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Coexpression cluster:C843: Difference between revisions

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{{Coexpression_clusters
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coat of endocytic vesicle!0.0322402009543343!1175$GO:0030669!clathrin-coated endocytic vesicle membrane!0.0322402009543343!1175$GO:0030122!AP-2 adaptor complex!0.0322402009543343!1175$GO:0030666!endocytic vesicle membrane!0.0322402009543343!1175$GO:0003924!GTPase activity!0.0322402009543343!389;84617$GO:0045334!clathrin-coated endocytic vesicle!0.0322402009543343!1175$GO:0006901!vesicle coating!0.0322402009543343!1175$GO:0048268!clathrin cage assembly!0.0322402009543343!1175$GO:0006900!membrane budding!0.0322402009543343!1175$GO:0005515!protein binding!0.0322402009543343!389;26262;54849;10494;1175;30851$GO:0030132!clathrin coat of coated pit!0.0418403982307954!1175$GO:0016050!vesicle organization and biogenesis!0.047192048562374!1175$GO:0030178!negative regulation of Wnt receptor signaling 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0.536392,0.775775|tfbs_overrepresentation_for_novel_motifs=0.76751,1.9417,0.273994,0.404877,0.237701,0.403356,0.474413,0.434224,0.138703,1.04851,0.375531,0.515448,1.16754,0.46359,0.236531,0.256724,0.68716,0.191625,0.371758,0.400542,0.274046,2.5877,1.02534,0.233338,0.844704,2.28298,0.0930454,1.02097,1.94395,0.590419,0.355553,0.722879,0.958783,1.17821,1.1315,0.0928746,0.593726,0.404426,0.186493,2.52061,0.207288,0.340749,0.302519,0.235234,1.62511,0.814459,0.47544,0.365597,0.116302,0.240465,0.550604,0.486559,0.468946,0.797754,0.947672,0.466348,0.244111,1.11117,0.994052,0.434711,0.762758,1.20168,0.139078,0.660336,1.23797,0.627106,1.0348,1.4,0.712787,1.2388,2.39225,0.144996,0.210881,0.945703,1.68253,1.08678,0.292851,1.55336,0.709631,0.309107,0.11972,0.659298,0.49429,0.142768,0.89511,6.3077,0.175904,0.0795497,0.575506,1.4989,1.12715,0.868602,0.739223,0.171001,0.238337,0.18161,0.368981,0.780743,0.579925,0.896538,0.187593,0.733724,0.775299,0.690713,0.616014,0.970906,0.675372,0.460348,0.31439,1.19204,0.283874,0.772599,0.269151,0.384185,1.07963,0.204477,2.50286,0.354459,0.624851,0.515375,0.937551,0.57318,0.400807,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,0.182384,0.869279,0.358161,0.993705,0.50181,1.13991,0.0752959,0.350108,0.394712,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,0.337738,0.503344