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Coexpression cluster:C4716: Difference between revisions

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{{Coexpression_clusters
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645155,0.388328,1.86765,2.72118,0.534793,0.439574,0.599922,1.96994,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,4.3166,1.45054,0.430728,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,5.10954,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,1.7605,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,1.98143,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,2.36206,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,2.45299,2.31409,0.773313,3.36921,1.54007,1.99724,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,2.24188,0.936473,0.56135|tfbs_overrepresentation_jaspar=MA0003.1;0.401049,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;3.90467,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;0.904546,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;2.4146,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;2.75836,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;22.76,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;0.715722,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;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;2.7939,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;2.26598,MA0145.1;0.273764,MA0146.1;0.707589,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;2.15877,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;1.60005,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;1.34467,MA0065.2;1.39232,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;1.31345,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;2.05956,MA0163.1;2.48891,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;10.17,MA0102.2;1.88331,MA0258.1;2.22591,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4716_cerebellum_Myoblast_tridermal_osteosarcoma_skeletal_myxofibrosarcoma_synovial
|id=C4716
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4716_cerebellum_Myoblast_tridermal_osteosarcoma_skeletal_myxofibrosarcoma_synovial



Phase1 CAGE Peaks

Hg19::chr8:106330543..106330554,+p4@ZFPM2
Hg19::chr8:106330656..106330684,+p1@ZFPM2
Hg19::chr8:106330696..106330719,+p2@ZFPM2


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
anatomical conduit1.62e-27240
tube6.97e-26192
anatomical cluster1.34e-25373
adult organism2.34e-24114
cell layer2.75e-21309
epithelium3.14e-21306
neural tube4.69e-2056
neural rod4.69e-2056
future spinal cord4.69e-2056
neural keel4.69e-2056
nervous system1.11e-1989
central nervous system1.44e-1981
brain1.45e-1968
future brain1.45e-1968
regional part of nervous system6.24e-1953
regional part of brain6.24e-1953
structure with developmental contribution from neural crest2.83e-18132
splanchnic layer of lateral plate mesoderm5.73e-1783
vessel1.42e-1568
multi-tissue structure1.97e-15342
neural plate3.07e-1582
presumptive neural plate3.07e-1582
neurectoderm5.89e-1586
regional part of forebrain6.07e-1541
forebrain6.07e-1541
anterior neural tube6.07e-1541
future forebrain6.07e-1541
vasculature1.04e-1478
vascular system1.04e-1478
brain grey matter2.54e-1434
gray matter2.54e-1434
epithelial tube open at both ends3.07e-1459
blood vessel3.07e-1459
blood vasculature3.07e-1459
vascular cord3.07e-1459
telencephalon7.57e-1434
circulatory system9.53e-14112
cerebral hemisphere9.94e-1432
regional part of telencephalon1.37e-1332
multi-cellular organism2.75e-13656
regional part of cerebral cortex5.46e-1322
cardiovascular system1.03e-12109
cerebral cortex1.13e-1225
pallium1.13e-1225
neocortex1.23e-1120
muscle tissue6.16e-1164
musculature6.16e-1164
musculature of body6.16e-1164
anatomical system6.28e-11624
organ system subdivision7.77e-11223
anatomical group9.90e-11625
skeletal muscle tissue1.55e-1062
striated muscle tissue1.55e-1062
myotome1.55e-1062
artery3.01e-1042
arterial blood vessel3.01e-1042
arterial system3.01e-1042
epithelial tube4.91e-10117
germ layer5.04e-10560
germ layer / neural crest5.04e-10560
embryonic tissue5.04e-10560
presumptive structure5.04e-10560
germ layer / neural crest derived structure5.04e-10560
epiblast (generic)5.04e-10560
embryonic structure8.62e-10564
systemic artery3.43e-0933
systemic arterial system3.43e-0933
ecto-epithelium3.45e-09104
ectoderm-derived structure4.06e-09171
ectoderm4.06e-09171
presumptive ectoderm4.06e-09171
pre-chordal neural plate5.11e-0961
unilaminar epithelium6.92e-09148
dense mesenchyme tissue7.44e-0973
primary circulatory organ1.12e-0827
paraxial mesoderm1.31e-0872
presumptive paraxial mesoderm1.31e-0872
somite2.53e-0871
presomitic mesoderm2.53e-0871
presumptive segmental plate2.53e-0871
dermomyotome2.53e-0871
trunk paraxial mesoderm2.53e-0871
developing anatomical structure2.63e-08581
embryo8.51e-08592
epithelial vesicle8.74e-0878
trunk mesenchyme9.84e-08122


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
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.90467
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.12.4146
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.12.75836
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.122.76
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.12.7939
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
MA0144.12.26598
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.210.17
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#90536.336201576962630.003930750035764890.0191208012568817
E2F6#187635.017155731697390.00791769806886330.032442091436071
ETS1#211339.728760922202340.001085840092584840.00765519464219439
HMGN3#932438.178547723350590.001827766942164210.0109248641717329
ZBTB7A#5134137.35190930787590.002516255860282270.0140969448445456
ZNF263#1012738.221841637010680.001799043925565870.0110167310784036



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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