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{{Coexpression_clusters
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281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=1.66899,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,1.23863,0.491742,1.84557,0.820209,0.985163,1.94915,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,3.26509,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,4.47361,1.21459,0.534793,1.11965,0.599922,0.427404,0.596053,1.99037,0.567465,0.469078,0.598234,4.39555,0.259059,0.63803,0.151453,1.72524,0.939121,0.808003,0.247669,0.645308,1.02504,2.18821,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,2.20718,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,4.08917,0.381882,1.053,2.0169,1.63834,3.03421,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,4.55594,1.16312,0.921547,0.743661,2.55998,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,0.794219,2.50498,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,3.2678,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,4.54113,0.318511,2.79286,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408|tfbs_overrepresentation_jaspar=MA0003.1;0.708947,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;15.8547,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;2.67616,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;0.557638,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;0.0185922,MA0074.1;0.935474,MA0076.1;2.91768,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;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;2.96208,MA0035.2;0.894194,MA0039.2;3.37171,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,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;1.60572,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.481578,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4084_peripheral_osteoclastoma_mesenchymal_Preadipocyte_Adipocyte_melanoma_bone
|id=C4084
|ontology_enrichment_celltype=CL:0000222!8.97e-27!119;CL:0000220!1.76e-22!246;CL:0002321!1.26e-21!248;CL:0000213!3.62e-18!57;CL:0000215!3.62e-18!57;CL:0000055!1.62e-17!180;CL:0002078!2.83e-16!44;CL:0000115!1.66e-14!35;CL:0002139!1.20e-13!24;CL:0000144!2.38e-11!625;CL:0000071!1.21e-10!18;CL:0002546!1.21e-10!18;CL:0000359!4.04e-10!32;CL:0000066!1.20e-09!254;CL:0000548!2.17e-09!679;CL:0000004!2.17e-09!679;CL:0000255!2.17e-09!679;CL:0002371!2.24e-09!591;CL:0000012!4.16e-09!682;CL:0000192!1.76e-08!42;CL:0000514!1.76e-08!42;CL:0000183!2.42e-08!59;CL:0000680!2.55e-08!57;CL:0000056!2.55e-08!57;CL:0000355!2.55e-08!57;CL:0000187!2.49e-07!54;CL:1000497!3.44e-07!18;CL:0002518!3.44e-07!18
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!1.84e-25!118;UBERON:0002049!1.03e-23!79;UBERON:0007798!1.03e-23!79;UBERON:0000055!2.44e-21!69;UBERON:0001981!6.34e-19!60;UBERON:0007500!6.34e-19!60;UBERON:0004537!6.34e-19!60;UBERON:0006965!6.34e-19!60;UBERON:0004872!2.25e-18!84;UBERON:0004535!1.52e-17!110;UBERON:0001009!2.61e-17!113;UBERON:0000468!1.37e-15!659;UBERON:0000490!1.83e-15!138;UBERON:0001637!1.83e-15!42;UBERON:0003509!1.83e-15!42;UBERON:0004572!1.83e-15!42;UBERON:0000467!7.96e-13!625;UBERON:0005256!1.20e-12!143;UBERON:0000480!1.60e-12!626;UBERON:0002100!6.90e-12!216;UBERON:0004573!1.06e-11!33;UBERON:0004571!1.06e-11!33;UBERON:0000926!1.10e-11!448;UBERON:0004120!1.10e-11!448;UBERON:0006603!1.10e-11!448;UBERON:0000487!2.21e-11!22;UBERON:0006914!2.65e-11!25;UBERON:0001986!1.21e-10!18;UBERON:0004638!1.21e-10!18;UBERON:0004852!1.21e-10!18;UBERON:0000119!1.67e-10!312;UBERON:0004111!5.95e-10!241;UBERON:0000483!8.55e-10!309;UBERON:0000477!3.77e-09!286;UBERON:0000025!3.98e-09!194;UBERON:0000923!1.22e-08!604;UBERON:0005291!1.22e-08!604;UBERON:0006598!1.22e-08!604;UBERON:0002532!1.22e-08!604;UBERON:0003081!1.24e-08!216;UBERON:0002050!1.39e-08!605;UBERON:0005423!1.39e-08!605;UBERON:0000922!7.20e-08!612;UBERON:0000947!1.28e-07!21;UBERON:0010191!1.28e-07!21;UBERON:0001134!5.85e-07!61;UBERON:0002036!5.85e-07!61;UBERON:0003082!5.85e-07!61;UBERON:0002385!6.47e-07!63;UBERON:0001015!6.47e-07!63;UBERON:0000383!6.47e-07!63;UBERON:0002417!8.99e-07!61;UBERON:0000916!8.99e-07!61
}}

Latest revision as of 12:39, 17 September 2013


Full id: C4084_peripheral_osteoclastoma_mesenchymal_Preadipocyte_Adipocyte_melanoma_bone



