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Coexpression cluster:C4714: Difference between revisions

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{{Coexpression_clusters
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tfbs_overrepresentation_jaspar=MA0003.1;1.54338,MA0004.1;1.93041,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,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;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;4.13609,MA0059.1;4.12962,MA0060.1;0.492218,MA0061.1;2.01615,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;0.0834661,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;1.84783,MA0093.1;2.626,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;2.63873,MA0103.1;0.628063,MA0105.1;3.21605,MA0106.1;0.986396,MA0107.1;3.44314,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;1.3784,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;1.16674,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;2.74132,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;2.07067,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;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;3.52399,MA0163.1;0.776149,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;3.61229,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4714_Adipocyte_Osteoblast_Preadipocyte_Fibroblast_Mesenchymal_tenocyte_mesenchymal
|id=C4714
|ontology_enrichment_celltype=CL:0000055!1.74e-35!180;CL:0000057!3.63e-20!75;CL:0000183!9.58e-18!59;CL:0000680!1.26e-16!57;CL:0000056!1.26e-16!57;CL:0000355!1.26e-16!57;CL:0000187!1.13e-15!54;CL:0000393!1.61e-13!60;CL:0000211!1.61e-13!60;CL:0000222!3.61e-13!119;CL:0000192!4.86e-13!42;CL:0000514!4.86e-13!42;CL:0002371!1.56e-09!591;CL:0000359!1.90e-09!32;CL:0002334!2.03e-08!12;CL:0000144!1.47e-07!625;CL:0000048!2.41e-07!430;CL:0000548!3.21e-07!679;CL:0000004!3.21e-07!679;CL:0000255!3.21e-07!679;CL:0002620!3.74e-07!23;CL:0000012!9.33e-07!682
|ontology_enrichment_disease=DOID:2394!9.54e-07!14
|ontology_enrichment_uberon=UBERON:0000914!5.95e-18!83;UBERON:0002329!5.95e-18!83;UBERON:0003077!5.95e-18!83;UBERON:0003059!5.95e-18!83;UBERON:0007282!5.95e-18!83;UBERON:0009618!5.95e-18!83;UBERON:0007285!5.95e-18!83;UBERON:0002049!1.41e-17!79;UBERON:0007798!1.41e-17!79;UBERON:0005256!2.55e-17!143;UBERON:0004290!3.53e-17!70;UBERON:0001134!7.51e-16!61;UBERON:0002036!7.51e-16!61;UBERON:0003082!7.51e-16!61;UBERON:0002385!1.52e-15!63;UBERON:0001015!1.52e-15!63;UBERON:0000383!1.52e-15!63;UBERON:0004872!1.49e-14!84;UBERON:0000055!4.00e-14!69;UBERON:0000486!5.44e-14!82;UBERON:0003914!5.62e-14!118;UBERON:0000475!1.35e-13!365;UBERON:0002100!2.12e-13!216;UBERON:0000490!1.14e-12!138;UBERON:0001009!3.97e-12!113;UBERON:0004535!4.65e-12!110;UBERON:0001981!1.73e-11!60;UBERON:0007500!1.73e-11!60;UBERON:0004537!1.73e-11!60;UBERON:0006965!1.73e-11!60;UBERON:0000468!2.74e-11!659;UBERON:0000119!1.40e-10!312;UBERON:0000483!4.54e-10!309;UBERON:0001637!4.03e-09!42;UBERON:0003509!4.03e-09!42;UBERON:0004572!4.03e-09!42;UBERON:0003102!5.84e-09!95;UBERON:0003104!6.49e-09!238;UBERON:0009142!6.49e-09!238;UBERON:0000477!7.26e-09!286;UBERON:0001013!1.33e-08!14;UBERON:0000481!1.71e-08!347;UBERON:0002199!2.67e-08!45;UBERON:0002416!2.67e-08!45;UBERON:0004111!8.35e-08!241;UBERON:0000480!9.73e-08!626;UBERON:0004573!1.19e-07!33;UBERON:0004571!1.19e-07!33;UBERON:0000467!1.35e-07!625
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4714_Adipocyte_Osteoblast_Preadipocyte_Fibroblast_Mesenchymal_tenocyte_mesenchymal



Phase1 CAGE Peaks

Hg19::chr8:104383700..104383709,+p4@CTHRC1
Hg19::chr8:104383728..104383756,+p2@CTHRC1
Hg19::chr8:104383759..104383821,+p1@CTHRC1


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>

Uber Anatomy
Ontology termp-valuen
epithelial vesicle1.03e-2078
somite1.80e-1871
presomitic mesoderm1.80e-1871
presumptive segmental plate1.80e-1871
dermomyotome1.80e-1871
trunk paraxial mesoderm1.80e-1871
dense mesenchyme tissue1.99e-1873
paraxial mesoderm3.08e-1872
presumptive paraxial mesoderm3.08e-1872
vasculature2.24e-1778
vascular system2.24e-1778
mesenchyme3.11e-17160
entire embryonic mesenchyme3.11e-17160
trunk mesenchyme6.16e-17122
skeletal muscle tissue7.85e-1762
striated muscle tissue7.85e-1762
myotome7.85e-1762
muscle tissue1.99e-1664
musculature1.99e-1664
musculature of body1.99e-1664
splanchnic layer of lateral plate mesoderm3.35e-1583
multilaminar epithelium5.56e-1583
unilaminar epithelium6.48e-15148
epithelial tube1.25e-14117
organism subdivision4.63e-14264
vessel6.42e-1468
circulatory system2.24e-13112
cardiovascular system2.68e-13109
trunk2.58e-12199
epithelial tube open at both ends2.72e-1159
blood vessel2.72e-1159
blood vasculature2.72e-1159
vascular cord2.72e-1159
cell layer3.24e-10309
epithelium1.25e-09306
multi-cellular organism1.54e-09656
surface structure3.78e-0999
integument5.79e-0946
integumental system5.79e-0946
artery6.82e-0942
arterial blood vessel6.82e-0942
arterial system6.82e-0942
adipose tissue7.81e-0914
mesoderm1.49e-08315
mesoderm-derived structure1.49e-08315
presumptive mesoderm1.49e-08315
multi-tissue structure6.37e-08342
systemic artery1.44e-0733
systemic arterial system1.44e-0733
anatomical conduit6.45e-07240
anatomical group6.92e-07625
anatomical cluster7.19e-07373
skin of body8.89e-0741
anatomical system9.16e-07624
Disease
Ontology termp-valuen
ovarian cancer8.42e-0714


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)
MA0003.11.54338
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.14.13609
MA0059.14.12962
MA0060.10.492218
MA0061.12.01615
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
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
MA0092.11.84783
MA0093.12.626
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.12.63873
MA0103.10.628063
MA0105.13.21605
MA0106.10.986396
MA0107.13.44314
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0146.11.16674
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.22.07067
MA0065.20.277623
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
MA0162.13.52399
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.61229
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
CTCF#1066435.360256373075030.0064925092527670.0281369008610205
E2F6#187635.017155731697390.00791769806886330.0324408186980782
EGR1#195834.988179094810140.008056488137383440.0322577658557042
NFKB1#479035.488063424193840.006049381815655430.0270876087911695
ZBTB7A#5134137.35190930787590.002516255860282270.0140961886923789
ZEB1#6935316.88843201754390.0002075486917327580.00243799098142813



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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