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Coexpression cluster:C4549: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4549_cholangiocellular_Preadipocyte_Fibroblast_Adipocyte_mesenchymal_Aortic_Smooth
|id=C4549
}}

Latest revision as of 14:15, 17 September 2013


Full id: C4549_cholangiocellular_Preadipocyte_Fibroblast_Adipocyte_mesenchymal_Aortic_Smooth



Phase1 CAGE Peaks

Hg19::chr6:116832767..116832787,+p3@FAM26E
Hg19::chr6:116832789..116832811,+p2@FAM26E
Hg19::chr6:116832823..116832853,+p1@FAM26E


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><br>

Uber Anatomy
Ontology termp-valuen
circulatory system2.57e-25112
cardiovascular system7.93e-25109
splanchnic layer of lateral plate mesoderm1.69e-2383
vasculature2.65e-2178
vascular system2.65e-2178
vessel1.45e-1968
dense mesenchyme tissue2.68e-1973
somite6.18e-1971
presomitic mesoderm6.18e-1971
presumptive segmental plate6.18e-1971
dermomyotome6.18e-1971
trunk paraxial mesoderm6.18e-1971
paraxial mesoderm6.63e-1972
presumptive paraxial mesoderm6.63e-1972
epithelial tube open at both ends1.14e-1859
blood vessel1.14e-1859
blood vasculature1.14e-1859
vascular cord1.14e-1859
muscle tissue1.62e-1864
musculature1.62e-1864
musculature of body1.62e-1864
skeletal muscle tissue3.13e-1862
striated muscle tissue3.13e-1862
myotome3.13e-1862
artery5.93e-1842
arterial blood vessel5.93e-1842
arterial system5.93e-1842
epithelial vesicle6.57e-1878
multilaminar epithelium1.63e-1683
systemic artery5.84e-1533
systemic arterial system5.84e-1533
epithelial tube1.62e-13117
unilaminar epithelium2.94e-13148
trunk mesenchyme7.99e-13122
mesenchyme6.09e-12160
entire embryonic mesenchyme6.09e-12160
surface structure4.69e-1199
multi-cellular organism8.15e-11656
aorta2.37e-1021
aortic system2.37e-1021
mesoderm2.92e-10315
mesoderm-derived structure2.92e-10315
presumptive mesoderm2.92e-10315
anatomical cluster4.41e-10373
organism subdivision9.92e-10264
primary circulatory organ1.97e-0927
anatomical system2.58e-09624
anatomical group2.92e-09625
cell layer3.17e-09309
integument3.36e-0946
integumental system3.36e-0946
heart4.02e-0924
primitive heart tube4.02e-0924
primary heart field4.02e-0924
anterior lateral plate mesoderm4.02e-0924
heart tube4.02e-0924
heart primordium4.02e-0924
cardiac mesoderm4.02e-0924
cardiogenic plate4.02e-0924
heart rudiment4.02e-0924
multi-tissue structure7.31e-09342
epithelium1.24e-08306
anatomical conduit3.42e-08240
skin of body9.73e-0841
trunk3.13e-07199
smooth muscle tissue7.46e-0715


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
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
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
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
MA0139.12.91906
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.12.29531
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.23.41713
MA0039.20.195278
MA0138.21.04628
MA0002.21.20011
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
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
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
CEBPB#105137.971147625824820.001974187055288560.0115683174475274
CTCF#1066435.360256373075030.0064925092527670.0280995886556601
EP300#203336.77394172622320.003216880500103790.0168244670514467
GATA2#2624312.7449317335540.0004829527704283790.00438715355229795
JUN#3725312.51282919233630.0005103313992726250.00446087219690607
JUNB#3726330.61063265982113.4847716247536e-050.000682313580273044
JUND#372736.994663941871030.002921845042734990.0157539790613423
RAD21#5885310.35503389545630.0009004912073565420.00667848325558229
SETDB1#9869340.32002617801051.52461559299059e-050.000359758987610358
SMC3#9126315.04493284493280.0002935825420371870.00310558767424509
TAL1#6886329.86861667744023.75103522793067e-050.000722261003263
TRIM28#10155318.59052504526250.0001555969297255280.00197813606130303



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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