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Coexpression cluster:C4355: Difference between revisions

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{{Coexpression_clusters
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013,0.0900729,0.0953646,0.166124,0.252184,0.0828367,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.0532009,0.180606,0.000773769,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.0377035,0.211332,0.187731,0.233626,0.00132285,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.00168003,0.295769,0.286691,0.347036,0.141729,1.71764e-05,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.00756988,0.000283503,0.218052,0.00224487,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.0133429,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,1.06031e-06,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,1.14835,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,2.63304,0.388328,0.795576,1.21459,0.534793,1.11965,1.46099,0.137917,3.61775,0.855276,0.567465,2.05816,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,1.5923,1.45054,7.45568,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,3.76231,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,2.62406,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,2.55998,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.66424,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,4.11334,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,3.22076|tfbs_overrepresentation_jaspar=MA0003.1;4.57391,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;1.88666,MA0009.1;1.3275,MA0014.1;1.80735,MA0017.1;1.64148,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;6.58497,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;0.904546,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;1.59304,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;0.0834661,MA0074.1;0.935474,MA0076.1;4.21544,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;8.72191,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.715722,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;0.31555,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;1.35563,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;1.12079,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;2.94723,MA0146.1;4.51393,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;7.63558,MA0035.2;0.894194,MA0039.2;1.62945,MA0138.2;1.04628,MA0002.2;2.08438,MA0137.2;0.666381,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.760954,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;1.60572,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;2.76014,MA0163.1;0.776149,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;3.61229,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;2.40872,MA0442.1;0}}
|full_id=C4355_Smooth_CD14_Alveolar_Astrocyte_Meningeal_Fibroblast_Renal
|id=C4355
}}

Latest revision as of 12:44, 17 September 2013


Full id: C4355_Smooth_CD14_Alveolar_Astrocyte_Meningeal_Fibroblast_Renal



Phase1 CAGE Peaks

Hg19::chr4:10118348..10118395,-p1@WDR1
Hg19::chr4:10118405..10118430,-p2@WDR1
Hg19::chr4:10118443..10118454,-p4@WDR1


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>

Cell Type
Ontology termp-valuen
somatic cell6.60e-46588
animal cell7.29e-33679
eukaryotic cell7.29e-33679
mesodermal cell1.31e-25121
native cell3.37e-23722
embryonic cell5.63e-18250
multi fate stem cell2.34e-17427
somatic stem cell3.09e-17433
contractile cell1.45e-1659
stem cell7.22e-16441
smooth muscle cell1.16e-1543
smooth muscle myoblast1.16e-1543
muscle cell5.91e-1555
muscle precursor cell6.05e-1558
myoblast6.05e-1558
multi-potent skeletal muscle stem cell6.05e-1558
vascular associated smooth muscle cell1.15e-1432
non-terminally differentiated cell4.82e-13106
electrically responsive cell5.17e-1261
electrically active cell5.17e-1261
fibroblast8.33e-1176
endothelial cell4.19e-1036
meso-epithelial cell6.74e-1045
lining cell1.84e-0958
barrier cell1.84e-0958
defensive cell6.44e-0948
phagocyte6.44e-0948
classical monocyte1.42e-0842
CD14-positive, CD16-negative classical monocyte1.42e-0842
monopoietic cell7.76e-0859
monocyte7.76e-0859
monoblast7.76e-0859
promonocyte7.76e-0859
macrophage dendritic cell progenitor8.77e-0861
myeloid leukocyte9.62e-0872
endothelial cell of vascular tree1.46e-0724
connective tissue cell2.11e-07361
epithelial cell of nephron2.18e-0715
stuff accumulating cell3.60e-0787
blood vessel endothelial cell5.32e-0718
embryonic blood vessel endothelial progenitor cell5.32e-0718
mesenchymal cell6.26e-07354
motile cell9.72e-07386
Uber Anatomy
Ontology termp-valuen
mesoderm3.26e-24315
mesoderm-derived structure3.26e-24315
presumptive mesoderm3.26e-24315
vasculature3.47e-2378
vascular system3.47e-2378
lateral plate mesoderm6.83e-23203
cardiovascular system4.07e-21109
circulatory system1.03e-20112
vessel8.40e-2068
musculoskeletal system1.37e-18167
epithelial tube2.45e-18117
epithelial tube open at both ends1.27e-1759
blood vessel1.27e-1759
blood vasculature1.27e-1759
vascular cord1.27e-1759
artery1.55e-1742
arterial blood vessel1.55e-1742
arterial system1.55e-1742
splanchnic layer of lateral plate mesoderm2.21e-1783
epithelial vesicle3.96e-1778
somite4.76e-1471
presomitic mesoderm4.76e-1471
presumptive segmental plate4.76e-1471
dermomyotome4.76e-1471
trunk paraxial mesoderm4.76e-1471
multilaminar epithelium1.17e-1383
systemic artery1.36e-1333
systemic arterial system1.36e-1333
unilaminar epithelium1.99e-13148
dense mesenchyme tissue2.33e-1373
paraxial mesoderm2.80e-1372
presumptive paraxial mesoderm2.80e-1372
skeletal muscle tissue3.10e-1362
striated muscle tissue3.10e-1362
myotome3.10e-1362
muscle tissue5.56e-1364
musculature5.56e-1364
musculature of body5.56e-1364
trunk mesenchyme1.48e-11122
mesenchyme3.53e-10160
entire embryonic mesenchyme3.53e-10160
trunk3.80e-08199
aorta6.79e-0821
aortic system6.79e-0821
skeletal element1.44e-0790
organism subdivision1.81e-07264
nephron epithelium2.18e-0715
renal tubule2.18e-0715
nephron tubule2.18e-0715
nephron2.18e-0715
uriniferous tubule2.18e-0715
nephrogenic mesenchyme2.18e-0715
skeletal system3.05e-07100
parenchyma3.32e-0715
excretory tube3.94e-0716
kidney epithelium3.94e-0716
bone element4.33e-0782


