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Coexpression cluster:C4734: Difference between revisions

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{{Coexpression_clusters
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9,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,1.54465,0.667627,1.17594,1.40888,0.452865,0.305559,1.65118,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,1.00813,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,1.10051,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,2.82894,0.684398,0.830777,1.58942,1.44883,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,2.36206,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,2.14918,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,1.29196,1.37083,4.21132,0.941179,1.78371,1.03563,0.624795,0.744018,2.84192,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,5.4618|tfbs_overrepresentation_jaspar=MA0003.1;1.0927,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.80735,MA0017.1;0.686276,MA0019.1;3.71555,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;0.557638,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;1.79391,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;1.31954,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;0.531867,MA0145.1;0.273764,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.432958,MA0138.2;1.04628,MA0002.2;1.20011,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;2.97249,MA0150.1;2.94916,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.711948,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;1.38935,MA0160.1;0.871361,MA0161.1;0,MA0162.1;3.52399,MA0163.1;3.19905,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;2.08754,MA0079.2;0.311277,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4734_Fibroblast_Smooth_Mesenchymal_Preadipocyte_Keratocytes_Chondrocyte_melanoma
|id=C4734
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4734_Fibroblast_Smooth_Mesenchymal_Preadipocyte_Keratocytes_Chondrocyte_melanoma



Phase1 CAGE Peaks

Hg19::chr8:145025046..145025061,-p7@PLEC
Hg19::chr8:145025063..145025073,-p16@PLEC
Hg19::chr8:145025074..145025102,-p2@PLEC


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
fibroblast3.82e-2876
somatic cell1.18e-26588
animal cell1.17e-23679
eukaryotic cell1.17e-23679
multi fate stem cell1.04e-16427
somatic stem cell1.29e-16433
mesodermal cell9.27e-16121
stem cell1.50e-14441
native cell5.74e-13722
skin fibroblast2.72e-1123
muscle precursor cell3.51e-1158
myoblast3.51e-1158
multi-potent skeletal muscle stem cell3.51e-1158
contractile cell5.69e-1159
connective tissue cell2.94e-10361
muscle cell3.03e-1055
classical monocyte5.19e-1042
CD14-positive, CD16-negative classical monocyte5.19e-1042
defensive cell9.60e-1048
phagocyte9.60e-1048
mesenchymal cell2.73e-09354
smooth muscle cell2.92e-0943
smooth muscle myoblast2.92e-0943
non-terminally differentiated cell1.49e-08106
macrophage dendritic cell progenitor3.03e-0861
monopoietic cell4.67e-0859
monocyte4.67e-0859
monoblast4.67e-0859
promonocyte4.67e-0859
preadipocyte1.09e-0712
embryonic cell1.23e-07250
electrically responsive cell1.98e-0761
electrically active cell1.98e-0761
motile cell2.12e-07386
granulocyte monocyte progenitor cell3.73e-0767
Uber Anatomy
Ontology termp-valuen
mesoderm5.23e-23315
mesoderm-derived structure5.23e-23315
presumptive mesoderm5.23e-23315
musculoskeletal system7.70e-23167
epithelial vesicle2.19e-1478
lateral plate mesoderm2.60e-14203
somite1.82e-1371
presomitic mesoderm1.82e-1371
presumptive segmental plate1.82e-1371
dermomyotome1.82e-1371
trunk paraxial mesoderm1.82e-1371
dense mesenchyme tissue2.40e-1373
anatomical group4.03e-13625
anatomical system4.49e-13624
multilaminar epithelium5.02e-1383
paraxial mesoderm5.47e-1372
presumptive paraxial mesoderm5.47e-1372
multi-cellular organism7.73e-13656
skeletal system8.34e-12100
connective tissue7.78e-11371
skeletal muscle tissue2.26e-1062
striated muscle tissue2.26e-1062
myotome2.26e-1062
splanchnic layer of lateral plate mesoderm5.98e-1083
artery6.12e-1042
arterial blood vessel6.12e-1042
arterial system6.12e-1042
muscle tissue7.12e-1064
musculature7.12e-1064
musculature of body7.12e-1064
integument7.20e-1046
integumental system7.20e-1046
surface structure9.02e-1099
epithelial tube open at both ends1.23e-0959
blood vessel1.23e-0959
blood vasculature1.23e-0959
vascular cord1.23e-0959
skeletal element2.02e-0990
bone element2.10e-0982
vasculature5.66e-0978
vascular system5.66e-0978
skin of body5.85e-0941
vessel8.89e-0968
systemic artery1.94e-0833
systemic arterial system1.94e-0833
bone marrow2.47e-0876
germ layer9.84e-08560
germ layer / neural crest9.84e-08560
embryonic tissue9.84e-08560
presumptive structure9.84e-08560
germ layer / neural crest derived structure9.84e-08560
epiblast (generic)9.84e-08560
embryonic structure2.16e-07564
epithelial tube3.45e-07117
unilaminar epithelium5.55e-07148
trunk mesenchyme6.50e-07122
developing anatomical structure6.83e-07581
cardiovascular system7.78e-07109


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.13.71555
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
MA0055.10.557638
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
MA0073.11.79391
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
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
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.22.97249
MA0150.12.94916
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.13.52399
MA0163.13.19905
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.22.08754
MA0079.20.311277
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#90536.336201576962630.003930750035764890.0191252552054623
E2F6#187635.017155731697390.00791769806886330.0324471833868556
EGR1#195834.988179094810140.008056488137383440.0322614763460063
ETS1#211339.728760922202340.001085840092584840.00765622828986415
FOS#235338.99795530889440.001372499272417130.00902262551217804
MXI1#460139.96157162875930.001011470541259020.00723689606484558
MYC#460935.22228187160940.007020843755740150.0296190782438902
ZBTB7A#5134137.35190930787590.002516255860282270.0140984573922757
ZNF263#1012738.221841637010680.001799043925565870.0110173770694367



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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