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Coexpression cluster:C1142: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.01633,0.75236,0.384703,0.529489,0.90845,0.52784,0.604235,0.643217,0.637583,2.78041,0.497563,0.647852,0.541517,1.44576,0.341795,0.365029,0.827563,0.28906,1.70194,1.10853,0.384762,0.23059,0.520063,0.338096,0.430372,0.670692,0.164928,2.22004,0.915262,0.459534,1.1974,0.864517,1.31702,0.546594,1.50609,0.71891,0.305874,1.3112,0.282922,0.207499,0.307642,1.16235,0.0729319,0.340293,0.794027,1.06715,0.60533,0.486696,0.0670664,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.897759,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,1.13397,0.232216,0.744055,1.0929,0.531388,1.54605,0.156354,0.782748,0.850825,1.0864,0.200147,0.798651,0.625403,0.229431,1.04131,0.0324537,0.097572,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.194299,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,1.90834,0.589207,0.43012,0.873303,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,1.00084,1.19482,0.762789,0.736663,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,1.28879,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.722945,1.16062,0.241704,1.0153,0.619774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,2.75549,0.7715,0.624608,0.695791,0.602897,0.860909
|tfbs_overrepresentation_jaspar=MA0003.1;0.358813,MA0004.1;1.25543,MA0006.1;0.904424,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;2.12603,MA0017.1;0.991615,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.940207,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.382278,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.362619,MA0056.1;0,MA0057.1;0.369442,MA0058.1;1.04727,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.00958848,MA0074.1;0.60198,MA0076.1;1.08222,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;1.04478,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;1.37625,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.9112,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.340955,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;1.14351,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.760835,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.547495,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;1.46178,MA0146.1;0.547931,MA0147.1;0.768766,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;2.39331,MA0035.2;0.564239,MA0039.2;0.854285,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.95459,MA0104.2;1.85658,MA0047.2;0.636643,MA0112.2;0.944394,MA0065.2;0.282161,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;0.534073,MA0156.1;0.959643,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;1.55314,MA0163.1;0.382702,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;1.58069,MA0102.2;1.51913,MA0258.1;0.687127,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:43, 22 January 2013


Full id: C1142_Mesenchymal_Fibroblast_Pericytes_Smooth_Renal_Hepatic_Hair



Phase1 CAGE Peaks

Hg19::chr11:46958264..46958342,+p1@C11orf49
Hg19::chr20:327736..327767,+p1@NRSN2
Hg19::chr2:27545939..27545981,-p1@MPV17
Hg19::chrX:134156502..134156577,-p1@FAM127C
Hg19::chrX:134166360..134166371,+p2@FAM127A
Hg19::chrX:134166376..134166394,+p1@FAM127A
Hg19::chrX:48931650..48931681,-p1@PRAF2


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

GO IDGO nameFDR corrected p-value
GO:0000002mitochondrial genome maintenance0.0240980092024216
GO:0015813L-glutamate transport0.0240980092024216
GO:0015800acidic amino acid transport0.0240980092024216
GO:0005779integral to peroxisomal membrane0.0240980092024216
GO:0031231intrinsic to peroxisomal membrane0.0240980092024216
GO:0043025cell soma0.0321322983860711
GO:0031903microbody membrane0.0321322983860711
GO:0006800oxygen and reactive oxygen species metabolic process0.0321322983860711
GO:0005778peroxisomal membrane0.0321322983860711
GO:0044439peroxisomal part0.0321322983860711
GO:0044438microbody part0.0321322983860711
GO:0016020membrane0.036124967424513
GO:0030133transport vesicle0.0364189068602428
GO:0006865amino acid transport0.0375136993092468
GO:0015837amine transport0.0375136993092468
GO:0007005mitochondrion organization and biogenesis0.0375136993092468
GO:0046942carboxylic acid transport0.0375136993092468
GO:0015849organic acid transport0.0375136993092468
GO:0042579microbody0.0375136993092468
GO:0005777peroxisome0.0375136993092468
GO:0031301integral to organelle membrane0.0495754959062544



