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{{Coexpression_clusters
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|full_id=C4633_hepatic_spindle_chorionic_bone_Smooth_Fibroblast_basal
|id=C4633
|ontology_enrichment_celltype=CL:0000222!2.34e-35!119;CL:0000055!7.18e-29!180;CL:0000680!9.49e-24!57;CL:0000056!9.49e-24!57;CL:0000355!9.49e-24!57;CL:0000183!3.48e-23!59;CL:0000187!2.62e-22!54;CL:0000192!2.18e-20!42;CL:0000514!2.18e-20!42;CL:0000220!5.82e-20!246;CL:0000144!6.91e-20!625;CL:0002321!2.33e-19!248;CL:0000359!3.27e-19!32;CL:0002371!5.45e-18!591;CL:0000393!1.12e-17!60;CL:0000211!1.12e-17!60;CL:0000548!1.25e-15!679;CL:0000004!1.25e-15!679;CL:0000255!1.25e-15!679;CL:0000012!4.77e-15!682;CL:0000057!5.45e-13!75;CL:0000213!1.11e-12!57;CL:0000215!1.11e-12!57;CL:0002139!3.84e-11!24;CL:0000115!8.79e-10!35;CL:0002078!9.93e-09!44;CL:0000048!2.06e-08!430;CL:0000003!2.26e-08!722;CL:0002494!2.88e-08!16;CL:0000723!3.49e-08!436;CL:0000071!5.88e-08!18;CL:0002546!5.88e-08!18;CL:0002539!6.31e-08!10;CL:0000034!2.97e-07!444;CL:1000413!6.75e-07!9
|ontology_enrichment_disease=DOID:2394!4.45e-08!14
|ontology_enrichment_uberon=UBERON:0002049!2.12e-33!79;UBERON:0007798!2.12e-33!79;UBERON:0000055!1.14e-30!69;UBERON:0003914!7.69e-28!118;UBERON:0004872!4.23e-27!84;UBERON:0001981!5.32e-27!60;UBERON:0007500!5.32e-27!60;UBERON:0004537!5.32e-27!60;UBERON:0006965!5.32e-27!60;UBERON:0004535!1.05e-26!110;UBERON:0001009!3.10e-26!113;UBERON:0001637!4.37e-25!42;UBERON:0003509!4.37e-25!42;UBERON:0004572!4.37e-25!42;UBERON:0000486!4.36e-23!82;UBERON:0000490!6.10e-23!138;UBERON:0004290!8.31e-23!70;UBERON:0004573!3.16e-21!33;UBERON:0004571!3.16e-21!33;UBERON:0001134!3.92e-21!61;UBERON:0002036!3.92e-21!61;UBERON:0003082!3.92e-21!61;UBERON:0002385!1.18e-19!63;UBERON:0001015!1.18e-19!63;UBERON:0000383!1.18e-19!63;UBERON:0000914!1.58e-19!83;UBERON:0002329!1.58e-19!83;UBERON:0003077!1.58e-19!83;UBERON:0003059!1.58e-19!83;UBERON:0007282!1.58e-19!83;UBERON:0009618!1.58e-19!83;UBERON:0007285!1.58e-19!83;UBERON:0005256!3.18e-19!143;UBERON:0000947!2.18e-13!21;UBERON:0010191!2.18e-13!21;UBERON:0002100!3.34e-13!216;UBERON:0000119!1.24e-11!312;UBERON:0000483!3.23e-11!309;UBERON:0000926!4.95e-09!448;UBERON:0004120!4.95e-09!448;UBERON:0006603!4.95e-09!448;UBERON:0000487!1.02e-08!22;UBERON:0000468!2.16e-08!659;UBERON:0000467!2.89e-08!625;UBERON:0000480!4.00e-08!626;UBERON:0006914!4.60e-08!25;UBERON:0003104!5.26e-08!238;UBERON:0009142!5.26e-08!238;UBERON:0001986!5.88e-08!18;UBERON:0004638!5.88e-08!18;UBERON:0004852!5.88e-08!18;UBERON:0004237!6.31e-08!10;UBERON:0004695!6.31e-08!10;UBERON:0002111!6.31e-08!10;UBERON:0004178!6.31e-08!10;UBERON:0004111!8.43e-08!241;UBERON:0000475!2.68e-07!365;UBERON:0003081!3.42e-07!216;UBERON:0000025!4.02e-07!194;UBERON:0000477!4.63e-07!286;UBERON:0003915!6.75e-07!9;UBERON:0004700!6.75e-07!9;UBERON:0001917!6.75e-07!9
}}

