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Coexpression cluster:C2697: Difference between revisions

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}}
}}

Revision as of 20:50, 22 January 2013


Full id: C2697_Chondrocyte_mesenchymal_Fibroblast_Smooth_Anulus_hepatic_aorta



Phase1 CAGE Peaks

Hg19::chr2:33359579..33359590,+p4@LTBP1
Hg19::chr2:33359634..33359645,+p5@LTBP1
Hg19::chr2:33359646..33359686,+p1@LTBP1
Hg19::chr2:33359687..33359717,+p2@LTBP1


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
dense mesenchyme tissue4.11e-2873
somite1.42e-2771
presomitic mesoderm1.42e-2771
presumptive segmental plate1.42e-2771
dermomyotome1.42e-2771
trunk paraxial mesoderm1.42e-2771
paraxial mesoderm2.05e-2772
presumptive paraxial mesoderm2.05e-2772
epithelial vesicle1.43e-2378
muscle tissue5.38e-2364
musculature5.38e-2364
musculature of body5.38e-2364
skeletal muscle tissue8.33e-2362
striated muscle tissue8.33e-2362
myotome8.33e-2362
multilaminar epithelium1.10e-2183
circulatory system4.36e-20112
multi-tissue structure5.71e-20342
cardiovascular system1.01e-19109
mesenchyme8.39e-19160
entire embryonic mesenchyme8.39e-19160
cell layer3.77e-18309
epithelium3.79e-17306
trunk mesenchyme7.21e-17122
multi-cellular organism7.53e-17656
splanchnic layer of lateral plate mesoderm7.86e-1783
vasculature2.85e-1678
vascular system2.85e-1678
artery2.94e-1642
arterial blood vessel2.94e-1642
arterial system2.94e-1642
unilaminar epithelium9.72e-16148
anatomical system3.40e-15624
anatomical group6.20e-15625
systemic artery1.71e-1433
systemic arterial system1.71e-1433
surface structure3.46e-1499
epithelial tube open at both ends1.38e-1359
blood vessel1.38e-1359
blood vasculature1.38e-1359
vascular cord1.38e-1359
organism subdivision1.62e-13264
vessel3.81e-1368
anatomical cluster5.00e-13373
tissue2.51e-12773
structure with developmental contribution from neural crest4.82e-12132
anatomical conduit2.93e-11240
epithelial tube8.13e-11117
embryonic structure1.99e-10564
integument3.81e-1046
integumental system3.81e-1046
germ layer4.62e-10560
germ layer / neural crest4.62e-10560
embryonic tissue4.62e-10560
presumptive structure4.62e-10560
germ layer / neural crest derived structure4.62e-10560
epiblast (generic)4.62e-10560
developing anatomical structure7.02e-10581
primary circulatory organ4.33e-0927
skin of body4.84e-0941
heart6.23e-0924
primitive heart tube6.23e-0924
primary heart field6.23e-0924
anterior lateral plate mesoderm6.23e-0924
heart tube6.23e-0924
heart primordium6.23e-0924
cardiac mesoderm6.23e-0924
cardiogenic plate6.23e-0924
heart rudiment6.23e-0924
embryo1.03e-08592
tube1.95e-08192
aorta1.98e-0821
aortic system1.98e-0821
trunk5.38e-08199
mesoderm1.73e-07315
mesoderm-derived structure1.73e-07315
presumptive mesoderm1.73e-07315
adult organism2.65e-07114
subdivision of skeletal system3.43e-0716
smooth muscle tissue9.32e-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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.11.70187
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.12.93423
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.21.75253
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.12.08227
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
CTCF#1066445.360256373075030.001211145381643620.00818657773046911
EP300#203346.77394172622320.0004748459821442640.00434678232353097
NR3C1#2908414.9730233311731.98868032687801e-050.000443699604056425
RAD21#5885410.35503389545638.6948481184721e-050.00129688837852772
STAT3#6774410.51946499715428.16377768286615e-050.00123317439603827



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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