,3.35427,2.66605,0.869654,0.821366,0.477214,1.26919,0.560015,0.225815,0.314669,1.4338,1.05976,0.851493,0.708865,0.793294,0.633206,0.493542,0.931981,0.473159,7.52033|tfbs_overrepresentation_jaspar=MA0003.1;14.4878,MA0004.1;0.380329,MA0006.1;0.665232,MA0007.1;2.55746,MA0009.1;0.828613,MA0014.1;7.41786,MA0017.1;0.270554,MA0019.1;0.520264,MA0024.1;0.725404,MA0025.1;0.960689,MA0027.1;2.43535,MA0028.1;0.25013,MA0029.1;0.744375,MA0030.1;0.733118,MA0031.1;0.669876,MA0038.1;1.20033,MA0040.1;0.750125,MA0041.1;0.397617,MA0042.1;0.367902,MA0043.1;0.828925,MA0046.1;0.817858,MA0048.1;0.830349,MA0050.1;0.368721,MA0051.1;0.473017,MA0052.1;0.753928,MA0055.1;0.577037,MA0056.1;0,MA0057.1;0.802927,MA0058.1;0.293055,MA0059.1;0.291897,MA0060.1;0.848451,MA0061.1;0.757837,MA0063.1;0,MA0066.1;0.477449,MA0067.1;1.1435,MA0068.1;0.631708,MA0069.1;0.814052,MA0070.1;0.803003,MA0071.1;0.440254,MA0072.1;0.798564,MA0073.1;1.91004,MA0074.1;0.4723,MA0076.1;0.307383,MA0077.1;0.790956,MA0078.1;0.568317,MA0081.1;0.292043,MA0083.1;0.836033,MA0084.1;1.32998,MA0087.1;0.79615,MA0088.1;2.74176,MA0089.1;0,MA0090.1;0.320494,MA0091.1;0.382762,MA0092.1;0.347826,MA0093.1;0.238771,MA0095.1;0,MA0098.1;0,MA0100.1;0.49029,MA0101.1;0.678051,MA0103.1;0.228129,MA0105.1;1.60143,MA0106.1;0.516528,MA0107.1;1.01551,MA0108.2;0.666881,MA0109.1;0,MA0111.1;0.885497,MA0113.1;0.532314,MA0114.1;0.174997,MA0115.1;1.06753,MA0116.1;0.536665,MA0117.1;0.865782,MA0119.1;0.760742,MA0122.1;0.891407,MA0124.1;1.0263,MA0125.1;0.942948,MA0130.1;0,MA0131.1;0.585907,MA0132.1;0,MA0133.1;0,MA0135.1;0.858623,MA0136.1;0.483775,MA0139.1;2.34656,MA0140.1;0.437738,MA0141.1;0.290336,MA0142.1;0.638837,MA0143.1;0.532484,MA0144.1;0.163394,MA0145.1;0.332712,MA0146.1;8.98507,MA0147.1;0.543675,MA0148.1;0.403564,MA0149.1;0.428597,MA0062.2;0.366815,MA0035.2;0.437071,MA0039.2;9.67447,MA0138.2;0.569505,MA0002.2;0.407187,MA0137.2;0.255808,MA0104.2;0.428616,MA0047.2;0.504873,MA0112.2;6.91351,MA0065.2;0.147044,MA0150.1;0.315136,MA0151.1;0,MA0152.1;0.443956,MA0153.1;0.926242,MA0154.1;3.28929,MA0155.1;0.866026,MA0156.1;0.257809,MA0157.1;0.612166,MA0158.1;0,MA0159.1;0.185458,MA0160.1;0.417847,MA0161.1;0,MA0162.1;7.09323,MA0163.1;9.65096,MA0164.1;0.544294,MA0080.2;0.238846,MA0018.2;0.517858,MA0099.2;0.444294,MA0079.2;15.1741,MA0102.2;1.36707,MA0258.1;0.919347,MA0259.1;0.560522,MA0442.1;0}}
|full_id=C843_Alveolar_Mesenchymal_Hepatic_Placental_Renal_Smooth_Fibroblast
|id=C843
}}

