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Coexpression cluster:C3181: Difference between revisions

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|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;0.758317,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;2.15619,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;1.23283,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;1.36698,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;2.3269,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;1.35563,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;1.37817,MA0146.1;1.16674,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;2.04956,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.757898,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,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;2.02721,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;1.38935,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.8915,MA0163.1;2.48891,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;1.54885,MA0102.2;1.88331,MA0258.1;1.29138,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:11, 22 January 2013


Full id: C3181_Mesenchymal_Smooth_Hair_Aortic_Fibroblast_Hepatic_tridermal



Phase1 CAGE Peaks

Hg19::chr11:6341724..6341760,-p1@PRKCDBP
Hg19::chr19:48828788..48828853,+p1@EMP3
Hg19::chr22:38071636..38071652,+p1@LGALS1


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

GO IDGO nameFDR corrected p-value
GO:0016265death0.0394088188776617
GO:0008219cell death0.0394088188776617
GO:0045445myoblast differentiation0.0394088188776617
GO:0048741skeletal muscle fiber development0.0394088188776617
GO:0048747muscle fiber development0.0394088188776617
GO:0048468cell development0.0394088188776617
GO:0042692muscle cell differentiation0.0394088188776617
GO:0007519skeletal muscle development0.0487380796564191
GO:0014706striated muscle development0.0487380796564191
GO:0048869cellular developmental process0.0487380796564191
GO:0030154cell differentiation0.0487380796564191
GO:0043123positive regulation of I-kappaB kinase/NF-kappaB cascade0.0487380796564191
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0487380796564191
GO:0048856anatomical structure development0.0487380796564191



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
somatic cell1.68e-40588
mesodermal cell1.16e-31121
animal cell1.86e-27679
eukaryotic cell1.86e-27679
contractile cell6.13e-2459
muscle precursor cell2.35e-2358
myoblast2.35e-2358
multi-potent skeletal muscle stem cell2.35e-2358
muscle cell1.73e-2255
fibroblast6.10e-2176
smooth muscle cell5.75e-2043
smooth muscle myoblast5.75e-2043
multi fate stem cell1.18e-19427
somatic stem cell3.69e-19433
non-terminally differentiated cell2.76e-18106
electrically responsive cell4.12e-1861
electrically active cell4.12e-1861
stem cell4.00e-17441
embryonic cell4.16e-17250
native cell1.09e-16722
vascular associated smooth muscle cell4.32e-1632
meso-epithelial cell7.21e-1045
endothelial cell9.35e-1036
lining cell1.07e-0958
barrier cell1.07e-0958
skin fibroblast1.89e-0823
cardiocyte1.48e-0716
connective tissue cell3.60e-07361
endothelial cell of vascular tree4.66e-0724
Uber Anatomy
Ontology termp-valuen
epithelial vesicle3.41e-2878
somite2.69e-2571
presomitic mesoderm2.69e-2571
presumptive segmental plate2.69e-2571
dermomyotome2.69e-2571
trunk paraxial mesoderm2.69e-2571
dense mesenchyme tissue9.70e-2573
paraxial mesoderm1.78e-2472
presumptive paraxial mesoderm1.78e-2472
vasculature5.72e-2478
vascular system5.72e-2478
splanchnic layer of lateral plate mesoderm1.04e-2383
multilaminar epithelium1.17e-2383
mesoderm7.19e-23315
mesoderm-derived structure7.19e-23315
presumptive mesoderm7.19e-23315
vessel2.52e-2268
skeletal muscle tissue1.53e-2162
striated muscle tissue1.53e-2162
myotome1.53e-2162
epithelial tube open at both ends3.67e-2159
blood vessel3.67e-2159
blood vasculature3.67e-2159
vascular cord3.67e-2159
muscle tissue1.93e-2064
musculature1.93e-2064
musculature of body1.93e-2064
cardiovascular system5.35e-20109
artery2.53e-1942
arterial blood vessel2.53e-1942
arterial system2.53e-1942
circulatory system3.33e-19112
epithelial tube6.92e-17117
unilaminar epithelium1.28e-16148
musculoskeletal system1.95e-16167
systemic artery4.36e-1533
systemic arterial system4.36e-1533
trunk mesenchyme5.66e-15122
lateral plate mesoderm4.94e-14203
mesenchyme1.37e-13160
entire embryonic mesenchyme1.37e-13160
surface structure1.45e-0999
integument4.17e-0946
integumental system4.17e-0946
organism subdivision8.22e-09264
trunk2.01e-08199
aorta2.47e-0821
aortic system2.47e-0821
anatomical group2.88e-08625
anatomical system3.28e-08624
skin of body1.55e-0741
connective tissue1.83e-07371
multi-cellular organism3.71e-07656


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
MA0014.10.758317
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
MA0051.12.15619
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
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
MA0073.11.36698
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
MA0105.12.3269
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
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
MA0145.11.37817
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.12.04956
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.54885
MA0102.21.88331
MA0258.11.29138
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

No analysis results for this cluster

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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