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Coexpression cluster:C3191: Difference between revisions

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{{Coexpression_clusters
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428,0.138871,3.11417e-08,0.0147755,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.119167,0.351067,0.275347,0.0830022,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,0.201728,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.000750623,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.0132793,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.00618871,0.04411,0.00229305,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.00380229,0.316866,0.171683,0.0133429,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,1.99148,0.641468,0.853988,0.937929,0.494933,0.491742,1.84557,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,1.14835,0.305559,1.65118,0.242883,1.96998,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,2.47502,0.855276,0.567465,0.469078,0.598234,0.777097,1.32383,0.63803,0.151453,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,3.20105,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,1.10051,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,3.09034,2.95969,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,2.55998,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.42224|tfbs_overrepresentation_jaspar=MA0003.1;3.22681,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;5.56064,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;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,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;3.5636,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;1.79391,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;2.84236,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,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;1.36919,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;1.35563,MA0115.1;1.57693,MA0116.1;0.5607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|full_id=C3191_bile_Smooth_leiomyoma_Hair_prostate_Preadipocyte_Myoblast
|id=C3191
}}

Latest revision as of 12:21, 17 September 2013


Full id: C3191_bile_Smooth_leiomyoma_Hair_prostate_Preadipocyte_Myoblast



Phase1 CAGE Peaks

Hg19::chr11:65686732..65686756,+p2@DRAP1
Hg19::chr11:65686776..65686787,+p9@DRAP1
Hg19::chr11:65686802..65686818,+p6@DRAP1


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
multilaminar epithelium9.68e-2183
epithelial vesicle2.90e-2078
somite1.14e-1871
presomitic mesoderm1.14e-1871
presumptive segmental plate1.14e-1871
dermomyotome1.14e-1871
trunk paraxial mesoderm1.14e-1871
dense mesenchyme tissue1.81e-1873
paraxial mesoderm2.58e-1872
presumptive paraxial mesoderm2.58e-1872
artery1.83e-1642
arterial blood vessel1.83e-1642
arterial system1.83e-1642
surface structure1.10e-1599
unilaminar epithelium1.87e-15148
vessel2.40e-1568
epithelial tube open at both ends9.58e-1559
blood vessel9.58e-1559
blood vasculature9.58e-1559
vascular cord9.58e-1559
skeletal muscle tissue1.48e-1462
striated muscle tissue1.48e-1462
myotome1.48e-1462
vasculature2.26e-1478
vascular system2.26e-1478
trunk mesenchyme9.91e-14122
systemic artery1.81e-1333
systemic arterial system1.81e-1333
organism subdivision2.08e-13264
muscle tissue3.70e-1364
musculature3.70e-1364
musculature of body3.70e-1364
trunk7.58e-12199
splanchnic layer of lateral plate mesoderm1.19e-1183
epithelial tube1.76e-11117
mesenchyme6.69e-11160
entire embryonic mesenchyme6.69e-11160
mesoderm2.83e-10315
mesoderm-derived structure2.83e-10315
presumptive mesoderm2.83e-10315
integument4.48e-1046
integumental system4.48e-1046
skin of body5.39e-0941
musculoskeletal system2.06e-08167
cell layer5.53e-08309
cardiovascular system5.66e-08109
epithelium5.93e-08306
circulatory system2.50e-07112
anatomical system2.80e-07624
anatomical group3.71e-07625
aorta6.87e-0721
aortic system6.87e-0721


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)
MA0003.13.22681
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.15.56064
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.13.5636
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.11.79391
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.84236
MA0089.10
MA0090.10.751469
MA0091.10.829044
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
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.12.7939
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.12.4174
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.13.97071
MA0140.10.894983
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.212.5552
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
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
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.16.1256
MA0163.19.44515
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.210.17
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
BCL11A#53335328.36945510360714.37778126761649e-050.000776645316474602
BCL3#602334.54710280373832.42397750207122e-050.000526425007982567
BCLAF1#9774321.65264761012189.8473954032885e-050.00138867422160957
CCNT2#90536.336201576962630.003930750035764890.0189251153874815
CTCF#1066435.360256373075030.0064925092527670.0278457218943671
E2F1#186934.907389214879320.008460985347239390.0323814301982606
E2F4#1874312.66806031528440.0004917987006298980.00435759434080648
E2F6#187635.017155731697390.00791769806886330.0320646969100785
EBF1#187938.9064668465690.00141523283560980.00912661328300416
EGR1#195834.988179094810140.008056488137383440.0319224358669167
ELF1#199734.258097958807540.01295179875054610.0460280696103268
EP300#203336.77394172622320.003216880500103790.0166940513068492
ETS1#211339.728760922202340.001085840092584840.00760182688225417
FOSL1#8061339.7135797163731.59554825631833e-050.000370223204491514
FOSL2#2355316.93020060456170.0002060162053171620.00242407914230724
FOXA1#3169311.08141974938550.000734755275698670.00579672958443068
GABPB1#255337.067683836182170.002832212825417420.0153666930891875
GATA3#2625327.2365163572064.94721007899563e-050.000848967586986895
HDAC2#3066313.41562023662630.0004140761399857210.00389987356695542
HMGN3#932438.178547723350590.001827766942164210.0108367954398347
HNF4A#3172323.13229036295378.07584663437677e-050.00122520823162068
HNF4G#3174328.75342252644684.20470658818262e-050.00075517687250766
IRF1#365937.63716375356390.002244692747297240.0127666212402645
JUND#372736.994663941871030.002921845042734990.0156217146727859
MEF2A#4205318.74323090964410.0001518243905622470.00194867734127202
MEF2C#4208341.31135449262411.41744912101957e-050.000340002224965923
MXI1#460139.96157162875930.001011470541259020.00718423366829101
MYC#460935.22228187160940.007020843755740150.0293311692870013
NFKB1#479035.488063424193840.006049381815655430.0268675903655215
NR2C2#7182332.61461090524092.88098172333076e-050.000603947912892295
NR3C1#2908314.9730233311730.0002978331194675480.0030797418974328
PAX5#507936.669565531177830.003370290999677260.0172383477014199
PBX3#5090321.91451268674419.49854535978121e-050.00136135388888458
POU2F2#545239.106124057742520.001324165192682130.00879847872239019
RAD21#5885310.35503389545630.0009004912073565420.00662065478388665
RXRA#6256320.07461713913330.0001235730348432220.00164867708047922
SIN3A#2594235.408884726815140.006318961977991520.0275551594997685
SMC3#9126315.04493284493280.0002935825420371870.0030812448103529
SP1#666735.69838137814090.005403962701712170.0245544685927395
SP2#6668326.15353049384465.58768218891694e-050.000937766254424387
SRF#6722313.79717826216780.0003806615025800190.00374032427019989
STAT1#6772320.70658749719920.0001125992441046670.00154509952109411
STAT2#6773365.26377118644073.59360517547754e-060.000118171451801542
TAF7#6879311.43306940492390.0006690181981945830.00540843653543185
TCF12#6938310.63446490218640.0008313523990202070.0062794252694924
TCF7L2#6934310.77017656313730.0008003181298398380.00611981440638035
USF1#739136.361499277207960.00388404057290560.0189598183404388
YY1#752834.911170749853860.008441455341808260.032810463507373
ZEB1#6935316.88843201754390.0002075486917327580.00242056703694891
ZNF143#7702313.50087655222790.0004062804962997170.00387892209096317



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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