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{{Coexpression_clusters
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|full_id=C3897_Mesothelial_Multipotent_mesenchymal_Fibroblast_argyrophil_medial_leiomyoma
|id=C3897
|ontology_enrichment_celltype=CL:0000055!2.18e-27!180;CL:0000222!6.24e-21!119;CL:0000680!3.71e-19!57;CL:0000056!3.71e-19!57;CL:0000355!3.71e-19!57;CL:0000183!1.86e-18!59;CL:0000187!4.34e-18!54;CL:0000359!5.82e-18!32;CL:0000192!2.72e-17!42;CL:0000514!2.72e-17!42;CL:0000393!1.87e-16!60;CL:0000211!1.87e-16!60;CL:0000057!2.13e-13!75;CL:0000220!2.75e-08!246;CL:0002321!4.58e-08!248;CL:0002494!3.21e-07!16
|ontology_enrichment_disease=DOID:2394!1.86e-07!14
|ontology_enrichment_uberon=UBERON:0000119!5.76e-26!312;UBERON:0002049!1.10e-25!79;UBERON:0007798!1.10e-25!79;UBERON:0000025!3.07e-25!194;UBERON:0000483!6.71e-25!309;UBERON:0004872!3.68e-24!84;UBERON:0001981!6.61e-23!60;UBERON:0007500!6.61e-23!60;UBERON:0004537!6.61e-23!60;UBERON:0006965!6.61e-23!60;UBERON:0000475!1.13e-22!365;UBERON:0001637!3.20e-22!42;UBERON:0003509!3.20e-22!42;UBERON:0004572!3.20e-22!42;UBERON:0000055!7.21e-22!69;UBERON:0004111!1.30e-21!241;UBERON:0000477!7.64e-21!286;UBERON:0000914!3.89e-19!83;UBERON:0002329!3.89e-19!83;UBERON:0003077!3.89e-19!83;UBERON:0003059!3.89e-19!83;UBERON:0007282!3.89e-19!83;UBERON:0009618!3.89e-19!83;UBERON:0007285!3.89e-19!83;UBERON:0004535!5.78e-19!110;UBERON:0001009!2.00e-18!113;UBERON:0000481!2.12e-18!347;UBERON:0004290!3.02e-18!70;UBERON:0001134!6.77e-18!61;UBERON:0002036!6.77e-18!61;UBERON:0003082!6.77e-18!61;UBERON:0004573!1.13e-17!33;UBERON:0004571!1.13e-17!33;UBERON:0002385!1.52e-17!63;UBERON:0001015!1.52e-17!63;UBERON:0000383!1.52e-17!63;UBERON:0003914!5.68e-17!118;UBERON:0003075!2.60e-16!86;UBERON:0007284!2.60e-16!86;UBERON:0002616!3.31e-16!59;UBERON:0000073!3.59e-16!94;UBERON:0001016!3.59e-16!94;UBERON:0002346!1.01e-15!90;UBERON:0005743!1.93e-15!86;UBERON:0000955!3.26e-15!69;UBERON:0006238!3.26e-15!69;UBERON:0001017!9.34e-15!82;UBERON:0000468!1.22e-14!659;UBERON:0001049!2.91e-14!57;UBERON:0005068!2.91e-14!57;UBERON:0006241!2.91e-14!57;UBERON:0007135!2.91e-14!57;UBERON:0000490!1.10e-13!138;UBERON:0002780!3.50e-13!41;UBERON:0001890!3.50e-13!41;UBERON:0006240!3.50e-13!41;UBERON:0003056!5.50e-13!61;UBERON:0003080!6.96e-13!42;UBERON:0005256!7.24e-13!143;UBERON:0000486!1.11e-12!82;UBERON:0000033!1.24e-12!123;UBERON:0001869!1.57e-12!32;UBERON:0001893!2.68e-12!34;UBERON:0000467!3.53e-12!625;UBERON:0002020!3.66e-12!34;UBERON:0003528!3.66e-12!34;UBERON:0000480!6.07e-12!626;UBERON:0002791!1.11e-11!33;UBERON:0000153!1.58e-11!129;UBERON:0007811!1.58e-11!129;UBERON:0000947!6.91e-11!21;UBERON:0010191!6.91e-11!21;UBERON:0002619!9.06e-11!22;UBERON:0004121!9.18e-11!169;UBERON:0000924!1.35e-10!173;UBERON:0006601!1.35e-10!173;UBERON:0000956!3.64e-10!25;UBERON:0000203!3.64e-10!25;UBERON:0001950!3.75e-10!20;UBERON:0000922!3.20e-09!612;UBERON:0002050!4.98e-09!605;UBERON:0005423!4.98e-09!605;UBERON:0000923!7.13e-09!604;UBERON:0005291!7.13e-09!604;UBERON:0006598!7.13e-09!604;UBERON:0002532!7.13e-09!604;UBERON:0002100!1.54e-08!216;UBERON:0000948!8.19e-08!24;UBERON:0005498!8.19e-08!24;UBERON:0004140!8.19e-08!24;UBERON:0009881!8.19e-08!24;UBERON:0004141!8.19e-08!24;UBERON:0003084!8.19e-08!24;UBERON:0007005!8.19e-08!24;UBERON:0004139!8.19e-08!24;UBERON:0004291!8.19e-08!24;UBERON:0007023!1.38e-07!115;UBERON:0007100!5.58e-07!27
}}