Phase1 CAGE Peaks

Hg19::chr21:46293545..46293584,-p2@PTTG1IP
Hg19::chr21:46293586..46293641,-p1@PTTG1IP
Hg19::chr21:46293644..46293655,-p3@PTTG1IP


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
mesodermal cell1.91e-27121
embryonic cell1.84e-22250
lining cell5.26e-1958
barrier cell5.26e-1958
meso-epithelial cell9.12e-1845
endothelial cell5.11e-1636
endothelial cell of vascular tree4.66e-1424
blood vessel endothelial cell3.79e-1118
embryonic blood vessel endothelial progenitor cell3.79e-1118
non-terminally differentiated cell9.98e-11106
epithelial cell1.38e-10253
animal cell1.75e-10679
eukaryotic cell1.75e-10679
somatic cell2.83e-10588
vascular associated smooth muscle cell1.02e-0932
smooth muscle cell2.77e-0843
smooth muscle myoblast2.77e-0843
muscle precursor cell3.42e-0858
myoblast3.42e-0858
multi-potent skeletal muscle stem cell3.42e-0858
contractile cell7.47e-0859
kidney cell8.02e-0817
kidney epithelial cell8.02e-0817
muscle cell3.47e-0755
fibroblast4.70e-0776
epithelial cell of nephron5.77e-0715
Uber Anatomy
Ontology termp-valuen
epithelial tube1.66e-25117
vasculature2.52e-2378
vascular system2.52e-2378
vessel4.23e-2168
epithelial tube open at both ends1.42e-1859
blood vessel1.42e-1859
blood vasculature1.42e-1859
vascular cord1.42e-1859
splanchnic layer of lateral plate mesoderm2.67e-1883
cardiovascular system5.91e-17109
circulatory system7.84e-17112
multi-cellular organism3.76e-16656
artery5.16e-1542
arterial blood vessel5.16e-1542
arterial system5.16e-1542
unilaminar epithelium2.28e-14148
anatomical system7.78e-14624
anatomical group1.64e-13625
mesenchyme3.10e-12160
entire embryonic mesenchyme3.10e-12160
simple squamous epithelium1.09e-1122
squamous epithelium1.60e-1125
trunk2.09e-11199
systemic artery2.89e-1133
systemic arterial system2.89e-1133
mesoderm3.38e-11315
mesoderm-derived structure3.38e-11315
presumptive mesoderm3.38e-11315
blood vessel endothelium3.79e-1118
endothelium3.79e-1118
cardiovascular system endothelium3.79e-1118
cell layer8.22e-11309
trunk mesenchyme2.75e-10122
anatomical conduit4.12e-10240
epithelium4.72e-10306
anatomical cluster9.23e-10373
organism subdivision1.55e-09264
tube5.79e-09192
developing anatomical structure1.76e-08581
embryo7.56e-08592
epithelial vesicle1.24e-0778
aorta2.96e-0721
aortic system2.96e-0721
lateral plate mesoderm3.36e-07203
parenchyma4.24e-0715
nephron epithelium5.77e-0715
renal tubule5.77e-0715
nephron tubule5.77e-0715
nephron5.77e-0715
uriniferous tubule5.77e-0715
nephrogenic mesenchyme5.77e-0715
abdominal segment of trunk6.44e-0760
abdomen6.44e-0760
muscle tissue7.12e-0764
musculature7.12e-0764
musculature of body7.12e-0764
excretory tube7.12e-0716
kidney epithelium7.12e-0716
skeletal muscle tissue8.01e-0762
striated muscle tissue8.01e-0762
myotome8.01e-0762


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.115.8547
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.12.67616
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
MA0055.10.557638
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
MA0073.10.0185922
MA0074.10.935474
MA0076.12.91768
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
MA0114.10.549955
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
MA0062.22.96208
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
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
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.481578
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#90536.336201576962630.003930750035764890.0190348033099295
E2F6#187635.017155731697390.00791769806886330.0322913335135119
ELF1#199734.258097958807540.01295179875054610.046318069774972
ELK4#2005316.2356816584680.0002336043955745990.00255979534880029
ESR1#2099330.76860329615453.43136389821584e-050.000677700858861127
GABPB1#255337.067683836182170.002832212825417420.015437267119345
HMGN3#932438.178547723350590.001827766942164210.0108868570590104
IRF1#365937.63716375356390.002244692747297240.0128316073253956
MXI1#460139.96157162875930.001011470541259020.00721071480263147
MYC#460935.22228187160940.007020843755740150.0295022894103865
NFKB1#479035.488063424193840.006049381815655430.0269996319421042
NRF1#4899312.21027944771090.0005492172401020010.00471746848745891
PAX5#507936.669565531177830.003370290999677260.017317220393353
SIN3A#2594235.408884726815140.006318961977991520.027727661443614
SP1#666735.69838137814090.005403962701712170.0246973770612689
USF1#739136.361499277207960.00388404057290560.0190649674951209
YY1#752834.911170749853860.008441455341808260.0329946539836494



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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