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Coexpression cluster:C3859: Difference between revisions

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{{Coexpression_clusters
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0130.1;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;0.752137,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;0.264678,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;0.256269,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;0.776149,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.311277,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3859_CD14_Fibroblast_Preadipocyte_Smooth_leiomyoma_tenocyte_Myoblast
|id=C3859
}}

Latest revision as of 12:34, 17 September 2013


Full id: C3859_CD14_Fibroblast_Preadipocyte_Smooth_leiomyoma_tenocyte_Myoblast



Phase1 CAGE Peaks

Hg19::chr1:145096387..145096477,+p1@SEC22B
Hg19::chr1:145116327..145116343,+p@chr1:145116327..145116343
+
Hg19::chr4:122618095..122618161,-p1@ANXA5


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:0033116ER-Golgi intermediate compartment membrane0.0205762027448468
GO:0050819negative regulation of coagulation0.0205762027448468
GO:0050818regulation of coagulation0.0205762027448468
GO:0055102lipase inhibitor activity0.0205762027448468
GO:0004859phospholipase inhibitor activity0.0205762027448468
GO:0006888ER to Golgi vesicle-mediated transport0.0332505298680399
GO:0005793ER-Golgi intermediate compartment0.0332505298680399
GO:0005544calcium-dependent phospholipid binding0.0365310003594502
GO:0048770pigment granule0.0405595081249357
GO:0042470melanosome0.0405595081249357
GO:0048193Golgi vesicle transport0.0405595081249357
GO:0007596blood coagulation0.0405595081249357
GO:0050817coagulation0.0405595081249357
GO:0007599hemostasis0.0405595081249357
GO:0050878regulation of body fluid levels0.0442604929895272
GO:0042060wound healing0.0442604929895272



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
multi fate stem cell4.62e-31427
somatic stem cell1.62e-29433
stem cell3.77e-26441
somatic cell1.46e-21588
muscle precursor cell5.31e-1858
myoblast5.31e-1858
multi-potent skeletal muscle stem cell5.31e-1858
animal cell7.49e-18679
eukaryotic cell7.49e-18679
muscle cell1.27e-1655
connective tissue cell3.50e-16361
mesenchymal cell4.21e-15354
fibroblast4.38e-1576
contractile cell1.33e-1459
smooth muscle cell4.00e-1443
smooth muscle myoblast4.00e-1443
mesodermal cell5.30e-14121
native cell2.36e-13722
electrically responsive cell5.99e-1361
electrically active cell5.99e-1361
stuff accumulating cell1.30e-1287
defensive cell2.37e-1248
phagocyte2.37e-1248
vascular associated smooth muscle cell4.38e-1232
motile cell5.52e-12386
monopoietic cell1.60e-1159
monocyte1.60e-1159
monoblast1.60e-1159
promonocyte1.60e-1159
macrophage dendritic cell progenitor9.79e-1161
non-terminally differentiated cell1.39e-10106
classical monocyte3.37e-1042
CD14-positive, CD16-negative classical monocyte3.37e-1042
myeloid lineage restricted progenitor cell4.61e-1066
granulocyte monocyte progenitor cell1.69e-0867
myeloid leukocyte6.97e-0872
fat cell3.76e-0715
Uber Anatomy
Ontology termp-valuen
musculoskeletal system3.07e-27167
mesoderm5.72e-22315
mesoderm-derived structure5.72e-22315
presumptive mesoderm5.72e-22315
somite2.27e-1671
presomitic mesoderm2.27e-1671
presumptive segmental plate2.27e-1671
dermomyotome2.27e-1671
trunk paraxial mesoderm2.27e-1671
dense mesenchyme tissue2.46e-1673
paraxial mesoderm4.67e-1672
presumptive paraxial mesoderm4.67e-1672
connective tissue1.25e-15371
skeletal muscle tissue5.99e-1562
striated muscle tissue5.99e-1562
myotome5.99e-1562
muscle tissue2.98e-1464
musculature2.98e-1464
musculature of body2.98e-1464
multilaminar epithelium3.37e-1383
epithelial vesicle4.62e-1378
lateral plate mesoderm5.75e-12203
skeletal system1.34e-11100
trunk mesenchyme1.79e-11122
skeletal element1.41e-1090
unilaminar epithelium5.09e-10148
bone marrow6.15e-1076
artery1.25e-0942
arterial blood vessel1.25e-0942
arterial system1.25e-0942
bone element5.20e-0982
systemic artery7.94e-0933
systemic arterial system7.94e-0933
mesenchyme1.60e-08160
entire embryonic mesenchyme1.60e-08160
vasculature3.78e-0878
vascular system3.78e-0878
cardiovascular system1.79e-07109
splanchnic layer of lateral plate mesoderm1.96e-0783
immune system2.38e-0793
vessel7.60e-0768


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)
MA0003.10.178364
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
MA0041.11.97353
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
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
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
MA0105.10.31555
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
MA0145.10.752137
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
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
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
SMC3#9126210.02995522995520.0126656379767470.0457489992617238
ZZZ3#26009179.80440414507770.0124784379082580.0451618524690909



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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