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{{Coexpression_clusters
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0080978,0.000278838,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.00673322,0.223773,0.25788,0.181895,0.00336176,0.30702,0.202977,0.170837,0.327002,0.28543,0.00220735,0.228479,0.127111,0.259989,0.0888526,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.0472356,0.376537,0.322827,0.229571,0.359036,0.00844265,0.000968095,0.208256,0.265058,0.256405,0.00120337,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.000261968,0.398354,0.222091,0.205977,0.00915515,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.00732664,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,1.42265,0.741427,0.534346,0.739643,1.92131,0.395818,0.392841,0.151681,1.68405,0.867962,0.905351,0.809319,2.26901,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.169357,1.73475,0.528529,2.59358,0.892087,0.316693,0.728867,0.537869,0.806311,1.63433,1.09415,0.433165,0.911389,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.0946706,0.61613,1.92371,0.694903,0.173425,0.538016,2.09659,0.83543,0.25073,1.17354,1.33024,0.812467,1.34056,1.82985,0.297448,0.776148,1.13655,3.20268,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,4.2246,0.823598,1.00941,1.08,0.62601,3.50709,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,2.59018,1.05974,2.24329,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,3.52745,0.717043,1.46636,0.489254,1.27972,0.681522,5.27904,0.444962,1.31973,0.932085,1.74599,0.856196,1.57854,3.77577,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,3.28787,1.52813,0.283547,2.73245,0.729481,3.26642,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,3.5346,0.521611,1.24902,0.383416,4.5968,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.359498|tfbs_overrepresentation_jaspar=MA0003.1;1.45381,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;1.65296,MA0009.1;1.20602,MA0014.1;0.524262,MA0017.1;2.4142,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;1.35734,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;1.28333,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;2.95284,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;1.63368,MA0140.1;0.779643,MA0141.1;1.46638,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;1.05083,MA0065.2;0.577908,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;1.21162,MA0155.1;0.180766,MA0156.1;2.36058,MA0157.1;0.97481,MA0158.1;0,MA0159.1;2.03616,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;2.49771,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.122011,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2894_Preadipocyte_Adipocyte_tenocyte_pons_mesenchymal_Mesothelial_Smooth
|id=C2894
}}

Latest revision as of 12:15, 17 September 2013


Full id: C2894_Preadipocyte_Adipocyte_tenocyte_pons_mesenchymal_Mesothelial_Smooth



Phase1 CAGE Peaks

Hg19::chr7:37960416..37960421,+p11@EPDR1
Hg19::chr7:37960422..37960438,+p4@EPDR1
Hg19::chr7:37960439..37960448,+p10@EPDR1
Hg19::chr7:37960465..37960476,+p6@EPDR1


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
fat cell1.92e-1015
Uber Anatomy
Ontology termp-valuen
adult organism2.22e-16114
structure with developmental contribution from neural crest1.78e-13132
neural tube1.45e-1256
neural rod1.45e-1256
future spinal cord1.45e-1256
neural keel1.45e-1256
neural plate2.01e-1282
presumptive neural plate2.01e-1282
tube2.15e-12192
regional part of nervous system7.69e-1253
regional part of brain7.69e-1253
neurectoderm8.80e-1186
brain2.10e-1068
future brain2.10e-1068
anatomical conduit5.26e-10240
central nervous system4.59e-0981
cell layer1.08e-08309
multi-tissue structure1.97e-08342
primary circulatory organ3.05e-0827
posterior neural tube3.14e-0815
chordal neural plate3.14e-0815
epithelium4.03e-08306
tissue4.78e-08773
segmental subdivision of hindbrain1.13e-0712
hindbrain1.13e-0712
presumptive hindbrain1.13e-0712
anatomical cluster1.31e-07373
nervous system2.25e-0789
heart2.63e-0724
primitive heart tube2.63e-0724
primary heart field2.63e-0724
anterior lateral plate mesoderm2.63e-0724
heart tube2.63e-0724
heart primordium2.63e-0724
cardiac mesoderm2.63e-0724
cardiogenic plate2.63e-0724
heart rudiment2.63e-0724
ecto-epithelium3.82e-07104
regional part of forebrain8.89e-0741
forebrain8.89e-0741
anterior neural tube8.89e-0741
future forebrain8.89e-0741


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)
MA0003.11.45381
MA0004.10.71247
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.10.524262
MA0017.12.4142
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.12.95284
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.11.63368
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.05083
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.180766
MA0156.12.36058
MA0157.10.97481
MA0158.10
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.12.49771
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.122011
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
CHD2#1106410.34402283411698.73193255208051e-050.00129355220398119
CTCF#1066445.360256373075030.001211145381643620.00819931370412124
EBF1#187948.9064668465690.00015887907472010.00200086478773575
EP300#203346.77394172622320.0004748459821442640.00435403332126118
ETS1#211349.728760922202340.0001115955317418140.00154841580172489
HEY1#2346244.040111043105710.00375304636917980.0186623058492011
MAX#414946.452555509007120.0005767613195645490.00486640616044611
MYC#460945.22228187160940.001344309395272740.0089000525472513
RAD21#5885410.35503389545638.6948481184721e-050.00129948660939483
TAF1#687243.343046285745290.008005664898701650.0323344278890673
TBP#690843.706770687096390.005296377814784350.0245048687634901



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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