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Coexpression cluster:C2731: Difference between revisions

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{{Coexpression_clusters
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467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.0231432,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.0627948,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.0554083,0.0271466,0.25788,0.181895,0.253768,0.00626086,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.0102294,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0036839,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.00120337,0.302133,0.000213981,0.151361,0.279606,0.0457079,0.150674,0.251128,0.246177,0.0103202,0.35852,0.318525,0.213257,0.287217,0.122782,0.0167026,0.289049,0.266974,0.125746,0.112897,0.0926658,0.00218951,0.205977,0.000944652,0.00453107,0.343425,0.132374,0.00491013,0.00236186,0.203996,0.276721,0.0585101,0.264707,0.000388714|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,0.741427,0.534346,0.739643,0.821651,2.71307,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,2.39977,0.471262,0.356737,0.223552,0.581762,0.505745,0.731221,0.528529,1.53003,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.285913,0.491074,0.740899,2.0411,0.371755,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,1.46445,0.776148,1.13655,0.825354,2.70182,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,1.03936,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,2.68455,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,2.11789,0.518428,3.77839,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,6.0639,0.0401987|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.524262,MA0017.1;1.41335,MA0019.1;2.02743,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;1.66514,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;1.98521,MA0058.1;0.605914,MA0059.1;1.47051,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;16.4179,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;37.1392,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;3.33935,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;1.13665,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;2.47057,MA0140.1;0.779643,MA0141.1;1.46638,MA0142.1;1.00381,MA0143.1;3.39479,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;4.36159,MA0062.2;0.353589,MA0035.2;1.83323,MA0039.2;3.07509,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,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;0.180766,MA0156.1;0.560797,MA0157.1;2.23474,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;1.90765,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;19.9498,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2731_optic_Endothelial_small_corpus_Prostate_medulla_Pericytes
|id=C2731
}}

Latest revision as of 12:11, 17 September 2013


Full id: C2731_optic_Endothelial_small_corpus_Prostate_medulla_Pericytes



Phase1 CAGE Peaks

Hg19::chr3:170138971..170138982,+p11@CLDN11
Hg19::chr3:170138985..170138998,+p7@CLDN11
Hg19::chr3:170139006..170139041,+p3@CLDN11
Hg19::chr3:170139046..170139064,+p4@CLDN11


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>

Uber Anatomy
Ontology termp-valuen
cell layer1.51e-34309
epithelium5.06e-33306
anatomical conduit5.17e-31240
tube1.50e-28192
anatomical cluster3.82e-27373
vasculature9.96e-2778
vascular system9.96e-2778
structure with developmental contribution from neural crest4.57e-25132
neural plate1.72e-2382
presumptive neural plate1.72e-2382
cardiovascular system1.44e-21109
vessel2.21e-2168
circulatory system2.54e-21112
neurectoderm4.61e-2186
neural tube6.35e-2156
neural rod6.35e-2156
future spinal cord6.35e-2156
neural keel6.35e-2156
splanchnic layer of lateral plate mesoderm2.76e-1983
regional part of nervous system5.93e-1953
regional part of brain5.93e-1953
multi-tissue structure5.89e-18342
brain2.86e-1768
future brain2.86e-1768
epithelial tube open at both ends6.77e-1759
blood vessel6.77e-1759
blood vasculature6.77e-1759
vascular cord6.77e-1759
epithelial vesicle6.41e-1678
central nervous system7.65e-1681
adult organism2.75e-15114
pre-chordal neural plate2.81e-1561
ecto-epithelium2.88e-15104
dense mesenchyme tissue1.01e-1473
unilaminar epithelium1.12e-14148
paraxial mesoderm1.54e-1472
presumptive paraxial mesoderm1.54e-1472
epithelial tube2.88e-14117
somite4.37e-1471
presomitic mesoderm4.37e-1471
presumptive segmental plate4.37e-1471
dermomyotome4.37e-1471
trunk paraxial mesoderm4.37e-1471
nervous system5.33e-1489
anatomical system5.84e-14624
anatomical group8.62e-14625
regional part of forebrain3.77e-1341
forebrain3.77e-1341
anterior neural tube3.77e-1341
future forebrain3.77e-1341
muscle tissue2.11e-1264
musculature2.11e-1264
musculature of body2.11e-1264
skeletal muscle tissue3.12e-1262
striated muscle tissue3.12e-1262
myotome3.12e-1262
multi-cellular organism7.54e-12656
artery9.10e-1242
arterial blood vessel9.10e-1242
arterial system9.10e-1242
trunk mesenchyme1.65e-11122
multilaminar epithelium1.97e-1183
telencephalon8.70e-1134
brain grey matter1.05e-1034
gray matter1.05e-1034
systemic artery1.95e-1033
systemic arterial system1.95e-1033
regional part of telencephalon1.37e-0932
cerebral hemisphere1.68e-0932
posterior neural tube1.84e-0915
chordal neural plate1.84e-0915
germ layer2.12e-09560
germ layer / neural crest2.12e-09560
embryonic tissue2.12e-09560
presumptive structure2.12e-09560
germ layer / neural crest derived structure2.12e-09560
epiblast (generic)2.12e-09560
blood vessel endothelium3.82e-0918
endothelium3.82e-0918
cardiovascular system endothelium3.82e-0918
embryonic structure7.44e-09564


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.11.41335
MA0019.12.02743
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
MA0042.11.66514
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.98521
MA0058.10.605914
MA0059.11.47051
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.116.4179
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.137.1392
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
MA0106.13.33935
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
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
MA0139.12.47057
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.13.39479
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.14.36159
MA0062.20.353589
MA0035.21.83323
MA0039.23.07509
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.12.23474
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.11.90765
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.219.9498
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

No analysis results for this cluster

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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