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Coexpression cluster:C301: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.47689857423244,0.

Latest revision as of 11:17, 17 September 2013


Full id: C301_Smooth_mesenchymal_Endothelial_Hepatic_basal_hepatic_chorionic



Phase1 CAGE Peaks

Hg19::chr7:100770328..100770393,+p1@SERPINE1
Hg19::chr7:100770399..100770412,+p6@SERPINE1
Hg19::chr7:100770418..100770430,+p8@SERPINE1
Hg19::chr7:100770437..100770464,+p3@SERPINE1
Hg19::chr7:100770466..100770499,+p2@SERPINE1
Hg19::chr7:100771725..100771774,+p7@SERPINE1
Hg19::chr7:100771785..100771826,+p5@SERPINE1
Hg19::chr7:100771827..100771882,+p4@SERPINE1
Hg19::chr7:100771879..100771926,-p@chr7:100771879..100771926
-
Hg19::chr7:100771891..100771905,+p11@SERPINE1
Hg19::chr7:100773698..100773743,+p@chr7:100773698..100773743
+
Hg19::chr7:100773764..100773799,-p@chr7:100773764..100773799
-
Hg19::chr7:100773780..100773795,+p@chr7:100773780..100773795
+
Hg19::chr7:100773800..100773832,+p@chr7:100773800..100773832
+
Hg19::chr7:100773840..100773860,+p@chr7:100773840..100773860
+
Hg19::chr7:100773872..100773904,-p@chr7:100773872..100773904
-
Hg19::chr7:100773914..100773948,-p@chr7:100773914..100773948
-
Hg19::chr7:100775170..100775232,+p2@BX649164
Hg19::chr7:100775178..100775193,-p@chr7:100775178..100775193
-
Hg19::chr7:100775233..100775309,+p1@BX649164
Hg19::chr7:100775264..100775282,-p@chr7:100775264..100775282
-
Hg19::chr7:100776967..100777011,+p@chr7:100776967..100777011
+
Hg19::chr7:100777001..100777050,-p@chr7:100777001..100777050
-
Hg19::chr7:100777029..100777041,+p@chr7:100777029..100777041
+
Hg19::chr7:100777064..100777089,+p@chr7:100777064..100777089
+
Hg19::chr7:100780263..100780339,+p9@SERPINE1
Hg19::chr7:100780319..100780345,-p@chr7:100780319..100780345
-
Hg19::chr7:100780695..100780710,+p@chr7:100780695..100780710
+
Hg19::chr7:100780724..100780737,+p@chr7:100780724..100780737
+
Hg19::chr7:100781004..100781031,+p@chr7:100781004..100781031
+
Hg19::chr7:100781252..100781342,+p@chr7:100781252..100781342
+
Hg19::chr7:100781348..100781402,+p@chr7:100781348..100781402
+
Hg19::chr7:100781477..100781548,+p@chr7:100781477..100781548
+
Hg19::chr7:100781537..100781588,-p@chr7:100781537..100781588
-
Hg19::chr7:100781614..100781656,+p@chr7:100781614..100781656
+
Hg19::chr7:100781695..100781730,+p@chr7:100781695..100781730
+
Hg19::chr7:100781793..100781808,+p@chr7:100781793..100781808
+
Hg19::chr7:100781864..100781880,+p@chr7:100781864..100781880
+
Hg19::chr7:100781903..100781920,+p@chr7:100781903..100781920
+
Hg19::chr7:100781986..100782007,+p@chr7:100781986..100782007
+
Hg19::chr7:100782368..100782400,+p@chr7:100782368..100782400
+


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:0002020protease binding0.00302770348690518
GO:0008243plasminogen activator activity0.00302770348690518
GO:0042730fibrinolysis0.00302770348690518
GO:0030195negative regulation of blood coagulation0.00302770348690518
GO:0030193regulation of blood coagulation0.00302770348690518
GO:0050819negative regulation of coagulation0.00302770348690518
GO:0050818regulation of coagulation0.00302770348690518
GO:0045765regulation of angiogenesis0.00629194630872483
GO:0007596blood coagulation0.01171243190987
GO:0050817coagulation0.01171243190987
GO:0007599hemostasis0.01171243190987
GO:0050878regulation of body fluid levels0.01171243190987
GO:0001525angiogenesis0.01171243190987
GO:0042060wound healing0.01171243190987
GO:0048514blood vessel morphogenesis0.01171243190987
GO:0048646anatomical structure formation0.01171243190987
GO:0001568blood vessel development0.01171243190987
GO:0001944vasculature development0.01171243190987
GO:0004867serine-type endopeptidase inhibitor activity0.01171243190987
GO:0004866endopeptidase inhibitor activity0.0166902154715648
GO:0030414protease inhibitor activity0.0167785234899329
GO:0019899enzyme binding0.0183640538197232
GO:0004252serine-type endopeptidase activity0.0191781979021086
GO:0009887organ morphogenesis0.0192069939950547
GO:0008236serine-type peptidase activity0.0192069939950547
GO:0017171serine hydrolase activity0.0192069939950547
GO:0004857enzyme inhibitor activity0.0196730640919973
GO:0009611response to wounding0.0200112277337639
GO:0009605response to external stimulus0.028913263255338
GO:0004175endopeptidase activity0.0354556693747792
GO:0065008regulation of biological quality0.0407213910506945
GO:0009653anatomical structure morphogenesis0.0433399196397033
GO:0048513organ development0.0455154244672083
GO:0048519negative regulation of biological process0.0455154244672083
GO:0006950response to stress0.0455154244672083
GO:0008233peptidase activity0.0455154244672083



