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Coexpression cluster:C229: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0768018,0.003076,0.0712904,0.425275,0.535284,1.0174,0.602814,0.394636,0.160191,0.000687247,0.357096,0.406009,0.0422556,0.314461,0.205253,0.133565,0.119289,0.50685,0.0539391,0.125359,0.477556,0.313384,0.0826628,0.51569,0.406124,0.05514,0.161338,0.657708,0.213779,0.190464,0.313301,0.138021,0.002829,0.146427,0.0721405,1.28755e-07,0.00733302,0.0882274,0.674962,0.00381975,1.36765,0.0502504,0.785697,0.747292,0.0243818,0.0957998,0.143887,0.335042,0.188244,0.547812,0.0599013,0.635855,0.1376,0.534408,0.768131,0.319102,0.799151,0.111033,0.121184,0.498877,0.160351,0.145852,0.943777,0.344895,0.161182,0.0906885,0.913499,0.652367,0.41389,0.511132,0.0444509,0.178759,0.000494126,0.27936,0.0169642,0.0124199,0.0442451,0.0983574,0.130929,0.883564,0.109736,0.343576,0.160873,0.274579,0.244004,9.68579e-06,0.000676207,0.0339898,0.0692009,0.742187,0.418256,0.226174,0.146997,1.01927,0.00207973,0.0464855,0.0524612,0.170887,0.0709247,0.00371111,0.325353,0.869668,0.167668,0.384308,0.290293,0.0142485,0.113383,0.309042,0.109066,0.00155713,0.0261922,0.166081,0.949804,0.193216,0.990466,0.247247,0.0083361,0.0574421,0.0896888,0.164117,0.273551,0.0683023,0.680308,1.0624,0.469328,1.10862,0.137804,0.149715,0.303903,0.459477,0.64297,0.0594771,0.844198,0.381084,0.428622,0.013041,0.149277,0.207828,0.394746,1.17283,0.79037,0.365644,0.591113,0.504498,0.0865557,0.024611,0.0797291,1.0194,0.0487439,0.0126941,0.0181463,2.80452e-06,0.226872,0.0795979,0.956264,0.537178,0.846492,0.311904,0.0380709,0.0279811,0.956196,0.214937,0.811807,0.189747,0.311046,0.366261,0.00236202,0.940995,0.00101928
|tfbs_overrepresentation_for_novel_motifs=0.0768018,0.003076,0.0712904,0.425275,0.535284,1.0174,0.602814,0.394636,0.160191,0.000687247,0.357096,0.406009,0.0422556,0.314461,0.205253,0.133565,0.119289,0.50685,0.0539391,0.125359,0.477556,0.313384,0.0826628,0.51569,0.406124,0.05514,0.161338,0.657708,0.213779,0.190464,0.313301,0.138021,0.002829,0.146427,0.0721405,1.28755e-07,0.00733302,0.0882274,0.674962,0.00381975,1.36765,0.0502504,0.785697,0.747292,0.0243818,0.0957998,0.143887,0.335042,0.188244,0.547812,0.0599013,0.635855,0.1376,0.534408,0.768131,0.319102,0.799151,0.111033,0.121184,0.498877,0.160351,0.145852,0.943777,0.344895,0.161182,0.0906885,0.913499,0.652367,0.41389,0.511132,0.0444509,0.178759,0.000494126,0.27936,0.0169642,0.0124199,0.0442451,0.0983574,0.130929,0.883564,0.109736,0.343576,0.160873,0.274579,0.244004,9.68579e-06,0.000676207,0.0339898,0.0692009,0.742187,0.418256,0.226174,0.146997,1.01927,0.00207973,0.0464855,0.0524612,0.170887,0.0709247,0.00371111,0.325353,0.869668,0.167668,0.384308,0.290293,0.0142485,0.113383,0.309042,0.109066,0.00155713,0