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Coexpression cluster:C2969: Difference between revisions

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{{Coexpression_clusters
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91,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.0406636,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.035048,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,1.94915,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,1.55576,1.00813,0.795576,1.21459,0.534793,0.439574,0.599922,1.36391,1.45286,0.855276,0.567465,1.18324,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,1.28131,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.977977,0.303648,2.64731,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,1.37703,1.99742,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,1.50815,0.703975,2.82894,0.684398,0.830777,1.58942,0.594137,0.188952,1.86486,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,2.3415,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,1.76124,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,2.20464,0.524529,0.936473,0.0768232|tfbs_overrepresentation_jaspar=MA0003.1;0.401049,MA0004.1;0.826076,MA0006.1;1.5435,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;1.64148,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;2.45333,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;1.06172,MA0056.1;0,MA0057.1;3.3282,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;4.27202,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;3.33427,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;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;7.18823,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;1.66081,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;0.0526989,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;4.86005,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.838867,MA0155.1;0.711948,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.455568,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;6.90173,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C2969_Melanocyte_Meningeal_Fibroblast_gall_breast_glioblastoma_melanoma
|id=C2969
}}

Latest revision as of 12:16, 17 September 2013


Full id: C2969_Melanocyte_Meningeal_Fibroblast_gall_breast_glioblastoma_melanoma



Phase1 CAGE Peaks

Hg19::chr10:102106933..102106948,+p4@SCD
Hg19::chr10:102106957..102106970,+p5@SCD
Hg19::chr10:102106982..102107015,+p1@SCD


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell3.95e-15253
ectodermal cell1.31e-1272
embryonic cell4.75e-10250
neurectodermal cell9.37e-0959
migratory neural crest cell2.56e-0841
ecto-epithelial cell9.13e-0734
endodermal cell9.34e-0758
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure8.06e-20171
ectoderm8.06e-20171
presumptive ectoderm8.06e-20171
organ system subdivision1.62e-13223
nervous system9.49e-1389
ecto-epithelium1.37e-12104
anatomical cluster1.36e-11373
multi-tissue structure1.90e-11342
cell layer2.36e-11309
central nervous system3.42e-1181
organ part4.54e-11218
epithelium2.19e-10306
brain2.19e-0968
future brain2.19e-0968
neural plate3.73e-0982
presumptive neural plate3.73e-0982
neurectoderm5.99e-0986
subdivision of head1.20e-0749
head1.26e-0756
organism subdivision1.44e-07264
ectodermal placode1.52e-0731
structure with developmental contribution from neural crest1.80e-07132
pre-chordal neural plate4.17e-0761
organ segment4.95e-0798
neural tube7.89e-0756
neural rod7.89e-0756
future spinal cord7.89e-0756
neural keel7.89e-0756
posterior neural tube8.88e-0715
chordal neural plate8.88e-0715
Disease
Ontology termp-valuen
cancer2.62e-13235
disease of cellular proliferation2.86e-13239
cell type cancer4.54e-11143
carcinoma3.43e-08106


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)
MA0003.10.401049
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.11.64148
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.13.3282
MA0058.10.716037
MA0059.10.714521
MA0060.14.27202
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
MA0073.13.33427
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
MA0091.10.829044
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
MA0114.17.18823
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.11.66081
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
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.24.86005
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.26.90173
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
CCNT2#90536.336201576962630.003930750035764890.0188989781320896
CHD2#1106310.34402283411690.0009033701102746880.00658112939083274
E2F1#186934.907389214879320.008460985347239390.0323257553658302
EBF1#187938.9064668465690.00141523283560980.00912267017147589
ELF1#199734.258097958807540.01295179875054610.0459670679888634
EP300#203336.77394172622320.003216880500103790.0166733390843841
FOS#235338.99795530889440.001372499272417130.00894381053921336
FOSL2#2355316.93020060456170.0002060162053171620.00242244161980625
FOXA1#3169311.08141974938550.000734755275698670.0057914797161278
GTF2F1#2962312.73966087675770.0004835525047438590.00432563083879605
HDAC2#3066313.41562023662630.0004140761399857210.00389741330064606
HNF4A#3172323.13229036295378.07584663437677e-050.00122431898192434
IRF1#365937.63716375356390.002244692747297240.0127520379588216
MAX#414936.452555509007120.003721913834265510.0185605194545602
MYC#460935.22228187160940.007020843755740150.0292983538181063
NFKB1#479035.488063424193840.006049381815655430.0268390563910466
NFYA#4800318.42558069983050.0001598135507814160.00198960155323166
NFYB#4801316.75979325353650.0002123649923296180.00244884480886751
POU2F2#545239.106124057742520.001324165192682130.00879120771460994
REST#597839.650028716128020.001112636247114590.00765044552060048
RFX5#5993312.04791082719510.0005717246050312580.00482819972708495
SIN3A#2594235.408884726815140.006318961977991520.0275229823179355
SP1#666735.69838137814090.005403962701712170.0245267246362225
SREBF1#6720347.00584944048839.62099323994382e-060.000253995680734705
SREBF2#67213436.9432624113481.19027063774682e-088.89203684804295e-07
TCF7L2#6934310.77017656313730.0008003181298398380.00611354777372315
TFAP2A#7020316.5186343730450.0002218033880766340.00247250763660322
TFAP2C#7022310.80922860986020.0007916746575753130.00612593239701475
USF1#739136.361499277207960.00388404057290560.0189376897009191
ZNF263#1012738.221841637010680.001799043925565870.0108858834613079



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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