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
mesodermal cell1.20e-37121
somatic cell1.77e-31588
animal cell5.14e-25679
eukaryotic cell5.14e-25679
muscle precursor cell3.10e-2458
myoblast3.10e-2458
multi-potent skeletal muscle stem cell3.10e-2458
embryonic cell4.70e-24250
contractile cell2.03e-2359
muscle cell7.61e-2355
smooth muscle cell1.11e-2243
smooth muscle myoblast1.11e-2243
vascular associated smooth muscle cell5.69e-2232
fibroblast1.43e-2076
electrically responsive cell6.58e-1961
electrically active cell6.58e-1961
native cell3.15e-16722
lining cell4.60e-1558
barrier cell4.60e-1558
non-terminally differentiated cell5.10e-14106
endothelial cell7.28e-1336
endothelial cell of vascular tree8.03e-1324
multi fate stem cell3.35e-12427
somatic stem cell4.96e-12433
meso-epithelial cell4.94e-1145
stem cell1.02e-10441
blood vessel endothelial cell1.35e-0918
embryonic blood vessel endothelial progenitor cell1.35e-0918
aortic smooth muscle cell2.27e-0810
skin fibroblast5.10e-0823
cardiocyte1.19e-0716
endothelial cell of artery7.27e-079
Uber Anatomy
Ontology termp-valuen
vasculature3.22e-3778
vascular system3.22e-3778
vessel1.10e-3468
splanchnic layer of lateral plate mesoderm7.07e-3283
epithelial tube open at both ends7.79e-3159
blood vessel7.79e-3159
blood vasculature7.79e-3159
vascular cord7.79e-3159
epithelial tube2.35e-29117
unilaminar epithelium1.50e-28148
artery2.42e-2842
arterial blood vessel2.42e-2842
arterial system2.42e-2842
cardiovascular system3.08e-28109
epithelial vesicle7.72e-2878
circulatory system5.01e-27112
multilaminar epithelium7.93e-2583
somite1.56e-2471
presomitic mesoderm1.56e-2471
presumptive segmental plate1.56e-2471
dermomyotome1.56e-2471
trunk paraxial mesoderm1.56e-2471
dense mesenchyme tissue5.93e-2473
paraxial mesoderm8.54e-2472
presumptive paraxial mesoderm8.54e-2472
systemic artery3.77e-2233
systemic arterial system3.77e-2233
trunk mesenchyme4.88e-22122
skeletal muscle tissue4.72e-2162
striated muscle tissue4.72e-2162
myotome4.72e-2162
muscle tissue1.24e-1964
musculature1.24e-1964
musculature of body1.24e-1964
mesenchyme1.62e-18160
entire embryonic mesenchyme1.62e-18160
cell layer1.06e-15309
epithelium4.11e-15306
trunk5.35e-15199
mesoderm2.37e-14315
mesoderm-derived structure2.37e-14315
presumptive mesoderm2.37e-14315
aorta8.12e-1421
aortic system8.12e-1421
organism subdivision1.68e-13264
simple squamous epithelium3.14e-1022
blood vessel endothelium1.35e-0918
endothelium1.35e-0918
cardiovascular system endothelium1.35e-0918
squamous epithelium1.57e-0925
anatomical conduit4.92e-09240
anatomical system9.49e-09624
multi-cellular organism1.18e-08656
anatomical group1.30e-08625
blood vessel smooth muscle2.27e-0810
arterial system smooth muscle2.27e-0810
artery smooth muscle tissue2.27e-0810
aorta smooth muscle tissue2.27e-0810
integument3.36e-0846
integumental system3.36e-0846
tube5.64e-08192
lateral plate mesoderm4.23e-07203
smooth muscle tissue5.26e-0715
endothelial tube7.27e-079
arterial system endothelium7.27e-079
endothelium of artery7.27e-079
Disease
Ontology termp-valuen
ovarian cancer1.67e-0814


