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Coexpression cluster:C574: Difference between revisions

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{{Coexpression_clusters
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703435,0.472747,0.56823,0.0138618,0.610746,0.750105,0.626829,0.188899,0.30561,0.248678,0.220147,0.811616,0.699044,0.669428,0.59256,7.87826e-05,0.425392,0.00360725,0.279289,0.372245,0.601575,0.382821,0.685986,0.507062,0.21748,0.859567,0.654357,0.60511,0.00580424,0.21706,0.72894,0.157744,0.00516718,0.298487,0.0616639,0.00595364,0.8018,0.703398,0.722807,0.710828,0.196964,0.681406,0.783012,0.00462762,0.742427,0.00455105,0.269111,0.696683,0.552042,0.689905,0.769388,0.596464,0.527328,0.00126235,0.739277,0.634865,0.645683,0.419455,0.700117,0.862225,0.827785,0.730872,0.367255,0.699974,0.452288,0.254606,0.0357859,0.582662,0.351578,0.198874,0.0357387,0.872068,0.801772,0.718094,0.026406,0.758074,0.674028,0.0760648,0.42349,0.297824,0.500117,0.296723,0.445268,0.306508,0.0678287,0.520488,0.460196,0.213844,0.308984,0.0904162,0.180997,0.00121718,0.704612,0.120234,0.835001,0.897022,0.557415,0.08282,0.79337,0.696022,0.160874,0.848907,0.461827,0.647685,0.831214,0.805592,0.529302,0.240004,0.00029352,0.694264,0.835246,0.762813,0.349666,0.481329,0.730672,0.74112,0.479646,0.685494,0.105779,0.828783,0.529957,0.784325,0.616883,0.741876,0.0162729,0.0211653,0.744519,0.711279,0.101794,0.380706,0.868972,0.0192706,0.602504,0.0288445,0.325254,0.81416,0.43333,0.738828,0.643716,0.598522,0.726332,0.788647,0.348167,0.908569|tfbs_overrepresentation_for_novel_motifs=0.928065,1.36836,2.79647,0.258928,0.395738,0.25764,1.54124,0.470337,0.463955,0.914578,2.68272,0.355038,2.44482,0.832947,0.124662,0.851457,0.511522,1.06688,2.56666,0.791358,0.152859,0.521809,0.251588,0.12232,0.18461,0.374311,0.89505,2.78878,0.127478,1.18369,0.217756,0.544857,0.260283,0.15896,0.104423,2.27421,0.102549,0.717201,0.0891992,1.13158,0.103604,1.12058,1.90995,0.391064,0.675783,0.994428,0.856196,1.86782,0.790901,0.798822,0.386472,0.329494,0.932856,0.615394,0.758742,2.30833,0.130259,0.2852,1.60819,1.41706,0.582323,0.321692,0.465207,2.11666,0.893874,0.456015,0.843028,1.20113,0.535417,1.04233,1.70383,0.0621482,0.0158491,0.756844,1.39608,0.580064,0.120629,0.471562,0.532468,0.18023,0.0470011,0.48568,0.336303,0.219253,0.70821,3.28272,0.149619,0.791038,1.85519,1.29895,0.932961,0.68283,0.560183,0.0788172,0.12599,0.0858933,0.0444202,0.599297,0.412954,0.0920994,0.0899484,1.36635,0.594155,0.514828,1.98025,1.21768,1.25067,0.306566,0.542462,0.7457,0.160439,0.591605,0.149112,0.241506,0.886618,0.333119,8.22236,0.216858,2.00748,0.275094,0.748992,0.406842,0.255485,0.345739,0.993708,0.472239,0.313614,0.564749,0.78949,0.291925,0.683478,0.219902,0.803201,0.342946,0.945426,0.469273,0.21329,0.250344,0.904406,1.74999,1.35069,0.868456,0.315034,0.596045,0.447394,0.278424,0.432737,1.59165,2.46528,0.562706,2.48777,0.0889833,0.683836,1.65867,0.859679,1.07219,0.394947,0.373254,0.184652,0.493594,0.867287,0