Latest revision as of 11:32, 17 September 2013


Full id: C843_Alveolar_Mesenchymal_Hepatic_Placental_Renal_Smooth_Fibroblast



Phase1 CAGE Peaks

Hg19::chr16:90015139..90015208,+p1@DEF8
Hg19::chr17:3571863..3571881,-p1@TAX1BP3
Hg19::chr18:12308232..12308252,+p1@TUBB6
Hg19::chr19:47354061..47354076,-p2@AP2S1
Hg19::chr1:113249721..113249731,-p3@RHOC
Hg19::chr1:113249734..113249762,-p1@RHOC
Hg19::chr1:113249948..113250035,-p4@RHOC
Hg19::chr2:242447692..242447726,-p4@STK25
Hg19::chr2:242447732..242447779,-p2@STK25
Hg19::chr5:176074455..176074519,+p1@TSPAN17


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:0030128clathrin coat of endocytic vesicle0.0322402009543343
GO:0030669clathrin-coated endocytic vesicle membrane0.0322402009543343
GO:0030122AP-2 adaptor complex0.0322402009543343
GO:0030666endocytic vesicle membrane0.0322402009543343
GO:0003924GTPase activity0.0322402009543343
GO:0045334clathrin-coated endocytic vesicle0.0322402009543343
GO:0006901vesicle coating0.0322402009543343
GO:0048268clathrin cage assembly0.0322402009543343
GO:0006900membrane budding0.0322402009543343
GO:0005515protein binding0.0322402009543343
GO:0030132clathrin coat of coated pit0.0418403982307954
GO:0016050vesicle organization and biogenesis0.047192048562374
GO:0030178negative regulation of Wnt receptor signaling pathway0.048998473354561



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>

Cell Type
Ontology termp-valuen
embryonic cell4.12e-38250
mesodermal cell1.14e-36121
animal cell1.59e-21679
eukaryotic cell1.59e-21679
somatic cell2.19e-21588
contractile cell8.90e-2159
muscle precursor cell1.76e-1958
myoblast1.76e-1958
multi-potent skeletal muscle stem cell1.76e-1958
non-terminally differentiated cell3.86e-19106
muscle cell1.03e-1855
smooth muscle cell3.16e-1743
smooth muscle myoblast3.16e-1743
electrically responsive cell7.96e-1761
electrically active cell7.96e-1761
epithelial cell5.69e-16253
meso-epithelial cell2.53e-1545
lining cell2.58e-1558
barrier cell2.58e-1558
vascular associated smooth muscle cell1.12e-1432
endothelial cell1.60e-1436
fibroblast9.02e-1376
endothelial cell of vascular tree2.33e-1224
blood vessel endothelial cell7.30e-1118
embryonic blood vessel endothelial progenitor cell7.30e-1118
native cell2.97e-09722
squamous epithelial cell8.52e-0963
epithelial cell of nephron1.40e-0815
kidney cell1.21e-0717
kidney epithelial cell1.21e-0717
kidney cortical cell1.65e-0712
renal cortical epithelial cell1.65e-0712
Uber Anatomy
Ontology termp-valuen
vasculature2.31e-2878
vascular system2.31e-2878
epithelial tube4.02e-27117
splanchnic layer of lateral plate mesoderm6.65e-2683
epithelial vesicle1.12e-2478
vessel1.16e-2468
unilaminar epithelium3.90e-24148
epithelial tube open at both ends3.58e-2359
blood vessel3.58e-2359
blood vasculature3.58e-2359
vascular cord3.58e-2359
organism subdivision1.31e-22264
multilaminar epithelium3.24e-2283
mesenchyme2.79e-21160
entire embryonic mesenchyme2.79e-21160
trunk6.77e-21199
somite1.29e-2071
presomitic mesoderm1.29e-2071
presumptive segmental plate1.29e-2071
dermomyotome1.29e-2071
trunk paraxial mesoderm1.29e-2071
dense mesenchyme tissue3.09e-2073
paraxial mesoderm5.06e-2072
presumptive paraxial mesoderm5.06e-2072
cardiovascular system1.18e-19109
circulatory system1.37e-19112
trunk mesenchyme1.72e-19122
cell layer2.22e-19309
epithelium9.07e-19306
artery9.95e-1942
arterial blood vessel9.95e-1942
arterial system9.95e-1942
skeletal muscle tissue1.01e-1762
striated muscle tissue1.01e-1762
myotome1.01e-1762
multi-cellular organism2.33e-17656
muscle tissue5.77e-1764
musculature5.77e-1764
musculature of body5.77e-1764
anatomical system1.58e-15624
anatomical group2.85e-15625
systemic artery1.08e-1333
systemic arterial system1.08e-1333
multi-tissue structure3.86e-12342
anatomical cluster1.12e-11373
simple squamous epithelium3.98e-1122
blood vessel endothelium7.30e-1118
endothelium7.30e-1118
cardiovascular system endothelium7.30e-1118
anatomical conduit1.02e-10240
squamous epithelium1.04e-1025
mesoderm1.39e-10315
mesoderm-derived structure1.39e-10315
presumptive mesoderm1.39e-10315
developing anatomical structure1.97e-09581
embryo3.05e-09592
surface structure5.96e-0999
compound organ7.85e-0968
nephron epithelium1.40e-0815
renal tubule1.40e-0815
nephron tubule1.40e-0815
nephron1.40e-0815
uriniferous tubule1.40e-0815
nephrogenic mesenchyme1.40e-0815
parenchyma1.88e-0815
tube2.60e-08192
excretory tube3.17e-0816
kidney epithelium3.17e-0816