.0261922,0.166081,0.949804,0.193216,0.990466,0.247247,0.0083361,0.0574421,0.0896888,0.164117,0.273551,0.0683023,0.680308,1.0624,0.469328,1.10862,0.137804,0.149715,0.303903,0.459477,0.64297,0.0594771,0.844198,0.381084,0.428622,0.013041,0.149277,0.207828,0.394746,1.17283,0.79037,0.365644,0.591113,0.504498,0.0865557,0.024611,0.0797291,1.0194,0.0487439,0.0126941,0.0181463,2.80452e-06,0.226872,0.0795979,0.956264,0.537178,0.846492,0.311904,0.0380709,0.0279811,0.956196,0.214937,0.811807,0.189747,0.311046,0.366261,0.00236202,0.940995,0.00101928
|tfbs_overrepresentation_jaspar=MA0003.1;1.9374e-07,MA0004.1;0.187985,MA0006.1;0.204381,MA0007.1;0.329382,MA0009.1;1.09942,MA0014.1;3.0773e-07,MA0017.1;0.95842,MA0019.1;1.58105,MA0024.1;0.139391,MA0025.1;0.290149,MA0027.1;1.6471,MA0028.1;0.0529791,MA0029.1;0.149877,MA0030.1;0.143615,MA0031.1;0.110677,MA0038.1;0.60992,MA0040.1;0.465611,MA0041.1;0.408002,MA0042.1;0.171568,MA0043.1;0.200452,MA0046.1;0.193494,MA0048.1;0.149132,MA0050.1;0.341919,MA0051.1;0.599051,MA0052.1;0.470992,MA0055.1;0.0046267,MA0056.1;0,MA0057.1;0.0121538,MA0058.1;0.191858,MA0059.1;0.342282,MA0060.1;0.0907347,MA0061.1;0.10636,MA0063.1;0,MA0066.1;0.145656,MA0067.1;0.431554,MA0068.1;0.000924356,MA0069.1;0.558619,MA0070.1;0.184309,MA0071.1;0.512993,MA0072.1;1.02527,MA0073.1;2.51606e-08,MA0074.1;0.141145,MA0076.1;0.0350181,MA0077.1;0.524407,MA0078.1;0.507832,MA0081.1;0.0290834,MA0083.1;0.204972,MA0084.1;0.59013,MA0087.1;0.532044,MA0088.1;0.0737429,MA0089.1;0,MA0090.1;0.242094,MA0091.1;0.619223,MA0092.1;0.29697,MA0093.1;0.210231,MA0095.1;0,MA0098.1;0,MA0100.1;0.646115,MA0101.1;0.112324,MA0103.1;0.0948626,MA0105.1;0.0330662,MA0106.1;0.182034,MA0107.1;0.0967296,MA0108.2;0.109215,MA0109.1;0,MA0111.1;0.0463494,MA0113.1;0.197766,MA0114.1;0.600931,MA0115.1;0.370769,MA0116.1;1.41001,MA0117.1;0.637527,MA0119.1;0.0742602,MA0122.1;0.677693,MA0124.1;0.338933,MA0125.1;1.39148,MA0130.1;0,MA0131.1;0.543404,MA0132.1;0,MA0133.1;0,MA0135.1;1.17465,MA0136.1;0.349036,MA0139.1;0.00740446,MA0140.1;0.0268183,MA0141.1;0.338045,MA0142.1;0.0959792,MA0143.1;0.197939,MA0144.1;0.0112872,MA0145.1;0.000738893,MA0146.1;7.65368e-05,MA0147.1;0.193449,MA0148.1;0.220479,MA0149.1;0.0247918,MA0062.2;0.0234785,MA0035.2;0.271242,MA0039.2;2.86463e-07,MA0138.2;0.066895,MA0002.2;0.478845,MA0137.2;0.00288294,MA0104.2;0.0441645,MA0047.2;0.170795,MA0112.2;0.0539276,MA0065.2;0.0724484,MA0150.1;1.60954,MA0151.1;0,MA0152.1;0.832978,MA0153.1;0.733339,MA0154.1;0.205443,MA0155.1;0.0252403,MA0156.1;0.0585425,MA0157.1;0.0841652,MA0158.1;0,MA0159.1;0.106727,MA0160.1;0.456767,MA0161.1;0,MA0162.1;6.68437e-06,MA0163.1;0.00273499,MA0164.1;0.210088,MA0080.2;0.108594,MA0018.2;0.410474,MA0099.2;0.282757,MA0079.2;0,MA0102.2;0.622942,MA0258.1;0.124014,MA0259.1;0.212038,MA0442.1;0
}}
}}