.66649,0.531753,0.166635,0.46162,0.335644,0.905857,2.33771,7.90377|tfbs_overrepresentation_jaspar=MA0003.1;6.70538,MA0004.1;0.238283,MA0006.1;0.784773,MA0007.1;2.61107,MA0009.1;1.55479,MA0014.1;3.85087,MA0017.1;0.45828,MA0019.1;0.359322,MA0024.1;0.547222,MA0025.1;0.771296,MA0027.1;2.23171,MA0028.1;0.134741,MA0029.1;0.565022,MA0030.1;0.554453,MA0031.1;0.495474,MA0038.1;0.321141,MA0040.1;0.570428,MA0041.1;0.252793,MA0042.1;0.227947,MA0043.1;0.644989,MA0046.1;0.634468,MA0048.1;0.390294,MA0050.1;0.228625,MA0051.1;0.317617,MA0052.1;0.574006,MA0055.1;0.0396796,MA0056.1;0,MA0057.1;4.97033,MA0058.1;0.167587,MA0059.1;0.964661,MA0060.1;0.212419,MA0061.1;0.700397,MA0063.1;0,MA0066.1;0.860141,MA0067.1;0.948938,MA0068.1;0.55611,MA0069.1;0.630852,MA0070.1;0.620368,MA0071.1;0.289163,MA0072.1;0.616162,MA0073.1;0.47148,MA0074.1;0.316991,MA0076.1;0.178863,MA0077.1;0.608956,MA0078.1;1.039,MA0081.1;0.166796,MA0083.1;0.651755,MA0084.1;1.13204,MA0087.1;0.613875,MA0088.1;4.36613,MA0089.1;0,MA0090.1;0.189305,MA0091.1;1.94375,MA0092.1;0.607109,MA0093.1;0.12631,MA0095.1;0,MA0098.1;0,MA0100.1;1.59075,MA0101.1;0.802624,MA0103.1;0.118522,MA0105.1;0.836818,MA0106.1;0.355999,MA0107.1;1.0064,MA0108.2;0.492699,MA0109.1;0,MA0111.1;3.22643,MA0113.1;0.370073,MA0114.1;1.46864,MA0115.1;0.874839,MA0116.1;0.607827,MA0117.1;0.680135,MA0119.1;0.155538,MA0122.1;0.70466,MA0124.1;0.834787,MA0125.1;0.75419,MA0130.1;0,MA0131.1;1.07372,MA0132.1;0,MA0133.1;0,MA0135.1;0.673296,MA0136.1;0.327047,MA0139.1;4.35781,MA0140.1;0.7823,MA0141.1;0.165463,MA0142.1;0.4668,MA0143.1;0.370225,MA0144.1;0.25687,MA0145.1;4.05715,MA0146.1;3.52664,MA0147.1;1.03443,MA0148.1;0.257816,MA0149.1;1.39788,MA0062.2;0.0439512,MA0035.2;0.286421,MA0039.2;2.0977,MA0138.2;0.403517,MA0002.2;0.434729,MA0137.2;0.138998,MA0104.2;1.22215,MA0047.2;0.345656,MA0112.2;3.38114,MA0065.2;3.03792,MA0150.1;0.185024,MA0151.1;0,MA0152.1;0.794472,MA0153.1;0.738108,MA0154.1;0.542249,MA0155.1;0.837529,MA0156.1;0.433955,MA0157.1;0.442323,MA0158.1;0,MA0159.1;1.53699,MA0160.1;0.26995,MA0161.1;0,MA0162.1;3.29979,MA0163.1;3.96526,MA0164.1;0.380804,MA0080.2;0.126365,MA0018.2;0.357181,MA0099.2;0.292649,MA0079.2;21.1843,MA0102.2;1.16862,MA0258.1;0.520754,MA0259.1;1.06828,MA0442.1;0}}
|full_id=C574_Mesenchymal_Fibroblast_Smooth_Prostate_Adipocyte_Hair_mesenchymal
|id=C574
|ontology_enrichment_celltype=CL:0000057!2.77e-16!75;CL:0000055!2.12e-15!180;CL:0000048!1.47e-11!430;CL:0000723!1.22e-10!436;CL:0000034!1.26e-10!444;CL:0002320!1.04e-08!365;CL:0000136!4.67e-08!15;CL:0002334!8.36e-08!12;CL:0000134!1.44e-07!358
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!7.01e-10!83;UBERON:0002329!7.01e-10!83;UBERON:0003077!7.01e-10!83;UBERON:0003059!7.01e-10!83;UBERON:0007282!7.01e-10!83;UBERON:0009618!7.01e-10!83;UBERON:0007285!7.01e-10!83;UBERON:0000479!2.36e-09!787;UBERON:0005256!6.55e-09!143;UBERON:0001013!3.39e-08!14;UBERON:0002384!4.93e-08!375;UBERON:0003102!5.18e-08!95;UBERON:0000468!5.19e-08!659;UBERON:0004290!5.26e-08!70;UBERON:0004923!2.63e-07!57
}}

