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Coexpression cluster:C2357: Difference between revisions

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2813,0.222656,0.228479,1.27686e-05,0.259989,0.390754,0.0725176,0.279739,0.108118,0.0371525,0.0102507,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.0944985,0.332746,0.271338,0.242121,0.298673,0.244395,6.21704e-06,0.128632,0.0036839,3.27633e-05,0.0842401,0.00984212,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.00401466,0.117657,0.0486914,0.175784,8.59317e-07,0.0805224,0.0109087,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.00142707,0.322827,0.0286371,1.25911e-09,0.00844265,4.51574e-05,0.208256,0.265058,0.0361085,0.0756763,0.302133,0.40806,0.151361,0.279606,0.0457079,0.150674,0.251128,0.246177,0.0011123,0.35852,0.000664446,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.00825997,0.000261968,0.398354,0.0267226,0.205977,0.34423,3.60457e-06,0.343425,0.132374,0.285122,0.22741,9.41269e-05,0.0424072,0.00732664,0.000291619,0.121257
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,5.25238,1.68405,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,1.73475,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,6.49933,1.23038,0.740899,0.463978,2.59922,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,3.55571,0.650393,0.402607,1.28263,1.32819,0.336329,2.35456,0.305238,1.00941,1.08,2.5716,0.95118,1.02594,0.844168,0.399165,1.27559,1.72726,6.25838,6.04591,2.1528,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,1.66879,1.15558,2.16273,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,2.81371,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,4.5548,2.52313,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,5.58091,1.48509,2.34913,1.94535,1.44718,1.91113,1.15194,0.980848,1.811,0.963351,2.1895,0.661255,1.95303,0.66252,2.26519,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.644569
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,5.25238,1.68405,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,1.73475,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,6.49933,1.23038,0.740899,0.463978,2.59922,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,3.55571,0.650393,0.402607,1.28263,1.32819,0.336329,2.35456,0.305238,1.00941,1.08,2.5716,0.95118,1.02594,0.844168,0.399165,1.27559,1.72726,6.25838,6.04591,2.1528,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,1.66879,1.15558,2.16273,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,2.81371,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,4.5548,2.52313,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,5.58091,1.48509,2.34913,1.94535,1.44718,1.91113,1.15194,0.980848,1.811,0.963351,2.1895,0.661255,1.95303,0.66252,2.26519,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.644569
|tfbs_overrepresentation_jaspar=MA0003.1;0.233555,MA0004.1;0.71247,MA0006.1;2.26728,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;1.41335,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;1.30988,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;2.54431,MA0055.1;11.6485,MA0056.1;0,MA0057.1;0.69331,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;0.0343867,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;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;0.344952,MA0140.1;1.83481,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.221129,MA0147.1;1.16748,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;1.01696,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;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.06783,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;1.6798,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;1.1888,MA0442.1;0
}}
}}

Revision as of 20:36, 22 January 2013


Full id: C2357_extraskeletal_small_Pericytes_alveolar_epithelioid_Fibroblast_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr15:96874063..96874074,+p10@NR2F2
Hg19::chr15:96874145..96874166,+p7@NR2F2
Hg19::chr15:96874216..96874236,+p13@NR2F2
Hg19::chr15:96874244..96874259,+p5@NR2F2