Latest revision as of 12:35, 17 September 2013


Full id: C3897_Mesothelial_Multipotent_mesenchymal_Fibroblast_argyrophil_medial_leiomyoma



Phase1 CAGE Peaks

Hg19::chr1:163038648..163038667,+p3@RGS4
Hg19::chr1:163038669..163038763,+p2@RGS4
Hg19::chr1:163039143..163039159,+p1@RGS4


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>

Uber Anatomy
Ontology termp-valuen
artery1.75e-2142
arterial blood vessel1.75e-2142
arterial system1.75e-2142
tube1.57e-19192
systemic artery1.29e-1833
systemic arterial system1.29e-1833
structure with developmental contribution from neural crest2.49e-17132
neural tube5.28e-1756
neural rod5.28e-1756
future spinal cord5.28e-1756
neural keel5.28e-1756
epithelial tube open at both ends1.34e-1659
blood vessel1.34e-1659
blood vasculature1.34e-1659
vascular cord1.34e-1659
brain1.76e-1668
future brain1.76e-1668
cell layer3.59e-16309
regional part of nervous system3.68e-1653
regional part of brain3.68e-1653
nervous system8.10e-1689
vasculature9.51e-1678
vascular system9.51e-1678
splanchnic layer of lateral plate mesoderm9.88e-1683
epithelium1.19e-15306
central nervous system2.11e-1581
neural plate2.18e-1582
presumptive neural plate2.18e-1582
skeletal muscle tissue3.76e-1562
striated muscle tissue3.76e-1562
myotome3.76e-1562
muscle tissue5.55e-1564
musculature5.55e-1564
musculature of body5.55e-1564
paraxial mesoderm8.49e-1572
presumptive paraxial mesoderm8.49e-1572
anatomical conduit1.26e-14240
dense mesenchyme tissue2.34e-1473
somite3.55e-1471
presomitic mesoderm3.55e-1471
presumptive segmental plate3.55e-1471
dermomyotome3.55e-1471
trunk paraxial mesoderm3.55e-1471
regional part of forebrain5.15e-1441
forebrain5.15e-1441
anterior neural tube5.15e-1441
future forebrain5.15e-1441
epithelial vesicle6.10e-1478
vessel8.24e-1468
neurectoderm8.33e-1486
cerebral hemisphere4.80e-1332
anatomical cluster5.90e-13373
regional part of cerebral cortex9.67e-1322
telencephalon1.32e-1234
brain grey matter1.63e-1234
gray matter1.63e-1234
cardiovascular system4.70e-12109
multi-tissue structure8.19e-12342
regional part of telencephalon1.43e-1132
neocortex1.51e-1120
pre-chordal neural plate2.77e-1161
circulatory system3.29e-11112
cerebral cortex2.40e-1025
pallium2.40e-1025
ecto-epithelium6.14e-10104
multilaminar epithelium8.05e-1083
aorta8.94e-1021
aortic system8.94e-1021
epithelial tube2.49e-09117
trunk mesenchyme1.62e-08122
unilaminar epithelium3.77e-08148
adult organism6.64e-08114
anatomical system7.08e-08624
multi-cellular organism8.30e-08656
anatomical group9.01e-08625
ectoderm-derived structure1.53e-07171
ectoderm1.53e-07171
presumptive ectoderm1.53e-07171
mesenchyme1.81e-07160
entire embryonic mesenchyme1.81e-07160
embryonic structure3.67e-07564
gyrus7.92e-076
blood vessel smooth muscle7.96e-0710
arterial system smooth muscle7.96e-0710
artery smooth muscle tissue7.96e-0710
aorta smooth muscle tissue7.96e-0710

Disease
Ontology termp-valuen


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
MA0038.12.16573
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
MA0057.10.333427
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
MA0090.11.77664
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
MA0131.12.4174
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
MA0148.11.98824
MA0149.10.884158
MA0062.21.141
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
MA0163.10.122425
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

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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