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Coexpression cluster:C4324: Difference between revisions

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{{Coexpression_clusters
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15,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.00632223,0.0173907,0.159884,0.00351525,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.00350063,0.222798,0.172134,0.176789,0.0969345,0.0219648,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.00132285,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.0687209,0.141729,0.263159,0.255956,0.200105,0.227491,0.00569858,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.00756988,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.000324864,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.0228361,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.84557,0.820209,2.25583,0.436625,2.13378,1.54465,0.667627,1.17594,0.575162,1.14835,0.824321,1.65118,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,3.25755,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.843849,1.45286,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,1.14422,1.27663,1.05794,1.68795,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,1.7605,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,2.36218,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,2.24188,0.936473,0.0768232|tfbs_overrepresentation_jaspar=MA0003.1;0.178364,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;1.62115,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;1.06172,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.211629,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;3.21421,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.846801,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.0526989,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;2.23118,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.8915,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.00160703,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4324_Endothelial_Lymphatic_Hepatic_Smooth_Neutrophils_adipose_breast
|id=C4324
}}

Latest revision as of 12:43, 17 September 2013


Full id: C4324_Endothelial_Lymphatic_Hepatic_Smooth_Neutrophils_adipose_breast



Phase1 CAGE Peaks

Hg19::chr3:30647997..30648010,+p4@TGFBR2
Hg19::chr3:30648011..30648061,+p2@TGFBR2
Hg19::chr3:30648066..30648167,+p1@TGFBR2


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><br>

Uber Anatomy
Ontology termp-valuen
circulatory system2.03e-29112
cardiovascular system3.43e-28109
vasculature1.14e-2478
vascular system1.14e-2478
vessel2.96e-2468
splanchnic layer of lateral plate mesoderm3.61e-2283
epithelial tube open at both ends3.54e-2159
blood vessel3.54e-2159
blood vasculature3.54e-2159
vascular cord3.54e-2159
epithelial tube2.23e-20117
unilaminar epithelium2.11e-17148
artery2.39e-1542
arterial blood vessel2.39e-1542
arterial system2.39e-1542
systemic artery1.78e-1333
systemic arterial system1.78e-1333
trunk mesenchyme3.30e-12122
muscle tissue2.35e-1164
musculature2.35e-1164
musculature of body2.35e-1164
skeletal muscle tissue5.61e-1162
striated muscle tissue5.61e-1162
myotome5.61e-1162
blood vessel endothelium7.66e-1118
endothelium7.66e-1118
cardiovascular system endothelium7.66e-1118
multilaminar epithelium1.77e-1083
epithelial vesicle2.13e-1078
mesoderm2.26e-10315
mesoderm-derived structure2.26e-10315
presumptive mesoderm2.26e-10315
somite4.25e-1071
presomitic mesoderm4.25e-1071
presumptive segmental plate4.25e-1071
dermomyotome4.25e-1071
trunk paraxial mesoderm4.25e-1071
paraxial mesoderm1.17e-0972
presumptive paraxial mesoderm1.17e-0972
dense mesenchyme tissue1.19e-0973
aorta1.82e-0921
aortic system1.82e-0921
mesenchyme3.18e-09160
entire embryonic mesenchyme3.18e-09160
trunk7.26e-09199
simple squamous epithelium1.26e-0822
anatomical conduit1.50e-08240
organism subdivision2.17e-08264
squamous epithelium3.36e-0825
primary circulatory organ3.51e-0827
cell layer8.52e-08309
epithelium1.38e-07306
heart4.12e-0724
primitive heart tube4.12e-0724
primary heart field4.12e-0724
anterior lateral plate mesoderm4.12e-0724
heart tube4.12e-0724
heart primordium4.12e-0724
cardiac mesoderm4.12e-0724
cardiogenic plate4.12e-0724
heart rudiment4.12e-0724
lateral plate mesoderm4.44e-07203
anatomical system5.02e-07624
anatomical group7.89e-07625


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.13.21421
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.22.23118
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
CTCF#1066435.360256373075030.0064925092527670.0280530873298471
E2F1#186934.907389214879320.008460985347239390.0326699515187938
E2F6#187635.017155731697390.00791769806886330.0323469124007985
EGR1#195834.988179094810140.008056488137383440.0321689694364654
ELF1#199734.258097958807540.01295179875054610.0463911417006751
EP300#203336.77394172622320.003216880500103790.0167975492500545
FOS#235338.99795530889440.001372499272417130.0090005306738649
FOSL2#2355316.93020060456170.0002060162053171620.00243643148761398
FOXA1#3169311.08141974938550.000734755275698670.00582842976140767
FOXA2#3170324.63046375266526.68983856509345e-050.00107489238446122
GATA2#2624312.7449317335540.0004829527704283790.00437991528228287
GTF2F1#2962312.73966087675770.0004835525047438590.00435097269259446
HDAC2#3066313.41562023662630.0004140761399857210.00392571695569796
HNF4A#3172323.13229036295378.07584663437677e-050.00123164916274485
HNF4G#3174328.75342252644684.20470658818262e-050.000758961893126866
JUN#3725312.51282919233630.0005103313992726250.00445416187603491
JUND#372736.994663941871030.002921845042734990.0157247539120993
MAX#414936.452555509007120.003721913834265510.0187106117418462
MXI1#460139.96157162875930.001011470541259020.00721909190586694
MYC#460935.22228187160940.007020843755740150.0295438938315704
NR3C1#2908314.9730233311730.0002978331194675480.00309629635318249
PBX3#5090321.91451268674419.49854535978121e-050.00137113832595742
RAD21#5885310.35503389545630.0009004912073565420.0066652304185053
RXRA#6256320.07461713913330.0001235730348432220.00165671940770107
SIN3A#2594235.408884726815140.006318961977991520.0277649909554233
SMARCB1#6598318.25271578115740.000164397760679890.00203527000090648
SMARCC1#6599343.66335931963151.20046018043203e-050.000302180912952858
SMC3#9126315.04493284493280.0002935825420371870.00310056295963411
SP1#666735.69838137814090.005403962701712170.0247341774302795
TCF12#6938310.63446490218640.0008313523990202070.00630541853313518
TCF7L2#6934310.77017656313730.0008003181298398380.00615995468806418
TFAP2A#7020316.5186343730450.0002218033880766340.00248978117447717
TFAP2C#7022310.80922860986020.0007916746575753130.00617626873552761



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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