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Coexpression cluster:C809: Difference between revisions

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{{Coexpression_clusters
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.622646,0.479007,0.671084,0.640709,0.375599,0.44222,0.536945,0.523194,0.676017,0.593153,0.377025,0.336551,2.21217e-07,0.570279,0.335207,7.77484e-08,0.506629,0.668131,0.670422,0.616624,0.450988,0.571064,0.279276,0.733696,0.573814,0.539957,2.69879e-05,0.2588,0.719228,0.46627,0.438198,0.65176,0.217989,0.650689,0.298817,0.567905,0.475347,0.434688,0.555097,0.621443,0.536392,0.775775|tfbs_overrepresentation_for_novel_motifs=2.99125,1.18574,0.273994,0.404877,0.237701,0.403356,0.474413,0.140612,0.138703,1.44021,1.74033,0.515448,2.32572,0.46359,0.236531,0.256724,0.68716,0.191625,0.116269,0.400542,0.274046,0.111654,0.396189,0.233338,0.314616,0.537051,0.0930454,0.39419,1.25378,0.994584,0.355553,0.722879,0.165252,1.72495,0.600053,0.0928746,0.20579,0.404426,0.186493,0.125439,0.597291,0.340749,0.031261,0.235234,2.97013,1.47796,3.08066,3.52638,0.0278865,0.240465,0.550604,0.486559,0.812657,1.87214,0.947672,0.466348,0.244111,0.435652,0.59006,0.434711,0.762758,0.477672,0.139078,1.58745,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,1.57684,0.144996,2.85306,0.945703,2.29033,0.0955465,0.0867529,1.55336,0.709631,0.309107,0.11972,0.659298,0.49429,0.142768,0.89511,3.26868,0.0463436,0.971783,1.40961,1.4989,4.13461,0.868602,0.739223,0.171001,0.238337,0.18161,0.115206,0.780743,0.579925,0.0696508,0.187593,0.733724,0.775299,0.690713,0.616014,0.37138,2.72959,0.460348,0.31439,0.22412,0.7752,0.772599,0.269151,1.77024,1.07963,0.204477,1.58987,0.933543,0.624851,0.173291,0.937551,0.57318,1.03543,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,0.182384,0.869279,0.358161,0.993705,0.50181,1.13991,0.0752959,0.350108,0.394712,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,0.337738,0.503344,5.48408,0.0287097,0.869654,0.132719,0.477214,1.26919,0.560015,0.225815,0.314669,0.28899,1.05976,0.851493,0.708865,0.291837,0.633206,1.23566,0.158769,0.473159,12.1915|tfbs_overrepresentation_jaspar=MA0003.1;5.81753,MA0004.1;0.380329,MA0006.1;0.665232,MA0007.1;0.363007,MA0009.1;0.828613,MA0014.1;0.284587,MA0017.1;0.270554,MA0019.1;0.520264,MA0024.1;0.725404,MA0025.1;0.960689,MA0027.1;2.43535,MA0028.1;0.25013,MA0029.1;0.744375,MA0030.1;0.733118,MA0031.1;0.669876,MA0038.1;0.477043,MA0040.1;0.750125,MA0041.1;0.397617,MA0042.1;0.367902,MA0043.1;1.93626,MA0046.1;0.817858,MA0048.1;0.480635,MA0050.1;8.05539,MA0051.1;7.85935,MA0052.1;0.753928,MA0055.1;0.0662377,MA0056.1;0,MA0057.1;1.22133,MA0058.1;0.293055,MA0059.1;1.44436,MA0060.1;0.138988,MA0061.1;1.80643,MA0063.1;0,MA0066.1;0.477449,MA0067.1;1.1435,MA0068.1;0.0911063,MA0069.1;0.814052,MA0070.1;0.803003,MA0071.1;0.440254,MA0072.1;0.798564,MA0073.1;0.311193,MA0074.1;0.4723,MA0076.1;0.307383,MA0077.1;0.790956,MA0078.1;0.568317,MA0081.1;0.292043,MA0083.1;0.836033,MA0084.1;1.32998,MA0087.1;0.79615,MA0088.1;2.74176,MA0089.1;0,MA0090.1;0.320494,MA0091.1;0.382762,MA0092.1;0.347826,MA0093.1;0.238771,MA0095.1;0,MA0098.1;0,MA0100.1;0.49029,MA0101.1;2.7329,MA0103.1;0.228129,MA0105.1;8.73034,MA0106.1;12.5864,MA0107.1;3.04541,MA0108.2;0.666881,MA0109.1;0,MA0111.1;0.33284,MA0113.1;0.532314,MA0114.1;0.174997,MA0115.1;1.06753,MA0116.1;1.62509,MA0117.1;0.865782,MA0119.1;0.277531,MA0122.1;0.891407,MA0124.1;1.0263,MA0125.1;0.942948,MA0130.1;0,MA0131.1;0.585907,MA0132.1;0,MA0133.1;0,MA0135.1;0.858623,MA0136.1;0.483775,MA0139.1;0.716757,MA0140.1;0.437738,MA0141.1;0.290336,MA0142.1;0.638837,MA0143.1;0.532484,MA0144.1;0.163394,MA0145.1;0.14293,MA0146.1;6.99972,MA0147.1;1.03863,MA0148.1;0.403564,MA0149.1;0.428597,MA0062.2;0.740103,MA0035.2;0.437071,MA0039.2;1.47377,MA0138.2;0.569505,MA0002.2;0.129981,MA0137.2;0.255808,MA0104.2;0.845907,MA0047.2;0.504873,MA0112.2;0.313961,MA0065.2;0.0371828,MA0150.1;0.315136,MA0151.1;0,MA0152.1;0.443956,MA0153.1;0.926242,MA0154.1;0.414714,MA0155.1;0.296882,MA0156.1;1.31919,MA0157.1;0.612166,MA0158.1;0,MA0159.1;0.544949,MA0160.1;0.417847,MA0161.1;0,MA0162.1;1.59966,MA0163.1;0.162989,MA0164.1;0.544294,MA0080.2;0.238846,MA0018.2;0.517858,MA0099.2;0.444294,MA0079.2;3.92995,MA0102.2;13.2221,MA0258.1;0.155735,MA0259.1;0.191914,MA0442.1;0}}
|full_id=C809_CD14_Olfactory_Synoviocyte_Monocytederived_Mesothelial_Fibroblast_Smooth
|id=C809
}}

