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Coexpression cluster:C1357: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.97464,1.82196,0.436508,0.58616,0.393082,0.584466,0.662701,0.742622,0.267027,0.555913,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.800617,0.436569,0.6169,1.41165,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.640661,0.35719,0.134746,0.35388,0.585658,1.5795,0.248856,0.355745,0.513952,0.0979105,0.390088,0.154075,1.18176,1.59472,0.542147,0.0909286,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,2.54967,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.624519,0.206105,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,1.55864,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,1.80351,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,1.35291,0.877269,0.647343,0.483695,0.982236,0.44815,0.978783,1.10061,1.38333,1.29401,0.352243,1.21803,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,1.35665,4.24288,1.07915,0.258882,0.665754,1.48627,0.755083,1.75096,1.21528,2.00817,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,3.39081
|tfbs_overrepresentation_jaspar=MA0003.1;4.63763,MA0004.1;0.558729,MA0006.1;1.79433,MA0007.1;1.33289,MA0009.1;1.03681,MA0014.1;0.788761,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;2.36158,MA0046.1;1.02569,MA0048.1;0.464411,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.465994,MA0056.1;0,MA0057.1;0.450439,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.671725,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.347876,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;1.09824,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.830067,MA0106.1;1.68738,MA0107.1;0.857383,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;1.86787,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;1.16614,MA0146.1;2.91645,MA0147.1;1.57246,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.658749,MA0035.2;0.621793,MA0039.2;0.82735,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;2.08061,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.65596,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;2.40092,MA0163.1;0.813808,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;5.47519,MA0099.2;0.629739,MA0079.2;0.476723,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;2.42942,MA0442.1;0
}}
}}

Revision as of 19:52, 22 January 2013


Full id: C1357_Mesenchymal_Alveolar_Renal_Placental_acantholytic_Tracheal_Bronchial



Phase1 CAGE Peaks

Hg19::chr12:132628963..132629027,+p1@NOC4L
Hg19::chr12:53895052..53895143,+p1@TARBP2
Hg19::chr16:2022036..2022112,+p1@TBL3
Hg19::chr16:88772866..88772947,+p1@CTU2
Hg19::chr19:59055814..59055835,+p1@TRIM28
Hg19::chr19:984313..984357,+p1@WDR18


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:0007199G-protein signaling, coupled to cGMP nucleotide second messenger0.011538404895764
GO:0019934cGMP-mediated signaling0.011538404895764
GO:0006357regulation of transcription from RNA polymerase II promoter0.0172999664284364
GO:0030515snoRNA binding0.0172999664284364
GO:0005634nucleus0.0172999664284364
GO:0043193positive regulation of gene-specific transcription0.0172999664284364
GO:0001837epithelial to mesenchymal transition0.0172999664284364
GO:0032583regulation of gene-specific transcription0.0172999664284364
GO:0005732small nucleolar ribonucleoprotein complex0.0192196385985799
GO:0006366transcription from RNA polymerase II promoter0.0203185721744452
GO:0048762mesenchymal cell differentiation0.0230544017185297
GO:0014031mesenchymal cell development0.0230544017185297
GO:0043231intracellular membrane-bound organelle0.0295162839166376
GO:0043227membrane-bound organelle0.0295162839166376
GO:0003723RNA binding0.0295162839166376
GO:0044452nucleolar part0.0295162839166376
GO:0003725double-stranded RNA binding0.0358917455404646



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
embryonic cell8.42e-28250
animal cell3.59e-25679
eukaryotic cell3.59e-25679
epithelial cell4.84e-21253
mesodermal cell7.82e-17121
native cell2.20e-15722
non-terminally differentiated cell1.04e-14106
electrically responsive cell8.70e-1261
electrically active cell8.70e-1261
contractile cell3.04e-1159
somatic cell3.33e-11588
muscle cell1.95e-0955
muscle precursor cell7.00e-0958
myoblast7.00e-0958
multi-potent skeletal muscle stem cell7.00e-0958
epithelial cell of nephron1.91e-0815
meso-epithelial cell3.39e-0845
smooth muscle cell3.78e-0843
smooth muscle myoblast3.78e-0843
endothelial cell4.11e-0836
lining cell5.32e-0858
barrier cell5.32e-0858
blood vessel endothelial cell7.79e-0818
embryonic blood vessel endothelial progenitor cell7.79e-0818
ectodermal cell9.40e-0872
squamous epithelial cell1.48e-0763
kidney cortical cell2.28e-0712
renal cortical epithelial cell2.28e-0712
vascular associated smooth muscle cell4.42e-0732
kidney cell5.47e-0717
kidney epithelial cell5.47e-0717
neurectodermal cell6.20e-0759
Uber Anatomy
Ontology termp-valuen
unilaminar epithelium1.15e-14148
epithelial vesicle1.02e-1378
epithelial tube7.07e-13117
vasculature7.32e-1278
vascular system7.32e-1278
epithelial tube open at both ends2.58e-1159
blood vessel2.58e-1159
blood vasculature2.58e-1159
vascular cord2.58e-1159
vessel2.82e-1168
multilaminar epithelium6.05e-1183
somite1.03e-1071
presomitic mesoderm1.03e-1071
presumptive segmental plate1.03e-1071
dermomyotome1.03e-1071
trunk paraxial mesoderm1.03e-1071
splanchnic layer of lateral plate mesoderm1.98e-1083
artery2.18e-1042
arterial blood vessel2.18e-1042
arterial system2.18e-1042
mesenchyme3.59e-10160
entire embryonic mesenchyme3.59e-10160
paraxial mesoderm3.61e-1072
presumptive paraxial mesoderm3.61e-1072
dense mesenchyme tissue5.94e-1073
trunk2.51e-09199
trunk mesenchyme1.07e-08122
cell layer1.41e-08309
nephron epithelium1.91e-0815
renal tubule1.91e-0815
nephron tubule1.91e-0815
nephron1.91e-0815
uriniferous tubule1.91e-0815
nephrogenic mesenchyme1.91e-0815
organism subdivision2.66e-08264
epithelium3.50e-08306
skeletal muscle tissue4.42e-0862
striated muscle tissue4.42e-0862
myotome4.42e-0862
blood vessel endothelium7.79e-0818
endothelium7.79e-0818
cardiovascular system endothelium7.79e-0818
excretory tube1.50e-0716
kidney epithelium1.50e-0716
parenchyma1.60e-0715
simple squamous epithelium1.81e-0722
cortex of kidney2.28e-0712
renal parenchyma2.28e-0712
muscle tissue3.12e-0764
musculature3.12e-0764
musculature of body3.12e-0764
squamous epithelium4.59e-0725
systemic artery9.96e-0733
systemic arterial system9.96e-0733
Disease
Ontology termp-valuen
cancer3.81e-07235
disease of cellular proliferation7.76e-07239