Latest revision as of 14:16, 17 September 2013


Full id: C4633_hepatic_spindle_chorionic_bone_Smooth_Fibroblast_basal



Phase1 CAGE Peaks

Hg19::chr7:100781146..100781169,+p@chr7:100781146..100781169
+
Hg19::chr7:100781561..100781583,+p@chr7:100781561..100781583
+
Hg19::chr7:100782236..100782279,+p@chr7:100782236..100782279
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
mesodermal cell3.15e-35121
muscle precursor cell3.36e-2358
myoblast3.36e-2358
multi-potent skeletal muscle stem cell3.36e-2358
vascular associated smooth muscle cell9.57e-2232
muscle cell1.27e-2155
smooth muscle cell4.04e-2143
smooth muscle myoblast4.04e-2143
contractile cell9.79e-2159
embryonic cell3.77e-20250
electrically responsive cell1.00e-1761
electrically active cell1.00e-1761
somatic cell2.44e-17588
non-terminally differentiated cell4.21e-15106
lining cell6.75e-1458
barrier cell6.75e-1458
animal cell8.49e-14679
eukaryotic cell8.49e-14679
endothelial cell of vascular tree3.91e-1324
endothelial cell1.53e-1236
fibroblast1.99e-1276
meso-epithelial cell6.09e-1045
blood vessel endothelial cell2.81e-0918
embryonic blood vessel endothelial progenitor cell2.81e-0918
aortic smooth muscle cell8.55e-0910
cardiocyte1.48e-0816
native cell1.84e-08722
endothelial cell of artery7.77e-089
somatic stem cell8.57e-08433
multi fate stem cell9.32e-08427
skin fibroblast2.62e-0723
stem cell5.81e-07441
Uber Anatomy
Ontology termp-valuen
vasculature2.50e-3578
vascular system2.50e-3578
vessel8.75e-3468
epithelial tube open at both ends2.82e-2959
blood vessel2.82e-2959
blood vasculature2.82e-2959
vascular cord2.82e-2959
epithelial tube8.26e-29117
splanchnic layer of lateral plate mesoderm9.62e-2983
artery1.30e-2842
arterial blood vessel1.30e-2842
arterial system1.30e-2842
cardiovascular system1.37e-28109
circulatory system8.80e-28112
epithelial vesicle2.46e-2478
systemic artery1.45e-2333
systemic arterial system1.45e-2333
unilaminar epithelium1.50e-21148
somite2.06e-2171
presomitic mesoderm2.06e-2171
presumptive segmental plate2.06e-2171
dermomyotome2.06e-2171
trunk paraxial mesoderm2.06e-2171
skeletal muscle tissue3.14e-2162
striated muscle tissue3.14e-2162
myotome3.14e-2162
paraxial mesoderm7.99e-2172
presumptive paraxial mesoderm7.99e-2172
dense mesenchyme tissue2.98e-2073
muscle tissue5.83e-2064
musculature5.83e-2064
musculature of body5.83e-2064
multilaminar epithelium5.98e-2083
trunk mesenchyme1.73e-19122
mesenchyme1.32e-15160
entire embryonic mesenchyme1.32e-15160
aorta5.32e-1421
aortic system5.32e-1421
trunk3.53e-13199
mesoderm6.31e-12315
mesoderm-derived structure6.31e-12315
presumptive mesoderm6.31e-12315
cell layer1.33e-10309
epithelium2.26e-10306
simple squamous epithelium2.26e-1022
tube5.20e-10192
anatomical conduit1.09e-09240
blood vessel endothelium2.81e-0918
endothelium2.81e-0918
cardiovascular system endothelium2.81e-0918
blood vessel smooth muscle8.55e-0910
arterial system smooth muscle8.55e-0910
artery smooth muscle tissue8.55e-0910
aorta smooth muscle tissue8.55e-0910
organism subdivision1.84e-08264
squamous epithelium2.58e-0825
endothelial tube7.77e-089
arterial system endothelium7.77e-089
endothelium of artery7.77e-089
umbilical blood vessel1.78e-079
lateral plate mesoderm1.90e-07203
smooth muscle tissue2.21e-0715
Disease
Ontology termp-valuen
ovarian cancer5.46e-0914


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
MA0048.10.341392
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
MA0073.10.211629
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
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
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
MA0162.10.149099
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.181755
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
JUNB#3726220.40708843988080.003131462199438740.0164560119073756



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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