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Coexpression cluster:C4619: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,2.70919,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,1.91835,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,5.12046,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.843849,1.45286,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,3.55152,0.726632,2.16194,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,4.53202,0.941709,0.492369,1.14672,2.20718,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,1.10051,1.06461,1.02656,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,2.22068,0.303648,1.76229,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,1.7605,1.50815,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,1.66424,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,3.38286,1.08214,2.31409,1.82176,0.539692,0.853445,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,2.56478
|tfbs_overrepresentation_for_novel_motifs=0.699513,2.70919,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,1.91835,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,5.12046,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.843849,1.45286,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,3.55152,0.726632,2.16194,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,4.53202,0.941709,0.492369,1.14672,2.20718,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,1.10051,1.06461,1.02656,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,2.22068,0.303648,1.76229,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,1.7605,1.50815,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,1.66424,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,3.38286,1.08214,2.31409,1.82176,0.539692,0.853445,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,2.56478
|tfbs_overrepresentation_jaspar=MA0003.1;2.61626,MA0004.1;0.826076,MA0006.1;1.5435,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,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;3.9895,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;0.0185922,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;1.93651,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;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;1.12079,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;1.70974,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.195278,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;2.13189,MA0047.2;0.973066,MA0112.2;0.731309,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;3.48527,MA0160.1;2.02335,MA0161.1;0,MA0162.1;0.8915,MA0163.1;3.19905,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.311277,MA0102.2;1.88331,MA0258.1;2.22591,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 22:11, 22 January 2013


Full id: C4619_smooth_bladder_left_Synoviocyte_Fibroblast_Hep2_heart



Phase1 CAGE Peaks

Hg19::chr6:57037421..57037481,+p2@BAG2
Hg19::chr6:57037487..57037509,+p3@BAG2
Hg19::chr6:57037538..57037554,+p4@BAG2


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
fibroblast8.28e-1376
skin fibroblast2.62e-1023
Uber Anatomy
Ontology termp-valuen
mesenchyme9.51e-09160
entire embryonic mesenchyme9.51e-09160
dense mesenchyme tissue3.70e-0773
somite4.15e-0771
presomitic mesoderm4.15e-0771
presumptive segmental plate4.15e-0771
dermomyotome4.15e-0771
trunk paraxial mesoderm4.15e-0771
paraxial mesoderm5.46e-0772
presumptive paraxial mesoderm5.46e-0772
trunk mesenchyme6.46e-07122


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)
MA0003.12.61626
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0055.13.9895
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
MA0073.10.0185922
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
MA0091.11.93651
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
MA0114.10.549955
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.11.70974
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.731309
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
MA0159.13.48527
MA0160.12.02335
MA0161.10
MA0162.10.8915
MA0163.13.19905
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.12.22591
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
CCNT2#90536.336201576962630.003930750035764890.0191056733366803
CTCF#1066435.360256373075030.0064925092527670.0281159005618333
CTCFL#140690319.74647435897440.0001298372005551160.0017230072920935
E2F1#186934.907389214879320.008460985347239390.0327498646757221
E2F6#187635.017155731697390.00791769806886330.0324141142493048
EGR1#195834.988179094810140.008056488137383440.0322330510488886
EP300#203336.77394172622320.003216880500103790.0168328965654762
FOSL2#2355316.93020060456170.0002060162053171620.00243974673626478
FOXA1#3169311.08141974938550.000734755275698670.0058395180152723
GTF2B#2959331.94382993432423.06634405746243e-050.000629537855351522
HMGN3#932438.178547723350590.001827766942164210.0109142453786557
JUND#372736.994663941871030.002921845042734990.0157613023303651
MYC#460935.22228187160940.007020843755740150.0295903914853005
NFKB1#479035.488063424193840.006049381815655430.0270783210802862
PAX5#507936.669565531177830.003370290999677260.0173624930555563
POU2F2#545239.106124057742520.001324165192682130.00885481422451844
RAD21#5885310.35503389545630.0009004912073565420.00668180470373782
RFX5#5993312.04791082719510.0005717246050312580.00486676550858746
SIN3A#2594235.408884726815140.006318961977991520.0278153110519875
SIX5#147912317.0867153554590.0002004060546325010.00240300894830813
SP1#666735.69838137814090.005403962701712170.0247787004699529
SRF#6722313.79717826216780.0003806615025800190.00376298217396636
TAF7#6879311.43306940492390.0006690181981945830.00545488262949833
TCF12#6938310.63446490218640.0008313523990202070.00631872594434694
TCF7L2#6934310.77017656313730.0008003181298398380.00617086933645942
TFAP2A#7020316.5186343730450.0002218033880766340.00249353326666691
TFAP2C#7022310.80922860986020.0007916746575753130.00618689835098085
YY1#752834.911170749853860.008441455341808260.0331074075047171
ZBTB7A#5134137.35190930787590.002516255860282270.0140863660909101
ZEB1#6935316.88843201754390.0002075486917327580.00243716863232263
ZNF263#1012738.221841637010680.001799043925565870.0110070502953822



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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