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
trunk2.39e-27199
organism subdivision5.79e-22264
mesenchyme1.81e-21160
entire embryonic mesenchyme1.81e-21160
epithelial tube8.45e-18117
trunk mesenchyme3.23e-17122
vasculature5.30e-1778
vascular system5.30e-1778
unilaminar epithelium1.20e-16148
anatomical cluster1.10e-15373
subdivision of trunk1.18e-14112
cell layer1.79e-14309
vessel5.22e-1468
epithelium1.46e-13306
multi-tissue structure1.50e-13342
splanchnic layer of lateral plate mesoderm8.05e-1383
anatomical conduit2.29e-12240
epithelial vesicle4.65e-1278
epithelial tube open at both ends1.51e-1159
blood vessel1.51e-1159
blood vasculature1.51e-1159
vascular cord1.51e-1159
multi-cellular organism7.65e-11656
immaterial anatomical entity8.22e-11117
skeletal muscle tissue3.16e-1062
striated muscle tissue3.16e-1062
myotome3.16e-1062
muscle tissue4.30e-1064
musculature4.30e-1064
musculature of body4.30e-1064
cardiovascular system5.99e-10109
abdominal segment of trunk6.85e-1060
abdomen6.85e-1060
circulatory system7.85e-10112
somite1.01e-0971
presomitic mesoderm1.01e-0971
presumptive segmental plate1.01e-0971
dermomyotome1.01e-0971
trunk paraxial mesoderm1.01e-0971
trunk region element1.51e-09101
body cavity precursor2.37e-0954
paraxial mesoderm2.45e-0972
presumptive paraxial mesoderm2.45e-0972
dense mesenchyme tissue3.03e-0973
tube3.42e-09192
anatomical space7.31e-0995
multilaminar epithelium1.07e-0883
anatomical cavity6.71e-0861
artery6.77e-0842
arterial blood vessel6.77e-0842
arterial system6.77e-0842
renal system1.27e-0748
abdomen element1.66e-0754
abdominal segment element1.66e-0754
urinary system structure2.14e-0747
systemic artery3.07e-0733
systemic arterial system3.07e-0733
compound organ3.41e-0768
anatomical system3.74e-07624
blood vessel endothelium4.88e-0718
endothelium4.88e-0718
cardiovascular system endothelium4.88e-0718
anatomical group6.01e-07625
simple squamous epithelium6.32e-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)
MA0003.10.233555
MA0004.10.71247
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.11.41335
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
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.12.54431
MA0055.111.6485
MA0056.10
MA0057.10.69331
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
MA0073.10.0343867
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
MA0114.11.13665
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
MA0139.10.344952
MA0140.11.83481
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.221129
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
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
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.6798
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
CEBPB#105147.971147625824820.0002476385788090830.00267845127715843
E2F1#186944.907389214879320.001724022357361790.0106409296720352
E2F4#187439.501045236463330.001850751034728270.0109259277212133
FOSL1#8061219.85678985818650.003677050009233230.0185574285258679
GATA3#2625427.2365163572061.81561517799785e-066.76493162950114e-05
GTF2B#2959431.94382993432429.59435337635006e-074.08323012336033e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.000717094258844672
HEY1#2346244.040111043105710.00375304636917980.0185817962335626
HMGN3#932448.178547723350590.0002234570284440470.00247929763026324
HNF4A#3172423.13229036295373.48990320893214e-060.000115415453210153
HNF4G#3174428.75342252644681.46167379934821e-065.66020578161394e-05
IRF1#365947.63716375356390.0002938853996185490.00307176713878719
MAX#414946.452555509007120.0005767613195645490.00485112148296705
MXI1#460149.96157162875930.0001015224754950450.0014224451057455
NFYA#4800418.42558069983058.67100748407158e-060.000234305653461566
NR2C2#7182432.61461090524098.82887529809196e-073.81813212114876e-05
RXRA#6256420.07461713913336.1537798808435e-060.000182014901437387
SIN3A#2594245.408884726815140.001168172384885160.00795428059101714
SP1#666745.69838137814090.0009482606065333980.00683615582838003
SREBF1#6720447.00584944048832.04523668136926e-071.10047642331543e-05
SRF#6722413.79717826216782.75840773062708e-050.000583759564293741
TAF1#687243.343046285745290.008005664898701650.0321825880044458
TBP#690843.706770687096390.005296377814784350.0243892593738211
TCF7L2#6934410.77017656313737.42969445082454e-050.00115297155832045
ZNF263#1012748.221841637010680.0002187871180958320.0024855768331133



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2357&oldid=2570868"