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Coexpression cluster:C758: Difference between revisions

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{{Coexpression_clusters
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|full_id=C758_Chondrocyte_Amniotic_Smooth_Fibroblast_Pericytes_Endothelial_Urothelial
|id=C758
}}

Latest revision as of 11:30, 17 September 2013


Full id: C758_Chondrocyte_Amniotic_Smooth_Fibroblast_Pericytes_Endothelial_Urothelial



Phase1 CAGE Peaks

Hg19::chr14:75078662..75078675,-p6@LTBP2
Hg19::chr14:75078682..75078706,-p5@LTBP2
Hg19::chr14:75078725..75078734,-p15@LTBP2
Hg19::chr14:75079026..75079049,-p8@LTBP2
Hg19::chr14:75079066..75079077,-p13@LTBP2
Hg19::chr14:75079174..75079185,-p22@LTBP2
Hg19::chr14:75079186..75079202,-p11@LTBP2
Hg19::chr14:75079205..75079223,-p7@LTBP2
Hg19::chr14:75079261..75079277,-p9@LTBP2
Hg19::chr14:75079282..75079293,-p21@LTBP2
Hg19::chr14:75079294..75079329,-p2@LTBP2


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 cell4.38e-20121
somatic cell4.59e-20588
fibroblast9.21e-1976
embryonic cell5.55e-16250
endothelial cell6.46e-1336
contractile cell8.93e-1359
vascular associated smooth muscle cell1.47e-1232
muscle precursor cell5.80e-1258
myoblast5.80e-1258
multi-potent skeletal muscle stem cell5.80e-1258
smooth muscle cell1.15e-1143
smooth muscle myoblast1.15e-1143
endothelial cell of vascular tree1.26e-1124
animal cell2.21e-11679
eukaryotic cell2.21e-11679
muscle cell9.62e-1155
meso-epithelial cell1.28e-1045
blood vessel endothelial cell6.05e-1018
embryonic blood vessel endothelial progenitor cell6.05e-1018
lining cell5.17e-0958
barrier cell5.17e-0958
electrically responsive cell3.81e-0861
electrically active cell3.81e-0861
preadipocyte6.86e-0812
endothelial cell of artery1.57e-079
non-terminally differentiated cell4.94e-07106
skin fibroblast5.12e-0723
Uber Anatomy
Ontology termp-valuen
vasculature1.76e-3078
vascular system1.76e-3078
vessel8.52e-2668
epithelial tube open at both ends2.64e-2459
blood vessel2.64e-2459
blood vasculature2.64e-2459
vascular cord2.64e-2459
splanchnic layer of lateral plate mesoderm1.15e-2283
circulatory system1.70e-21112
cardiovascular system2.65e-21109
artery1.04e-1942
arterial blood vessel1.04e-1942
arterial system1.04e-1942
epithelial tube5.10e-18117
systemic artery2.20e-1533
systemic arterial system2.20e-1533
multilaminar epithelium1.43e-1483
epithelial vesicle3.07e-1478
organism subdivision6.87e-14264
unilaminar epithelium3.00e-13148
cell layer8.81e-13309
epithelium3.12e-12306
somite5.70e-1271
presomitic mesoderm5.70e-1271
presumptive segmental plate5.70e-1271
dermomyotome5.70e-1271
trunk paraxial mesoderm5.70e-1271
dense mesenchyme tissue9.57e-1273
paraxial mesoderm1.60e-1172
presumptive paraxial mesoderm1.60e-1172
surface structure1.71e-1199
aorta4.72e-1121
aortic system4.72e-1121
skeletal muscle tissue1.29e-1062
striated muscle tissue1.29e-1062
myotome1.29e-1062
muscle tissue3.71e-1064
musculature3.71e-1064
musculature of body3.71e-1064
blood vessel endothelium6.05e-1018
endothelium6.05e-1018
cardiovascular system endothelium6.05e-1018
anatomical system7.02e-10624
multi-cellular organism7.06e-10656
anatomical group1.00e-09625
simple squamous epithelium1.04e-0822
trunk mesenchyme1.23e-08122
squamous epithelium1.36e-0825
head1.47e-0856
mesenchyme4.49e-08160
entire embryonic mesenchyme4.49e-08160
trunk4.96e-08199
mesoderm6.69e-08315
mesoderm-derived structure6.69e-08315
presumptive mesoderm6.69e-08315
anatomical conduit8.93e-08240
subdivision of head9.80e-0849
anterior region of body1.37e-0762
craniocervical region1.37e-0762
endothelial tube1.57e-079
arterial system endothelium1.57e-079
endothelium of artery1.57e-079
integument6.50e-0746
integumental system6.50e-0746
organ component layer9.77e-0766
Disease
Ontology termp-valuen
ovarian cancer2.58e-0814


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)
MA0003.114.5901
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.15.54861
MA0017.10.24363
MA0019.12.11515
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.637069
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.0494179
MA0050.10.897608
MA0051.10.439895
MA0052.10.716602
MA0055.10.0496191
MA0056.10
MA0057.10.703296
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.11.64924
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.88546
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.11.10483
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.203171
MA0105.11.0054
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.12.26737
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.16.71888
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.11.24556
MA0144.10.142196
MA0145.14.44618
MA0146.13.16699
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.23.21617
MA0138.23.34637
MA0002.20.358551
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.22.53749
MA0065.20.28513
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.11.41082
MA0155.14.19662
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.11.37951
MA0163.11.7806
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.25.33306
MA0102.21.32663
MA0258.10.420151
MA0259.10.168926
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
ATF3#467816.33685420073362.24789214598075e-091.92117518685829e-07
CCNT2#90584.608146601427374.03688108190029e-050.000739273756466044
CTCF#1066483.898368271327290.0001406611760594710.00183425053895307
CTCFL#140690712.56593822843822.34732188916212e-071.23377931948769e-05
EGR1#195883.627766614407370.0002392247441646590.00260471153626072
POLR2A#5430112.147453176558070.0002231983422387430.00248540480489093
RAD21#588587.530933742150069.5260786570561e-074.06743306976403e-05
SMC3#912679.574048174048171.48666828013051e-065.73360961996125e-05
TAF1#687282.431306389632940.004204244189139110.0200185583509392
TAF7#687988.31495956721744.42802301552428e-072.11168171560886e-05
YY1#752883.571760545348260.0002682005866906720.00286494845795102
ZBTB7A#5134185.346843133000651.31319566009782e-050.000320816003613932
ZNF143#770289.81881931071121.21663595201433e-077.0007846937975e-06



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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