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Coexpression cluster:C2443: Difference between revisions

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{{Coexpression_clusters
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6166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.029604,0.0231432,0.0606443,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.0181825,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.0528669,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.037179,0.390754,0.0725176,0.0433915,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.0600054,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=1.44014,1.54039,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,1.44778,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.975621,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.911389,1.23824,0.598278,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,2.18092,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,1.28263,1.32819,1.6033,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,3.76398,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,1.32435,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,1.28386,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,1.23342,3.82793,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.91266|tfbs_overrepresentation_jaspar=MA0003.1;5.41581,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;1.65296,MA0009.1;1.20602,MA0014.1;2.45009,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,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;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;1.01899,MA0061.1;0.946082,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.841508,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;1.18043,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;8.10291,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;1.32557,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;1.33363,MA0103.1;0.521546,MA0105.1;1.22348,MA0106.1;0.869173,MA0107.1;1.1497,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;1.15856,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;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;1.70272,MA0146.1;4.2865,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.931615,MA0035.2;0.778873,MA0039.2;3.07509,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;1.05083,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;2.30186,MA0156.1;1.37856,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;3.50007,MA0163.1;1.90765,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;3.12283,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;1.1888,MA0442.1;0}}
|full_id=C2443_Mesenchymal_Hepatic_Alveolar_Smooth_Astrocyte_Renal_Hair
|id=C2443
}}

Latest revision as of 12:06, 17 September 2013


Full id: C2443_Mesenchymal_Hepatic_Alveolar_Smooth_Astrocyte_Renal_Hair



Phase1 CAGE Peaks

Hg19::chr17:79479822..79479830,-p1@ACTG1
Hg19::chr19:1026566..1026648,+p1@CNN2
Hg19::chr19:2096259..2096342,-p1@MOB3A
Hg19::chr7:143078379..143078454,+p1@ZYX


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

p.valueFDRnGenesnPathwayName
0.0001458532098643570.03077502728137932200Focal adhesion (KEGG):04510
8.75676438203826e-050.03077502728137932155Myometrial Relaxation and Contraction Pathways (Wikipathways):WP289
0.0001288708350416320.03077502728137932188Focal Adhesion (Wikipathways):WP306



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

GO IDGO nameFDR corrected p-value
GO:0005911intercellular junction0.00105713136868672
GO:0030054cell junction0.00326156077542858
GO:0005913cell-cell adherens junction0.0104577467891468
GO:0031032actomyosin structure organization and biogenesis0.0126684703362576
GO:0005856cytoskeleton0.0142566507029949
GO:0005912adherens junction0.0217068263005428
GO:0044459plasma membrane part0.0264873599816309
GO:0043232intracellular non-membrane-bound organelle0.0336456441217229
GO:0043228non-membrane-bound organelle0.0336456441217229
GO:0005516calmodulin binding0.0339637806473224
GO:0005886plasma membrane0.0470180521288173
GO:0030036actin cytoskeleton organization and biogenesis0.048091021929576
GO:0030029actin filament-based process0.048091021929576



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
somatic cell7.15e-44588
animal cell2.50e-28679
eukaryotic cell2.50e-28679
mesodermal cell2.09e-24121
native cell5.32e-24722
contractile cell4.80e-1959
embryonic cell3.20e-18250
muscle precursor cell5.50e-1758
myoblast5.50e-1758
multi-potent skeletal muscle stem cell5.50e-1758
muscle cell8.88e-1755
smooth muscle cell1.40e-1543
smooth muscle myoblast1.40e-1543
somatic stem cell1.43e-15433
multi fate stem cell1.87e-15427
stem cell7.20e-15441
electrically responsive cell1.80e-1461
electrically active cell1.80e-1461
non-terminally differentiated cell1.00e-12106
vascular associated smooth muscle cell2.64e-1232
fibroblast2.97e-1276
meso-epithelial cell5.36e-0945
endothelial cell7.01e-0936
lining cell8.67e-0858
barrier cell8.67e-0858
blood vessel endothelial cell2.25e-0718
embryonic blood vessel endothelial progenitor cell2.25e-0718
endothelial cell of vascular tree4.03e-0724
Uber Anatomy
Ontology termp-valuen
cardiovascular system2.58e-22109
mesoderm1.20e-21315
mesoderm-derived structure1.20e-21315
presumptive mesoderm1.20e-21315
vasculature2.02e-2178
vascular system2.02e-2178
circulatory system1.43e-20112
epithelial vesicle4.83e-1978
multilaminar epithelium2.80e-1783
vessel1.95e-1668
epithelial tube open at both ends3.62e-1659
blood vessel3.62e-1659
blood vasculature3.62e-1659
vascular cord3.62e-1659
somite4.22e-1671
presomitic mesoderm4.22e-1671
presumptive segmental plate4.22e-1671
dermomyotome4.22e-1671
trunk paraxial mesoderm4.22e-1671
lateral plate mesoderm4.88e-16203
splanchnic layer of lateral plate mesoderm1.46e-1583
dense mesenchyme tissue1.91e-1573
paraxial mesoderm2.74e-1572
presumptive paraxial mesoderm2.74e-1572
unilaminar epithelium1.84e-14148
skeletal muscle tissue2.55e-1462
striated muscle tissue2.55e-1462
myotome2.55e-1462
artery5.41e-1442
arterial blood vessel5.41e-1442
arterial system5.41e-1442
epithelial tube1.40e-13117
muscle tissue1.48e-1364
musculature1.48e-1364
musculature of body1.48e-1364
musculoskeletal system2.82e-13167
trunk mesenchyme1.63e-11122
mesenchyme4.57e-11160
entire embryonic mesenchyme4.57e-11160
organism subdivision8.97e-10264
systemic artery1.32e-0933
systemic arterial system1.32e-0933
trunk2.66e-08199
blood vessel endothelium2.25e-0718
endothelium2.25e-0718
cardiovascular system endothelium2.25e-0718
ectodermal placode3.20e-0731
surface structure5.17e-0799
simple squamous epithelium9.02e-0722


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)
MA0003.15.41581
MA0004.10.71247
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.12.45009
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
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
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.18043
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.18.10291
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.11.32557
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.70272
MA0146.14.2865
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.23.07509
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.21.05083
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.12.30186
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.13.50007
MA0163.11.90765
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.23.12283
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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#90546.336201576962630.0006203100587215640.00512090445204501
E2F6#187645.017155731697390.00157802193473060.00996776538292784
ELF1#199744.258097958807540.003041525565781240.016087814057464
EP300#203335.08045629466740.01144298405398240.0418904907853015
HEY1#2346244.040111043105710.00375304636917980.0186003136596958
HMGN3#932436.133910792512940.006640696683324720.0282942118517359
JUND#372735.245997956403270.01043432751748420.038687543723322
PAX5#507935.002174148383370.01196533174786410.0434917092686171
RXRA#6256315.055962854350.0004758307997303580.0043390633801658
SIN3A#2594245.408884726815140.001168172384885160.00796154761844302
SRF#6722310.34788369662590.001439893778401260.00923773366438045
TAF1#687243.343046285745290.008005664898701650.0322135864517627
TAF7#687938.574802053692940.00250055433515240.0140323139116104
TBP#690843.706770687096390.005296377814784350.0244140178575391
USF1#739134.771124457905970.01370465887188020.0483025400891027
ZBTB7A#5134147.35190930787590.000342223540015990.00346399343823706



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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