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)
MA0003.114.4878
MA0004.10.380329
MA0006.10.665232
MA0007.12.55746
MA0009.10.828613
MA0014.17.41786
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.11.20033
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.830349
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.577037
MA0056.10
MA0057.10.802927
MA0058.10.293055
MA0059.10.291897
MA0060.10.848451
MA0061.10.757837
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.631708
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.11.91004
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.12.74176
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.678051
MA0103.10.228129
MA0105.11.60143
MA0106.10.516528
MA0107.11.01551
MA0108.20.666881
MA0109.10
MA0111.10.885497
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.536665
MA0117.10.865782
MA0119.10.760742
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.12.34656
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.332712
MA0146.18.98507
MA0147.10.543675
MA0148.10.403564
MA0149.10.428597
MA0062.20.366815
MA0035.20.437071
MA0039.29.67447
MA0138.20.569505
MA0002.20.407187
MA0137.20.255808
MA0104.20.428616
MA0047.20.504873
MA0112.26.91351
MA0065.20.147044
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.13.28929
MA0155.10.866026
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.17.09323
MA0163.19.65096
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.215.1741
MA0102.21.36707
MA0258.10.919347
MA0259.10.560522
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
ATF3#46736.738952357802630.008358935771413540.0329110643531124
BRF2#552901107.4575581395350.009267350174716920.0350145714817039
CCNT2#90553.168100788481320.01227157669794290.0444840928380293
CHD2#110644.137609133646740.01136509692198320.0416637775083366
CTCF#1066484.288205098460024.59406669642002e-050.000807335910663656
CTCFL#14069035.923942307692310.01190857855768930.0433351928915162
E2F1#186962.944433528927590.007015119886153280.0296356324646049
E2F6#187673.512009012188170.0008453950419482970.00637350846647211
EGR1#195894.489361185329124.28342047930016e-060.000135562470132615
ELF1#199793.832288162926781.71269377095518e-050.000392091242316501
ESR1#2099412.30744131846180.0001999674803985190.00240050617072884
ETS1#211365.83725655332140.0001713587518742850.0020897403884865
GABPB1#255374.947378685327529.16652307636923e-050.00133557826949348
HEY1#2346293.636099938795142.70877685450303e-050.000578176876982306
IRF1#365953.818581876781950.005465628575453730.0247592618864373
PAX5#507974.668695871824480.0001341235735206540.0017595442651581
POLR2A#5430102.147453176558070.0004793377491637920.004366087143286
RAD21#588577.248523726819437.20863381607108e-060.000207686208859765
REST#597876.755020101289611.15734408021362e-050.000294593854236973
SIN3A#2594263.245330836089080.004223840630485730.0201045342998495
SMC3#912657.522466422466420.0002459581083513690.00267467918347654
STAT1#677248.282634998879680.0009022427883430250.00662746761652533
TAF1#687282.674437028596230.001556617278062390.00988517280211344
TBP#690882.965416549677110.0007302875668644710.00581729106824487
TCF12#693844.253785960874570.01031118060518840.0383016571071728
TFAP2A#702058.259317186522480.0001581829523935980.00199426235695738
TFAP2C#702277.566460026902165.39952747293911e-060.00016488925431178
YY1#7528104.911170749853861.22387217331053e-077.03080230519133e-06
ZBTB7A#5134185.881527446300724.0719212874727e-060.000129496768374653
ZNF143#7702810.80070124178233.55138054445481e-082.36998487336943e-06



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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