Latest revision as of 11:26, 17 September 2013


Full id: C574_Mesenchymal_Fibroblast_Smooth_Prostate_Adipocyte_Hair_mesenchymal



Phase1 CAGE Peaks

Hg19::chr4:1161154..1161170,-p@chr4:1161154..1161170
-
Hg19::chr4:1164223..1164265,-p@chr4:1164223..1164265
-
Hg19::chr4:1164305..1164316,-p@chr4:1164305..1164316
-
Hg19::chr4:1164817..1164847,-p5@SPON2
Hg19::chr4:1164865..1164905,-p4@SPON2
Hg19::chr4:1164925..1164936,-p11@SPON2
Hg19::chr4:1164956..1164968,-p16@SPON2
Hg19::chr4:1165106..1165131,-p15@SPON2
Hg19::chr4:1165213..1165245,+p@chr4:1165213..1165245
+
Hg19::chr4:1165260..1165276,-p17@SPON2
Hg19::chr4:1165666..1165705,-p7@SPON2
Hg19::chr4:1165755..1165774,-p12@SPON2
Hg19::chr4:1165811..1165842,-p10@SPON2
Hg19::chr4:1166363..1166378,-p1@SPON2
Hg19::chr4:1166587..1166600,-p2@SPON2
Hg19::chr4:1166623..1166634,-p3@SPON2


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

Cell Type
Ontology termp-valuen
multi fate stem cell1.53e-16427
somatic stem cell2.92e-16433
stem cell2.70e-15441
fibroblast1.39e-1376
connective tissue cell4.79e-12361
preadipocyte2.20e-1112
mesenchymal cell6.33e-11354
motile cell5.02e-10386
fat cell2.31e-0915
mesenchymal stem cell of adipose3.28e-098
somatic cell3.97e-09588
extraembryonic cell3.51e-0719
Uber Anatomy
Ontology termp-valuen
connective tissue8.78e-12371
adipose tissue6.97e-1114
organ component layer3.19e-1066
cavity lining1.15e-0812
serous membrane1.15e-0812
omentum1.18e-086
peritoneum1.18e-086
abdominal cavity1.18e-086
visceral peritoneum1.18e-086
somite2.85e-0871
presomitic mesoderm2.85e-0871
presumptive segmental plate2.85e-0871
dermomyotome2.85e-0871
trunk paraxial mesoderm2.85e-0871
trunk mesenchyme3.30e-08122
mesoderm4.27e-08315
mesoderm-derived structure4.27e-08315
presumptive mesoderm4.27e-08315
paraxial mesoderm4.89e-0872
presumptive paraxial mesoderm4.89e-0872
surface structure6.86e-0899
dense mesenchyme tissue8.24e-0873
integument1.06e-0746
integumental system1.06e-0746
epithelial vesicle1.87e-0778
hypodermis2.65e-075
mesenchyme4.09e-07160
entire embryonic mesenchyme4.09e-07160
trunk4.49e-07199
multilaminar epithelium4.91e-0783
Disease
Ontology termp-valuen
ovarian cancer4.41e-1114


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)
MA0003.16.70538
MA0004.10.238283
MA0006.10.784773
MA0007.12.61107
MA0009.11.55479
MA0014.13.85087
MA0017.10.45828
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.10.644989
MA0046.10.634468
MA0048.10.390294
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.10.0396796
MA0056.10
MA0057.14.97033
MA0058.10.167587
MA0059.10.964661
MA0060.10.212419
MA0061.10.700397
MA0063.10
MA0066.10.860141
MA0067.10.948938
MA0068.10.55611
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.10.47148
MA0074.10.316991
MA0076.10.178863
MA0077.10.608956
MA0078.11.039
MA0081.10.166796
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.14.36613
MA0089.10
MA0090.10.189305
MA0091.11.94375
MA0092.10.607109
MA0093.10.12631
MA0095.10
MA0098.10
MA0100.11.59075
MA0101.10.802624
MA0103.10.118522
MA0105.10.836818
MA0106.10.355999
MA0107.11.0064
MA0108.20.492699
MA0109.10
MA0111.13.22643
MA0113.10.370073
MA0114.11.46864
MA0115.10.874839
MA0116.10.607827
MA0117.10.680135
MA0119.10.155538
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.11.07372
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.327047
MA0139.14.35781
MA0140.10.7823
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.25687
MA0145.14.05715
MA0146.13.52664
MA0147.11.03443
MA0148.10.257816
MA0149.11.39788
MA0062.20.0439512
MA0035.20.286421
MA0039.22.0977
MA0138.20.403517
MA0002.20.434729
MA0137.20.138998
MA0104.21.22215
MA0047.20.345656
MA0112.23.38114
MA0065.23.03792
MA0150.10.185024
MA0151.10
MA0152.10.794472
MA0153.10.738108
MA0154.10.542249
MA0155.10.837529
MA0156.10.433955
MA0157.10.442323
MA0158.10
MA0159.11.53699
MA0160.10.26995
MA0161.10
MA0162.13.29979
MA0163.13.96526
MA0164.10.380804
MA0080.20.126365
MA0018.20.357181
MA0099.20.292649
MA0079.221.1843
MA0102.21.16862
MA0258.10.520754
MA0259.11.06828
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
CTCF#1066482.680128186537510.00449100386855960.0212473817906453
SUZ12#2351239.39670892082430.003659155081411430.0184769374630145



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.

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