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{{Coexpression_clusters
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95,0.106889,0.128632,0.0845989,0.159153,0.0842401,1.74481e-05,0.0874421,0.100355,4.10228e-05,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.000845912,0.171704,0.208256,0.265058,0.256405,0.0109327,0.302133,0.40806,0.151361,0.0433477,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.00707033,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.0926658,0.222091,0.0228412,0.0675312,0.00453107,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.121257|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,0.581696,1.75588,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.975621,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.297585,0.682839,1.09415,1.10579,0.344471,0.49475,0.0842336,0.491074,0.740899,2.0411,0.371755,0.493145,1.59701,0.183156,0.53106,0.0946706,1.49501,0.822818,0.694903,0.173425,1.33034,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,1.80204,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,2.27581,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.353274,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,1.52945,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,1.22649,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,2.78996,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,1.73115,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.4289|tfbs_overrepresentation_jaspar=MA0003.1;0.443649,MA0004.1;1.69588,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.896009,MA0017.1;2.4142,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;0.69331,MA0058.1;1.47358,MA0059.1;1.47051,MA0060.1;1.01899,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;2.36824,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;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;1.6149,MA0093.1;1.32557,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;1.98562,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;2.8366,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;1.25938,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;3.07509,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;1.37305,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;1.05083,MA0065.2;1.7213,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;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.309472,MA0163.1;0.539587,MA0164.1;3.43559,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;3.5408,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;1.1888,MA0442.1;0}}
|full_id=C2209_acute_testis_spinal_Endothelial_rectum_heart_substantia
|id=C2209
}}

Latest revision as of 12:01, 17 September 2013


Full id: C2209_acute_testis_spinal_Endothelial_rectum_heart_substantia



Phase1 CAGE Peaks

Hg19::chr12:49488535..49488546,-p3@DHH
Hg19::chr12:49488554..49488568,-p2@DHH
Hg19::chr12:49488573..49488590,-p1@DHH
Hg19::chr19:2247294..2247304,+p@chr19:2247294..2247304
+


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
adult organism8.13e-41114
endothelial tube2.29e-199
arterial system endothelium2.29e-199
endothelium of artery2.29e-199
blood vessel endothelium8.35e-1618
endothelium8.35e-1618
cardiovascular system endothelium8.35e-1618
neural tube3.48e-1556
neural rod3.48e-1556
future spinal cord3.48e-1556
neural keel3.48e-1556
neural plate1.31e-1382
presumptive neural plate1.31e-1382
anatomical conduit7.98e-13240
neurectoderm1.29e-1286
simple squamous epithelium2.39e-1222
regional part of nervous system7.37e-1253
regional part of brain7.37e-1253
tube7.48e-12192
central nervous system3.61e-1181
anatomical cluster7.76e-11373
structure with developmental contribution from neural crest1.11e-10132
squamous epithelium1.72e-1025
nervous system3.15e-1089
ecto-epithelium5.05e-10104
gland of diencephalon2.17e-094
neuroendocrine gland2.17e-094
regional part of forebrain3.54e-0941
forebrain3.54e-0941
anterior neural tube3.54e-0941
future forebrain3.54e-0941
brain9.12e-0968
future brain9.12e-0968
vessel2.18e-0868
posterior neural tube6.83e-0815
chordal neural plate6.83e-0815
diencephalon1.21e-077
future diencephalon1.21e-077
medulla oblongata1.86e-073
myelencephalon1.86e-073
future myelencephalon1.86e-073
spinal cord1.90e-073
dorsal region element1.90e-073
dorsum1.90e-073
epithelial tube open at both ends2.19e-0759
blood vessel2.19e-0759
blood vasculature2.19e-0759
vascular cord2.19e-0759
valve4.07e-073
cardiac mesenchyme4.07e-073
cardial valve4.07e-073
tunica intima4.07e-073
heart layer4.07e-073
endocardium4.07e-073
endocardial cushion4.07e-073
presumptive endocardium4.07e-073
splanchnic layer of lateral plate mesoderm8.16e-0783


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)
MA0003.10.443649
MA0004.11.69588
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
MA0017.12.4142
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
MA0057.10.69331
MA0058.11.47358
MA0059.11.47051
MA0060.11.01899
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
MA0073.12.36824
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.11.6149
MA0093.11.32557
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
MA0114.11.98562
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.12.8366
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
MA0146.11.25938
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.23.07509
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.21.01696
MA0047.20.856092
MA0112.21.05083
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.12.30186
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.539587
MA0164.13.43559
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.23.5408
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
USF1#739134.771124457905970.01370465887188020.0482846158594033
ZBTB7A#5134135.513931980906920.009038352821081090.0342310897258808



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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