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)
MA0003.11.42231e-06
MA0004.10.188666
MA0006.10.0601979
MA0007.10.0444559
MA0009.10.849154
MA0014.10.000149655
MA0017.11.00027
MA0019.10.11308
MA0024.10.240609
MA0025.10.422115
MA0027.11.82504
MA0028.10.18203
MA0029.10.254078
MA0030.10.246057
MA0031.11.1088
MA0038.10.0913067
MA0040.10.258207
MA0041.10.0569489
MA0042.10.0461274
MA0043.10.316837
MA0046.10.308386
MA0048.10.346045
MA0050.10.0464098
MA0051.10.0893845
MA0052.10.26095
MA0055.10.902548
MA0056.10
MA0057.11.55264
MA0058.10.103276
MA0059.10.102293
MA0060.10.01376
MA0061.10.0304331
MA0063.10
MA0066.11.05838
MA0067.10.579326
MA0068.10.0149273
MA0069.10.824176
MA0070.11.46337
MA0071.10.0744425
MA0072.10.293816
MA0073.10.0037693
MA0074.10.0890442
MA0076.10.115785
MA0077.10.784875
MA0078.10.139588
MA0081.10.251339
MA0083.11.55357
MA0084.10.748791
MA0087.10.292007
MA0088.10.269456
MA0089.10
MA0090.10.879166
MA0091.10.425566
MA0092.10.637632
MA0093.10.0619468
MA0095.10
MA0098.10
MA0100.11.10216
MA0101.10.0638765
MA0103.11.47061
MA0105.10.0990781
MA0106.11.74395
MA0107.10.00511893
MA0108.22.44703
MA0109.10
MA0111.10.139536
MA0113.11.2475
MA0114.10.520921
MA0115.11.27652
MA0116.10.0053958
MA0117.10.345453
MA0119.10.0904534
MA0122.10.365749
MA0124.10.477271
MA0125.10.407486
MA0130.10
MA0131.10.149857
MA0132.10
MA0133.10
MA0135.10.33984
MA0136.11.07991
MA0139.12.34076
MA0140.10.255482
MA0141.10.755354
MA0142.10.182439
MA0143.10.119599
MA0144.10.00375441
MA0145.10.607971
MA0146.10.000201099
MA0147.10.0312756
MA0148.10.469303
MA0149.10.0694357
MA0062.20.145863
MA0035.20.0730588
MA0039.20.0037385
MA0138.20.140273
MA0002.20.960842
MA0137.20.0738426
MA0104.20.109224
MA0047.20.697656
MA0112.21.10515
MA0065.20.348335
MA0150.10.539464
MA0151.10
MA0152.10.0760669
MA0153.10.39383
MA0154.10.250193
MA0155.10.370651
MA0156.14.37904
MA0157.10.165715
MA0158.10
MA0159.10.570514
MA0160.10.231485
MA0161.10
MA0162.10.000965435
MA0163.10.141384
MA0164.10.126046
MA0080.20.835604
MA0018.20.111815
MA0099.20.946837
MA0079.21.64939e-05
MA0102.20.783286
MA0258.12.75623
MA0259.10.0346422
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
BCL11A#5333553.459689646781350.01417894842491450.049744203518749
BHLHE40#855344.377737907022190.0129508009192390.0465488074200504
CEBPB#1051112.138600582538370.01040207561906880.038617317488267
CTCF#10664182.353283285740260.0001790636655242010.00217203602365645
CTCFL#140690125.779455909943715.61284338384473e-072.5938042042715e-05
ELK4#2005124.751906826868694.33602035203446e-060.000135950053901569
EP300#2033152.478271363252390.0004713635921470570.00432742107948721
FOS#2353112.414085570678990.0042001618863850.0200009441570383
FOSL1#806176.780367268649056.77450068925307e-050.00108250011855095
FOSL2#2355124.955180664749762.81473071835762e-069.72115282720077e-05
FOXA1#3169123.243342365673790.000188668566722630.00228086079869716
HDAC2#3066134.253733245759555.22766137706847e-060.000160062071697348
HEY1#23462272.660560930825713.31152556333363e-082.22270191715296e-06
HNF4G#317453.506514942249610.01344447461371720.0474977161282055
JUN#3725113.357100515017070.0002790631827148430.00297095614062747
JUNB#372685.972806372648034.70071774143001e-050.000822204421700232
NR3C1#2908114.017152601046435.66273002737155e-050.000949141167274365
POLR2A#5430412.147453176558072.44859392948639e-144.09165922242606e-12
PRDM1#639619.29233499182356.7551613882104e-073.05942020912102e-05
RAD21#5885133.283303430266648.21445987108688e-050.00123546943328981
SIRT6#51548622.4836688765892.77986037044944e-071.40934872441441e-05
SMARCC1#659988.519679867245163.66022406923874e-060.000120135179625149
SMC3#912682.935596652669820.0050164072030320.0234128145809295
STAT3#6774102.565723170037620.004261264991781040.0202734263154437
TAL1#688685.82802276632985.58419897508093e-050.000942939622891637
TCF7L2#6934123.152246798967030.000246461806644940.00267987762875491
ZBTB7A#51341173.048352639850981.06276796092639e-050.000276036864141236



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

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