Revision as of 18:47, 22 January 2013


Full id: C229_Mesenchymal_CD4_Melanocyte_acute_skeletal_left_heart



Phase1 CAGE Peaks

Hg19::chr11:17096287..17096292,-p1@SNORD14A
Hg19::chr11:62432889..62432899,+p1@SNORA57
Hg19::chr11:811679..811684,+p2@SNORA52
Hg19::chr11:93465662..93465665,-p1@SNORA8
Hg19::chr11:93466460..93466463,-p1@SNORD5
Hg19::chr11:93468399..93468405,-p19@TAF1D
p1@SNORA40
Hg19::chr12:57038878..57038884,-p1@SNORD59A
Hg19::chr13:27829202..27829226,+p1@SNORD102
Hg19::chr13:45910578..45910583,-p1@ENST00000517242
Hg19::chr14:20791482..20791485,-p1@ENST00000410557
Hg19::chr16:2013101..2013108,-p1@SNORA64
Hg19::chr16:2015179..2015182,+p3@SNORA78
Hg19::chr16:2205102..2205107,-p2@SNORD60
Hg19::chr16:33965418..33965444,+p1@RN5-8S2
Hg19::chr16:70563415..70563420,+p4@SNORD111B
Hg19::chr16:89627836..89627840,+p2@SNORD68
Hg19::chr17:27050447..27050450,+p1@SNORD42A
Hg19::chr17:27050702..27050704,+p1@SNORD4B
Hg19::chr17:7478029..7478035,+p1@SNORA48
Hg19::chr17:7480128..7480132,+p1@SNORD10
Hg19::chr18:47017713..47017717,-p1@SNORD58A
Hg19::chr18:47018091..47018115,-p1@SNORD58B
p4@RPL17
Hg19::chr19:10218330..10218339,+p1@SNORD105
Hg19::chr19:10220437..10220441,+p1@SNORD105B
Hg19::chr19:24187307..24187313,-p1@RN5-8S4
Hg19::chr19:49993222..49993226,+p1@SNORD32A
Hg19::chr19:49993872..49993876,+p1@SNORD33
Hg19::chr19:49994430..49994434,+p1@SNORD35A
Hg19::chr1:173833352..173833357,-p1@SNORD81
Hg19::chr1:173833579..173833584,-p1@SNORD47
Hg19::chr1:173835162..173835166,-p1@SNORD44
Hg19::chr1:173835843..173835856,-p1@SNORD76
Hg19::chr1:173836874..173836885,-p1@SNORD74
Hg19::chr1:235291248..235291252,-p2@SNORA14B
Hg19::chr1:28160911..28160914,+p1@SCARNA1
Hg19::chr1:28833864..28833907,+p1@SNORA73A
Hg19::chr1:28835067..28835078,+p1@SNORA73B
Hg19::chr1:28907004..28907024,-p1@SNORA44
Hg19::chr1:28907560..28907564,-p1@SNORA16A
Hg19::chr20:2634860..2634861,+p1@SNORD110
Hg19::chr20:2637264..2637276,+p1@SNORD56
Hg19::chr20:2637584..2637589,+p2@SNORD57
Hg19::chr20:47896855..47896877,+p1@SNORD12B
Hg19::chr20:47897225..47897227,+p2@SNORD12
Hg19::chr2:29150850..29150852,+p@chr2:29150850..29150852
+
Hg19::chr3:186505086..186505092,+p2@SNORA63
Hg19::chr4:119200341..119200348,+p2@SNORA24
Hg19::chr4:1976361..1976365,+p1@SCARNA22
Hg19::chr5:105889153..105889161,+p1@ENST00000478633
Hg19::chr5:137896795..137896800,-p1@SNORD63
Hg19::chr5:180668885..180668889,-p1@SNORD96A
Hg19::chr5:74063455..74063464,-p4@GFM2
Hg19::chr6:26305727..26305730,-p@chr6:26305727..26305730
-
Hg19::chr6:31804851..31804855,+p1@SNORD52
Hg19::chr8:56986457..56986460,-p1@SNORD54
Hg19::chr9:136216952..136216953,+p2@SNORD36B
Hg19::chr9:136217312..136217315,+p1@SNORD36A
Hg19::chr9:136217702..136217704,+p1@SNORD36C
p6@RPL7A
Hg19::chrM:12203..12214,+p3@uc004cow.1
Hg19::chrX:132286783..132286784,+p1@ENST00000384372
Hg19::chrX:153628621..153628623,+p2@SNORA70
Hg19::chrY:10037751..10037770,+p1@RN5-8S6


