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Coexpression cluster:C3095: Difference between revisions

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{{Coexpression_clusters
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084.1;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;0.846801,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;4.65896,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;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.15986,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;2.13692,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;3.19371,MA0155.1;0.711948,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.455568,MA0163.1;1.2663,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;7.52072,MA0102.2;1.88331,MA0258.1;1.29138,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3095_Endothelial_mature_Renal_aorta_Hepatic_melanoma_gall
|id=C3095
}}

Latest revision as of 12:19, 17 September 2013


Full id: C3095_Endothelial_mature_Renal_aorta_Hepatic_melanoma_gall



Phase1 CAGE Peaks

Hg19::chr11:119187829..119187847,-p1@MCAM
Hg19::chr17:1395929..1395942,-p8@MYO1C
Hg19::chr17:1395954..1396027,-p3@MYO1C


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:0016461unconventional myosin complex0.00865202040666745
GO:0016328lateral plasma membrane0.00865202040666745
GO:0031941filamentous actin0.00865202040666745
GO:0045178basal part of cell0.00865202040666745
GO:0009925basal plasma membrane0.00865202040666745
GO:0005902microvillus0.00865202040666745
GO:0005884actin filament0.0102989628262972
GO:0044459plasma membrane part0.0272109751028391
GO:0016323basolateral plasma membrane0.0272109751028391
GO:0016459myosin complex0.0308184393693123
GO:0005516calmodulin binding0.0369007816345632



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 cluster4.92e-26373
epithelium3.21e-20306
anatomical conduit5.13e-20240
cell layer6.58e-20309
multi-tissue structure4.52e-18342
tube2.00e-17192
multi-cellular organism2.20e-16656
adult organism1.24e-15114
organ part7.61e-15218
epithelial tube1.06e-13117
blood vessel endothelium1.30e-1318
endothelium1.30e-1318
cardiovascular system endothelium1.30e-1318
anatomical group1.18e-12625
anatomical system1.19e-12624
simple squamous epithelium3.10e-1122
compound organ4.36e-1168
embryo6.39e-11592
subdivision of trunk6.76e-11112
developing anatomical structure1.04e-10581
excretory tube1.55e-1016
kidney epithelium1.55e-1016
abdominal segment of trunk2.37e-1060
abdomen2.37e-1060
organism subdivision4.52e-10264
parenchyma4.58e-1015
nephron epithelium4.67e-1015
renal tubule4.67e-1015
nephron tubule4.67e-1015
nephron4.67e-1015
uriniferous tubule4.67e-1015
nephrogenic mesenchyme4.67e-1015
squamous epithelium8.15e-1025
vasculature3.55e-0978
vascular system3.55e-0978
abdomen element6.46e-0954
abdominal segment element6.46e-0954
renal system1.08e-0848
cavitated compound organ1.10e-0831
vessel1.75e-0868
cortex of kidney2.84e-0812
renal parenchyma2.84e-0812
urinary system structure3.05e-0847
embryonic structure3.63e-08564
kidney4.27e-0826
kidney mesenchyme4.27e-0826
upper urinary tract4.27e-0826
kidney rudiment4.27e-0826
kidney field4.27e-0826
endothelial tube6.80e-089
arterial system endothelium6.80e-089
endothelium of artery6.80e-089
trunk region element8.72e-08101
germ layer8.79e-08560
germ layer / neural crest8.79e-08560
embryonic tissue8.79e-08560
presumptive structure8.79e-08560
germ layer / neural crest derived structure8.79e-08560
epiblast (generic)8.79e-08560
neural plate1.33e-0782
presumptive neural plate1.33e-0782
trunk2.83e-07199
cortex3.14e-0715
structure with developmental contribution from neural crest3.21e-07132
primordium3.24e-07160
splanchnic layer of lateral plate mesoderm4.02e-0783
mesenchyme6.07e-07160
entire embryonic mesenchyme6.07e-07160
ecto-epithelium7.26e-07104
nephron tubule epithelium8.90e-0710


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)
MA0003.12.05336
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
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
MA0055.11.67416
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.11.70014
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
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
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.14.65896
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
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.22.13692
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.13.19371
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.27.52072
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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