Latest revision as of 11:31, 17 September 2013


Full id: C809_CD14_Olfactory_Synoviocyte_Monocytederived_Mesothelial_Fibroblast_Smooth



Phase1 CAGE Peaks

Hg19::chr12:102271087..102271111,+p7@DRAM1
Hg19::chr12:102271201..102271223,+p8@DRAM1
Hg19::chr12:102271229..102271245,+p9@DRAM1
Hg19::chr12:102271249..102271260,+p10@DRAM1
Hg19::chr12:102271313..102271322,+p12@DRAM1
Hg19::chr12:102271348..102271376,+p2@DRAM1
Hg19::chr12:102271387..102271426,+p3@DRAM1
Hg19::chr12:102271436..102271486,+p1@DRAM1
Hg19::chr12:102271492..102271516,+p5@DRAM1
Hg19::chr12:102271520..102271550,+p4@DRAM1


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><br>

Cell Type
Ontology termp-valuen
defensive cell1.76e-1948
phagocyte1.76e-1948
classical monocyte2.64e-1642
CD14-positive, CD16-negative classical monocyte2.64e-1642
animal cell8.89e-16679
eukaryotic cell8.89e-16679
monopoietic cell9.96e-1659
monocyte9.96e-1659
monoblast9.96e-1659
promonocyte9.96e-1659
myeloid lineage restricted progenitor cell1.15e-1466
myeloid leukocyte2.55e-1472
macrophage dendritic cell progenitor3.11e-1461
granulocyte monocyte progenitor cell8.04e-1467
mesodermal cell9.00e-14121
somatic cell8.50e-13588
multi fate stem cell1.19e-09427
stuff accumulating cell1.31e-0987
lining cell1.71e-0958
barrier cell1.71e-0958
somatic stem cell8.27e-09433
stem cell1.45e-08441
native cell4.08e-08722
smooth muscle cell9.90e-0843
smooth muscle myoblast9.90e-0843
mesothelial cell1.96e-0719
vascular associated smooth muscle cell2.99e-0732
embryonic cell5.56e-07250
Uber Anatomy
Ontology termp-valuen
mesoderm3.62e-19315
mesoderm-derived structure3.62e-19315
presumptive mesoderm3.62e-19315
lateral plate mesoderm1.38e-17203
musculoskeletal system1.71e-14167
immune system4.59e-1493
bone marrow2.07e-1376
hemolymphoid system3.76e-13108
hematopoietic system3.16e-1198
blood island3.16e-1198
skeletal system7.04e-11100
bone element7.92e-1182
skeletal element1.12e-1090
vessel7.57e-1068
anatomical group5.53e-09625
anatomical system6.67e-09624
vasculature8.69e-0978
vascular system8.69e-0978
cardiovascular system1.26e-08109
circulatory system3.72e-08112
splanchnic layer of lateral plate mesoderm5.16e-0883
multi-cellular organism5.65e-08656
epithelial tube open at both ends8.20e-0859
blood vessel8.20e-0859
blood vasculature8.20e-0859
vascular cord8.20e-0859
artery1.77e-0742
arterial blood vessel1.77e-0742
arterial system1.77e-0742
systemic artery7.66e-0733
systemic arterial system7.66e-0733
epithelial tube8.86e-07117