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)
MA0003.14.57391
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
MA0009.11.3275
MA0014.11.80735
MA0017.11.64148
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.16.58497
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.11.59304
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
MA0073.10.0834661
MA0074.10.935474
MA0076.14.21544
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.18.72191
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.94723
MA0146.14.51393
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.27.63558
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.22.08438
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.61229
MA0102.21.88331
MA0258.10.519674
MA0259.12.40872
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
CCNT2#90536.336201576962630.003930750035764890.0190701724803851
E2F1#186934.907389214879320.008460985347239390.0326796171849236
E2F6#187635.017155731697390.00791769806886330.0323595706587624
EGR1#195834.988179094810140.008056488137383440.0321788115565316
ELF1#199734.258097958807540.01295179875054610.0464038734033716
ETS1#211339.728760922202340.001085840092584840.0076407528250551
GABPB1#255337.067683836182170.002832212825417420.0154590506571428
GTF2B#2959331.94382993432423.06634405746243e-050.000629043227297818
GTF2F1#2962312.73966087675770.0004835525047438590.00435134758253868
HMGN3#932438.178547723350590.001827766942164210.010898044740391
JUND#372736.994663941871030.002921845042734990.0157288064748312
MAX#414936.452555509007120.003721913834265510.018715115981553
MYC#460935.22228187160940.007020843755740150.0295510378029962
NFKB1#479035.488063424193840.006049381815655430.0270389192606881
NRF1#4899312.21027944771090.0005492172401020010.00472601955499818
PAX5#507936.669565531177830.003370290999677260.0173436719248728
PBX3#5090214.60967512449610.006056122473217890.0268541321691676
POU2F2#545239.106124057742520.001324165192682130.00884348948449475
RDBP#79363153.6384039900252.75057764221434e-071.4033589564007e-05
REST#597839.650028716128020.001112636247114590.00769859659549494
SIN3A#2594235.408884726815140.006318961977991520.0277684957510501
SMARCB1#6598318.25271578115740.000164397760679890.0020359940386158
SP1#666735.69838137814090.005403962701712170.024741767594762
SRF#6722313.79717826216780.0003806615025800190.00375906833093368
TAF7#6879311.43306940492390.0006690181981945830.0054459541388343
TCF12#6938310.63446490218640.0008313523990202070.00630770891400446
YY1#752834.911170749853860.008441455341808260.0330540324851197
ZBTB7A#5134137.35190930787590.002516255860282270.0140652561438675
ZEB1#6935316.88843201754390.0002075486917327580.00243361152081256



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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