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Coexpression cluster:C3282: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;3.22681,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;2.44638,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;1.06172,MA0056.1;0,MA0057.1;1.59304,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;3.33427,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;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;1.84783,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;1.37817,MA0146.1;3.00132,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;6.2923,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,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;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;0.8915,MA0163.1;3.19905,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;10.8725,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:16, 22 January 2013


Full id: C3282_Mesenchymal_Renal_Endothelial_Hepatic_Fibroblast_Pericytes_Trabecular



Phase1 CAGE Peaks

Hg19::chr12:48213650..48213695,-p1@HDAC7
Hg19::chr19:54984354..54984463,-p1@CDC42EP5
Hg19::chr1:26126670..26126721,+p1@SEPN1


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:0031269pseudopodium formation0.00423847294024064
GO:0031268pseudopodium organization and biogenesis0.00423847294024064
GO:0031274positive regulation of pseudopodium formation0.00423847294024064
GO:0031272regulation of pseudopodium formation0.00423847294024064
GO:0017049GTP-Rho binding0.00423847294024064
GO:0030838positive regulation of actin filament polymerization0.00423847294024064
GO:0031344regulation of cell projection organization and biogenesis0.00423847294024064
GO:0031346positive regulation of cell projection organization and biogenesis0.00423847294024064
GO:0030833regulation of actin filament polymerization0.0119282334752735
GO:0030041actin filament polymerization0.0141190928522875
GO:0017048Rho GTPase binding0.0141190928522875
GO:0022603regulation of anatomical structure morphogenesis0.0141190928522875
GO:0008360regulation of cell shape0.0141190928522875
GO:0022604regulation of cell morphogenesis0.0141190928522875
GO:0008064regulation of actin polymerization and/or depolymerization0.0141190928522875
GO:0030832regulation of actin filament length0.0141190928522875
GO:0032535regulation of cellular component size0.0141190928522875
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0141190928522875
GO:0030031cell projection biogenesis0.0141190928522875
GO:0008430selenium binding0.0141190928522875
GO:0051493regulation of cytoskeleton organization and biogenesis0.0143745331790643
GO:0033043regulation of organelle organization and biogenesis0.0143745331790643
GO:0008154actin polymerization and/or depolymerization0.0149760890815889
GO:0007254JNK cascade0.0152923045578563
GO:0031098stress-activated protein kinase signaling pathway0.0153575003160227
GO:0017016Ras GTPase binding0.0167190430585973
GO:0031267small GTPase binding0.017135774408785
GO:0051247positive regulation of protein metabolic process0.017135774408785
GO:0051020GTPase binding0.0182047674899782
GO:0051258protein polymerization0.0182047674899782
GO:0051128regulation of cellular component organization and biogenesis0.0182047674899782
GO:0000165MAPKKK cascade0.0264343064197099
GO:0007266Rho protein signal transduction0.0319306848958582
GO:0032990cell part morphogenesis0.0319306848958582
GO:0030030cell projection organization and biogenesis0.0319306848958582
GO:0048858cell projection morphogenesis0.0319306848958582
GO:0050793regulation of developmental process0.0359240784781714
GO:0030036actin cytoskeleton organization and biogenesis0.0366031238167997
GO:0030029actin filament-based process0.0375344561401569
GO:0019899enzyme binding0.0429014915697675



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
vasculature3.43e-3378
vascular system3.43e-3378
splanchnic layer of lateral plate mesoderm4.51e-3183
vessel1.36e-2968
epithelial tube1.31e-28117
epithelial tube open at both ends1.21e-2659
blood vessel1.21e-2659
blood vasculature1.21e-2659
vascular cord1.21e-2659
circulatory system3.40e-26112
cardiovascular system5.67e-26109
cell layer1.38e-22309
multi-cellular organism1.01e-21656
epithelium1.37e-21306
mesenchyme2.91e-21160
entire embryonic mesenchyme2.91e-21160
unilaminar epithelium3.47e-21148
epithelial vesicle9.91e-2178
organism subdivision4.92e-19264
artery1.54e-1842
arterial blood vessel1.54e-1842
arterial system1.54e-1842
anatomical cluster3.83e-18373
multilaminar epithelium5.75e-1883
anatomical system1.03e-17624
anatomical group2.65e-17625
somite3.61e-1771
presomitic mesoderm3.61e-1771
presumptive segmental plate3.61e-1771
dermomyotome3.61e-1771
trunk paraxial mesoderm3.61e-1771
trunk mesenchyme4.15e-17122
dense mesenchyme tissue8.09e-1773
paraxial mesoderm8.84e-1772
presumptive paraxial mesoderm8.84e-1772
trunk1.54e-16199
skeletal muscle tissue8.65e-1662
striated muscle tissue8.65e-1662
myotome8.65e-1662
anatomical conduit1.04e-15240
muscle tissue1.26e-1564
musculature1.26e-1564
musculature of body1.26e-1564
systemic artery5.88e-1533
systemic arterial system5.88e-1533
multi-tissue structure2.11e-13342
tube2.12e-12192
blood vessel endothelium4.28e-1218
endothelium4.28e-1218
cardiovascular system endothelium4.28e-1218
squamous epithelium5.37e-1225
compound organ7.96e-1268
simple squamous epithelium2.48e-1122
mesoderm6.10e-11315
mesoderm-derived structure6.10e-11315
presumptive mesoderm6.10e-11315
embryo8.50e-11592
aorta1.01e-1021
aortic system1.01e-1021
developing anatomical structure3.07e-10581
germ layer4.25e-09560
germ layer / neural crest4.25e-09560
embryonic tissue4.25e-09560
presumptive structure4.25e-09560
germ layer / neural crest derived structure4.25e-09560
epiblast (generic)4.25e-09560
embryonic structure6.97e-09564
primary circulatory organ3.73e-0827
heart4.43e-0824
primitive heart tube4.43e-0824
primary heart field4.43e-0824
anterior lateral plate mesoderm4.43e-0824
heart tube4.43e-0824
heart primordium4.43e-0824
cardiac mesoderm4.43e-0824
cardiogenic plate4.43e-0824
heart rudiment4.43e-0824


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)
MA0003.13.22681
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
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
MA0055.11.06172
MA0056.10
MA0057.11.59304
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
MA0073.13.33427
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.11.84783
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
MA0145.11.37817
MA0146.13.00132
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.26.2923
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
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
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.13.19905
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.210.8725
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

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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