA0076.10.299048
MA0077.10.463589
MA0078.10.194571
MA0081.10.139784
MA0083.11.60449
MA0084.11.35694
MA0087.10.470858
MA0088.10.000924625
MA0089.10
MA0090.10.530463
MA0091.10.297728
MA0092.10.109133
MA0093.10.264179
MA0095.10
MA0098.10
MA0100.10.296489
MA0101.10.15613
MA0103.10.0636
MA0105.17.81066e-05
MA0106.10.613607
MA0107.10.121051
MA0108.20.627577
MA0109.10
MA0111.10.0320901
MA0113.10.160472
MA0114.10.0574343
MA0115.10.336593
MA0116.10.0096387
MA0117.10.196603
MA0119.13.01402
MA0122.10.212824
MA0124.10.305891
MA0125.10.690351
MA0130.10
MA0131.10.806233
MA0132.10
MA0133.10
MA0135.10.561121
MA0136.10.528777
MA0139.10.0242189
MA0140.11.00904
MA0141.10.0596471
MA0142.10.269716
MA0143.11.45011
MA0144.11.46528
MA0145.10.000205966
MA0146.10.000534134
MA0147.10.0689055
MA0148.10.860451
MA0149.15.12865
MA0062.20.256593
MA0035.20.680551
MA0039.22.982e-09
MA0138.20.195748
MA0002.22.79566
MA0137.23.15679
MA0104.20.0251613
MA0047.20.582934
MA0112.20.0409959
MA0065.20.0193641
MA0150.11.03578
MA0151.10
MA0152.11.42545
MA0153.11.91916
MA0154.10.172834
MA0155.10.00216724
MA0156.10.493351
MA0157.11.3302
MA0158.10
MA0159.10.133693
MA0160.10.617337
MA0161.10
MA0162.17.64521e-07
MA0163.11.5854e-07
MA0164.10.17148
MA0080.20.26439
MA0018.20.0373716
MA0099.20.226802
MA0079.21.98724e-12
MA0102.20.582837
MA0258.10.0155231
MA0259.10.0120686
MA0442.10



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#2351253.631578326888620.01235455260604420.0447305387097916



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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