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)
MA0003.14.63763
MA0004.10.558729
MA0006.11.79433
MA0007.11.33289
MA0009.11.03681
MA0014.10.788761
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.12.36158
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.347876
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.11.68738
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.86787
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.11.16614
MA0146.12.91645
MA0147.11.57246
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.82735
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.22.08061
MA0047.20.695777
MA0112.20.332548
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.12.40092
MA0163.10.813808
MA0164.10.738243
MA0080.20.394469
MA0018.25.47519
MA0099.20.629739
MA0079.20.476723
MA0102.21.58513
MA0258.10.289793
MA0259.12.42942
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#467518.71931210500731.00898122415384e-064.25765616442033e-05
BRCA1#672516.82019220268651.71529178571936e-066.474281127891e-05
CCNT2#90566.336201576962631.54467812014647e-050.000362364416419536
CHD2#110646.896015222744570.001115391320135990.00766031130950763
CTCFL#140690413.16431623931629.07806692187542e-050.00132416792074546
E2F1#186954.089491012399440.001749817597761990.0107569133022935
E2F4#187448.445373543522960.0005111193523770840.00443288440814734
E2F6#187654.180963109747820.001573598759586970.00997360607188393
EGR1#195864.988179094810146.48943962979974e-050.00105453646413047
ELF1#199764.258097958807540.0001677224776288830.00205162424936553
ETS1#211369.728760922202341.17854759771003e-064.80243201549895e-05
FOSL2#235538.465100302280850.003598315634615090.0182208235909608
GABPB1#255344.711789224121450.004730054311555960.0222854758083905
GTF2F1#296248.493107251171770.0005001017319378380.0044109555596534
HDAC2#306636.707810118313130.006973940027962660.0294867140026878
HEY1#2346264.040111043105710.0002298968555807510.00252978587082478
HMGN3#932445.452365148900390.002729616882333770.0149859884126614
IRF1#365956.364303127969920.000205667514205090.00243921298161088
JUN#372536.256414596168170.008486346850954870.0324084239712914
JUND#372755.828886618225860.0003155682485030750.00323431131554589
MAX#414966.452555509007121.3848964723355e-050.000334421277859532
MEF2A#420539.371615454822030.002687399947103910.0147993336712674
MEF2C#4208320.6556772463120.0002683563494060410.00286573300364187
MXI1#460158.301309690632755.60234779909565e-050.000939321884395169
MYC#460965.22228187160944.92821127172503e-050.000853419759588278
NFKB1#479065.488063424193843.65870229532191e-050.000706958758595976
NR3C1#290849.982015554115360.0002673219180401920.00285995019444782
NRF1#489936.105139723855450.009090162079396740.0344023567694635
PAX5#507966.669565531177831.13557256338955e-050.000289829088337832
POLR2A#543062.147453176558070.01019570676818780.038005190204967
RFX5#599348.03194055146340.0006204615428381410.00510963436937964
SETDB1#9869213.44000872600350.008631741208583420.0328795105435569
SIN3A#2594265.408884726815143.99207083571449e-050.000742525175442895
SIX5#147912514.23892946288253.91539088341565e-060.00012746867471105
SP1#666765.69838137814092.91961319085282e-050.000609233730348608
SRF#6722511.49764855180651.12681431027194e-050.000288016054210697
TAF1#687263.343046285745290.0007162474284635620.00572816947555755
TAF7#687959.52755783743662.84599232912077e-050.000599863961374459
TBP#690863.706770687096390.000385416472907960.00377603292814582
TCF7L2#693447.180117708758230.0009553297120679730.00687430617325803
THAP1#55145420.91276306856751.46974095435158e-050.000349097738302307
USF1#739155.30124939767330.0005003327549858890.00441075821709895
YY1#752854.092642291544880.001743365462849530.010723561197629
ZEB1#693538.444216008771930.003623843810733590.018335866660976
ZNF143#770236.750438276113950.006850259204468580.0290354797506288



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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