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Coexpression cluster:C2424: Difference between revisions

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{{Coexpression_clusters
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,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,2.01638,0.341754,0.809319,0.532789,1.37557,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,1.17228,0.371755,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.6318,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,1.70537,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.156682|tfbs_overrepresentation_jaspar=MA0003.1;0.233555,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.244769,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;0.393285,MA0061.1;0.360128,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;1.53734,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;1.4709,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;1.70187,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;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;0.195821,MA0146.1;0.221129,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.10559,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;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.327251,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2424_CD14_CD133_Dendritic_Natural_Basophils_chronic_Peripheral
|id=C2424
}}

Latest revision as of 12:05, 17 September 2013


Full id: C2424_CD14_CD133_Dendritic_Natural_Basophils_chronic_Peripheral



Phase1 CAGE Peaks

Hg19::chr17:56709188..56709203,-p1@ENST00000390893
Hg19::chr1:145382755..145382759,+p1@ENST00000364688
Hg19::chr1:63266602..63266609,-p@chr1:63266602..63266609
-
Hg19::chr2:88316053..88316067,-p1@ENST00000410792


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell3.70e-26168
angioblastic mesenchymal cell3.70e-26168
hematopoietic cell1.74e-23177
hematopoietic oligopotent progenitor cell1.79e-23161
hematopoietic multipotent progenitor cell1.79e-23161
leukocyte5.34e-21136
nongranular leukocyte2.27e-20115
hematopoietic lineage restricted progenitor cell8.88e-20120
lymphocyte3.55e-1453
common lymphoid progenitor3.55e-1453
nucleate cell4.72e-1455
lymphoid lineage restricted progenitor cell1.02e-1352
classical monocyte1.76e-1342
CD14-positive, CD16-negative classical monocyte1.76e-1342
animal cell2.39e-12679
eukaryotic cell2.39e-12679
lymphocyte of B lineage1.11e-1024
pro-B cell1.11e-1024
myeloid cell1.86e-10108
common myeloid progenitor1.86e-10108
connective tissue cell3.30e-10361
mesenchymal cell1.01e-09354
native cell1.18e-09722
motile cell1.76e-09386
defensive cell4.34e-0948
phagocyte4.34e-0948
stem cell5.94e-09441
multi fate stem cell2.41e-08427
somatic stem cell3.16e-08433
granulocyte monocyte progenitor cell1.26e-0767
macrophage dendritic cell progenitor1.29e-0761
B cell1.53e-0714
monopoietic cell6.03e-0759
monocyte6.03e-0759
monoblast6.03e-0759
promonocyte6.03e-0759
myeloid lineage restricted progenitor cell6.58e-0766
Uber Anatomy
Ontology termp-valuen
connective tissue8.34e-11371
bone marrow1.92e-0976
bone element1.16e-0882
skeletal element2.55e-0890
immune system5.82e-0793
Disease
Ontology termp-valuen
cancer6.35e-21235
disease of cellular proliferation1.07e-19239
organ system cancer2.65e-17137
hematologic cancer1.01e-1051
immune system cancer1.01e-1051
cell type cancer6.49e-09143
carcinoma5.31e-08106
leukemia8.24e-0739


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
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
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
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.53734
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.11.70187
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
MA0114.10.447443
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
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
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
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.327251
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
BATF#10538212.17890089615180.009566758805047810.0360155260197674
BCL11A#53335428.36945510360711.542446414682e-065.89215658752646e-05
BCL3#602325.91032710280379.48553136097325e-050.00137381695993439
BCLAF1#9774316.23948570759140.000380256706766480.00376646720390595
BRCA1#672210.09211532161190.0137713969900260.0484706949159615
BRF2#552902537.2877906976745.15958263355146e-060.000158163090890954
CCNT2#90534.752151182721970.01386206996689490.0487192329140037
CHD2#110637.758017125587640.003351522464536340.0172948097570884
EBF1#187936.679850134926750.005184294118278910.0240438071592403
EP300#203335.08045629466740.01144298405398240.0418875542958139
ETS1#211337.296570691651750.00400857377511390.019203313448884
FOSL1#8061219.85678985818650.003677050009233230.0185601191781117
FOSL2#2355312.69765045342130.000787568572975710.00616680718196207
FOXA1#316938.311064812039090.002740138182109850.0150358478222755
FOXA2#3170212.31523187633260.009361916285467240.0353437382496354
GATA1#2623310.17023110785030.001515158168498270.00966301929407616
GATA2#262439.55869880016550.001818151618357440.0108967024486189
GATA3#2625320.42738726790450.0001924415576258320.00231976036898479
GTF2B#2959323.95787245074320.0001197754562855920.00162436422269977
GTF2F1#296239.554745657568240.001820362319304780.010898069376089
HNF4A#3172211.56614518147680.01057585681762490.0390708139432589
HNF4G#3174214.37671126322340.006924169980439180.0293059405327885
IRF1#365935.727872815172930.008097114790333330.0320081215589562
IRF4#3662421.91451268674414.33289161192893e-060.000136343135600556
JUNB#3726322.95797449486590.0001359772504018780.001778946267659
JUND#372735.245997956403270.01043432751748420.0386861703148331
KAT2A#26483462.06751.69143680699618e-081.22419936719247e-06
MAFF#23764228.15767824497260.001846876180367150.0109246659153469
MAFK#7975320.32554985337240.0001953213688931110.00235094715291317
MEF2A#4205314.0574231822330.0005830038854186610.00488709710163251
MEF2C#4208330.9835158694685.56692972943475e-050.000941393416470913
NR2C2#7182324.46095817893070.0001125906063438030.00155519776959932
PAX5#507935.002174148383370.01196533174786410.0434886821790561
PBX3#5090316.43588451505810.0003669431395554610.00365783855607834
POU2F2#545236.829593043306890.004860473775203740.022758261403654
POU5F1#54602167.7196007259535.30170476996226e-050.000899455400373763
REST#597849.650028716128020.0001152825614219170.00156954705153743
RXRA#6256315.055962854350.0004758307997303580.00433830579598768
SETDB1#9869220.16001308900520.00356908685407640.018083338764512
STAT3#677437.889598747865680.003190760481680130.0167415138882789
TAF7#687938.574802053692940.00250055433515240.0140308061144889
TBP#690843.706770687096390.005296377814784350.0244064773472583
TCF12#693837.975848676639820.003090920396013070.0162773615993954
THAP1#55145215.68457230142570.005840469678357920.0262478081130007
USF1#739134.771124457905970.01370465887188020.0483009100637901
YY1#752844.911170749853860.00171871838055440.0106801468999061
ZBTB33#10009323.74854377248590.0001229451908818380.00165531426975742
ZEB1#6935312.66632401315790.000793336075912850.00613197353702355
ZNF263#1012736.166381227758010.006539814347975980.0279716467642011



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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