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)
MA0003.15.81753
MA0004.10.380329
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.10.284587
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.11.93626
MA0046.10.817858
MA0048.10.480635
MA0050.18.05539
MA0051.17.85935
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.11.22133
MA0058.10.293055
MA0059.11.44436
MA0060.10.138988
MA0061.11.80643
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.311193
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.12.74176
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.12.7329
MA0103.10.228129
MA0105.18.73034
MA0106.112.5864
MA0107.13.04541
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.11.62509
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.716757
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.14293
MA0146.16.99972
MA0147.11.03863
MA0148.10.403564
MA0149.10.428597
MA0062.20.740103
MA0035.20.437071
MA0039.21.47377
MA0138.20.569505
MA0002.20.129981
MA0137.20.255808
MA0104.20.845907
MA0047.20.504873
MA0112.20.313961
MA0065.20.0371828
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.414714
MA0155.10.296882
MA0156.11.31919
MA0157.10.612166
MA0158.10
MA0159.10.544949
MA0160.10.417847
MA0161.10
MA0162.11.59966
MA0163.10.162989
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.23.92995
MA0102.213.2221
MA0258.10.155735
MA0259.10.191914
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
CCNT2#90585.068961261570111.27971424775898e-050.000313810932899037
CEBPB#1051107.971147625824829.63949422428846e-108.96472962858827e-08
CTCF#1066484.288205098460024.59406669642002e-050.000807200086990933
CTCFL#140690611.84788461538462.96270758774739e-060.000101350218721503
E2F1#1869104.907389214879321.23333699071511e-077.07738911941182e-06
E2F6#1876105.017155731697399.88551667938738e-085.81980539164903e-06
EGR1#1958104.988179094810141.04750927020086e-076.12546588300717e-06
ELF1#199772.980668571165280.002378202870469130.0134745906574581
EP300#203396.096547553600882.8843323567924e-071.46089615427275e-05
ETS1#211365.83725655332140.0001713587518742850.00208949640245165
GATA1#26231013.56030814380044.74215757032704e-126.21413042016795e-10
GTF2B#2959412.77753197372970.000173128848581580.00210788106983115
HEY1#23462104.040111043105718.62472978604083e-073.74535615020507e-05
HMGN3#932486.542838178680471.78445645847134e-066.69902401388528e-05
MAX#414963.871533305404270.001649602786473820.0103169570283573
MYC#4609105.22228187160946.6214088608781e-084.04405450304824e-06
NFKB1#4790105.488063424193844.03027026544603e-082.66234912240935e-06
PAX5#507996.002608978060053.30907588058665e-071.6559490938792e-05
POLR2A#5430102.147453176558070.0004793377491637920.00436456453225085
SIN3A#2594263.245330836089080.004223840630485730.020101785901449
TAF1#6872103.343046285745295.73229241267096e-060.000172379754473637
TBP#6908103.706770687096392.04059382584877e-067.45426997474013e-05
TCF7L2#69341010.77017656313734.75049080034347e-115.3752601158946e-09
TFAP2A#70201016.5186343730456.58593123034545e-139.48728374849721e-11
TFAP2C#70221010.80922860986024.58158302019868e-115.18976083564566e-09
YY1#7528104.911170749853861.22387217331053e-077.02693710326434e-06
ZBTB7A#5134196.61671837708831.39690928008423e-077.92029361035381e-06
ZNF143#770268.100525931336742.6666044303864e-050.000571511389503642



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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