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
germ cell and embryonal cancer4.15e-0822
germ cell cancer4.15e-0822
cancer1.98e-07235
disease of cellular proliferation6.42e-07239


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)
MA0003.11.9374e-07
MA0004.10.187985
MA0006.10.204381
MA0007.10.329382
MA0009.11.09942
MA0014.13.0773e-07
MA0017.10.95842
MA0019.11.58105
MA0024.10.139391
MA0025.10.290149
MA0027.11.6471
MA0028.10.0529791
MA0029.10.149877
MA0030.10.143615
MA0031.10.110677
MA0038.10.60992
MA0040.10.465611
MA0041.10.408002
MA0042.10.171568
MA0043.10.200452
MA0046.10.193494
MA0048.10.149132
MA0050.10.341919
MA0051.10.599051
MA0052.10.470992
MA0055.10.0046267
MA0056.10
MA0057.10.0121538
MA0058.10.191858
MA0059.10.342282
MA0060.10.0907347
MA0061.10.10636
MA0063.10
MA0066.10.145656
MA0067.10.431554
MA0068.10.000924356
MA0069.10.558619
MA0070.10.184309
MA0071.10.512993
MA0072.11.02527
MA0073.12.51606e-08
MA0074.10.141145
MA0076.10.0350181
MA0077.10.524407
MA0078.10.507832
MA0081.10.0290834
MA0083.10.204972
MA0084.10.59013
MA0087.10.532044
MA0088.10.0737429
MA0089.10
MA0090.10.242094
MA0091.10.619223
MA0092.10.29697
MA0093.10.210231
MA0095.10
MA0098.10
MA0100.10.646115
MA0101.10.112324
MA0103.10.0948626
MA0105.10.0330662
MA0106.10.182034
MA0107.10.0967296
MA0108.20.109215
MA0109.10
MA0111.10.0463494
MA0113.10.197766
MA0114.10.600931
MA0115.10.370769
MA0116.11.41001
MA0117.10.637527
MA0119.10.0742602
MA0122.10.677693
MA0124.10.338933
MA0125.11.39148
MA0130.10
MA0131.10.543404
MA0132.10
MA0133.10
MA0135.11.17465
MA0136.10.349036
MA0139.10.00740446
MA0140.10.0268183
MA0141.10.338045
MA0142.10.0959792
MA0143.10.197939
MA0144.10.0112872
MA0145.10.000738893
MA0146.17.65368e-05
MA0147.10.193449
MA0148.10.220479
MA0149.10.0247918
MA0062.20.0234785
MA0035.20.271242
MA0039.22.86463e-07
MA0138.20.066895
MA0002.20.478845
MA0137.20.00288294
MA0104.20.0441645
MA0047.20.170795
MA0112.20.0539276
MA0065.20.0724484
MA0150.11.60954
MA0151.10
MA0152.10.832978
MA0153.10.733339
MA0154.10.205443
MA0155.10.0252403
MA0156.10.0585425
MA0157.10.0841652
MA0158.10
MA0159.10.106727
MA0160.10.456767
MA0161.10
MA0162.16.68437e-06
MA0163.10.00273499
MA0164.10.210088
MA0080.20.108594
MA0018.20.410474
MA0099.20.282757
MA0079.20
MA0102.20.622942
MA0258.10.124014
MA0259.10.212038
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
BCL3#60273.900479348809160.002073237162505470.0120172503060777
GTF2B#295963.091338380741050.01294097647149440.0465182983997521
POLR2A#5430421.454726345410310.0006197994584600220.00513739965413542
RDBP#793649.912155096130640.0007380870040578320.00581510777133342



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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