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 layer1.28e-32309
epithelium2.76e-31306
multi-tissue structure9.22e-27342
anatomical cluster9.11e-26373
multi-cellular organism2.99e-23656
tube1.41e-20192
structure with developmental contribution from neural crest4.32e-20132
anatomical system1.25e-19624
epithelial vesicle1.30e-1978
anatomical conduit2.34e-19240
anatomical group3.12e-19625
dense mesenchyme tissue8.97e-1873
paraxial mesoderm1.95e-1772
presumptive paraxial mesoderm1.95e-1772
somite5.26e-1771
presomitic mesoderm5.26e-1771
presumptive segmental plate5.26e-1771
dermomyotome5.26e-1771
trunk paraxial mesoderm5.26e-1771
ectoderm-derived structure8.00e-17171
ectoderm8.00e-17171
presumptive ectoderm8.00e-17171
multilaminar epithelium3.14e-1683
mesenchyme3.56e-16160
entire embryonic mesenchyme3.56e-16160
neural plate4.84e-1682
presumptive neural plate4.84e-1682
developing anatomical structure5.22e-16581
embryo9.85e-16592
ecto-epithelium1.29e-15104
skeletal muscle tissue2.10e-1562
striated muscle tissue2.10e-1562
myotome2.10e-1562
brain4.01e-1568
future brain4.01e-1568
central nervous system5.66e-1581
neurectoderm7.11e-1586
muscle tissue1.38e-1464
musculature1.38e-1464
musculature of body1.38e-1464
embryonic structure4.31e-14564
organ part5.33e-14218
germ layer6.09e-14560
germ layer / neural crest6.09e-14560
embryonic tissue6.09e-14560
presumptive structure6.09e-14560
germ layer / neural crest derived structure6.09e-14560
epiblast (generic)6.09e-14560
nervous system1.17e-1389
neural tube1.99e-1356
neural rod1.99e-1356
future spinal cord1.99e-1356
neural keel1.99e-1356
regional part of nervous system2.74e-1353
regional part of brain2.74e-1353
organism subdivision3.23e-13264
pre-chordal neural plate3.76e-1361
trunk mesenchyme6.03e-13122
vasculature3.86e-1278
vascular system3.86e-1278
splanchnic layer of lateral plate mesoderm2.28e-1183
epithelial tube3.80e-11117
unilaminar epithelium4.28e-11148
trunk6.57e-11199
regional part of forebrain2.02e-1041
forebrain2.02e-1041
anterior neural tube2.02e-1041
future forebrain2.02e-1041
telencephalon6.84e-1034
cerebral hemisphere1.76e-0932
epithelial tube open at both ends2.27e-0959
blood vessel2.27e-0959
blood vasculature2.27e-0959
vascular cord2.27e-0959
artery2.47e-0942
arterial blood vessel2.47e-0942
arterial system2.47e-0942
brain grey matter2.61e-0934
gray matter2.61e-0934
regional part of telencephalon5.03e-0932
vessel5.10e-0968
organ system subdivision5.10e-08223
regional part of cerebral cortex8.41e-0822
cerebral cortex8.81e-0825
pallium8.81e-0825
cardiovascular system1.16e-07109


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)
MA0003.10.358813
MA0004.11.25543
MA0006.10.904424
MA0007.10.483857
MA0009.10.973289
MA0014.12.12603
MA0017.10.991615
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.940207
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.10.369442
MA0058.11.04727
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.00958848
MA0074.10.60198
MA0076.11.08222
MA0077.10.934645
MA0078.10.703614
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.11.37625
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.9112
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.11.14351
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.760835
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.11.46178
MA0146.10.547931
MA0147.10.768766
MA0148.10.528066
MA0149.10.555119
MA0062.22.39331
MA0035.20.564239
MA0039.20.854285
MA0138.20.704862
MA0002.20.213296
MA0137.20.95459
MA0104.21.85658
MA0047.20.636643
MA0112.20.944394
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.534073
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.11.55314
MA0163.10.382702
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.21.58069
MA0102.21.51913
MA0258.10.687127
MA0259.10.289405
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
E2F6#187653.583682665498130.004598101897827240.0217235666383416
ELF1#199753.041498542005380.009719562269370750.0365591501783048
ELK4#200536.958149282200580.006773584590600160.0287513270090506
ETS1#211345.559291955544190.003022564475303460.0160484804898942
GABPB1#255355.048345597272980.0009267438350018040.00673637245154186
HEY1#2346252.885793602218360.01231366941853030.0446211901183818
MYC#460953.730201336863860.003821944222306690.0188683541779006
POLR2A#543072.147453176558070.004747636447610280.0223260121100441
SIX5#14791237.322878009482430.00586667625269160.0263304598691387
SREBF1#6720213.43024269728240.008849476021677450.0335900572861338
TAF1#687262.865468244924540.003728330207471460.0185836433225844
USF1#739154.543928055148540.001522788355968760.00970279379592589
YY1#752853.507979107038470.005072570672808980.0236116329499264
ZNF143#770235.786089950954810.0113300558873240.0415513626945795



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:C1142&oldid=2569653"