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{{Coexpression_clusters
{
|full_id=C2814_Smooth_mesenchymal_alveolar_Preadipocyte_pancreas_leiomyoma_Mast

Latest revision as of 12:13, 17 September 2013


Full id: C2814_Smooth_mesenchymal_alveolar_Preadipocyte_pancreas_leiomyoma_Mast



Phase1 CAGE Peaks

Hg19::chr5:150157847..150157859,+p6@C5orf62
Hg19::chr5:150157860..150157883,+p4@C5orf62
Hg19::chr5:150157886..150157917,+p3@C5orf62
Hg19::chr5:150157924..150157963,+p2@C5orf62


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
artery3.23e-1542
arterial blood vessel3.23e-1542
arterial system3.23e-1542
tube2.53e-14192
muscle tissue8.39e-1464
musculature8.39e-1464
musculature of body8.39e-1464
skeletal muscle tissue1.16e-1362
striated muscle tissue1.16e-1362
myotome1.16e-1362
somite5.01e-1271
presomitic mesoderm5.01e-1271
presumptive segmental plate5.01e-1271
dermomyotome5.01e-1271
trunk paraxial mesoderm5.01e-1271
systemic artery5.77e-1233
systemic arterial system5.77e-1233
paraxial mesoderm1.07e-1172
presumptive paraxial mesoderm1.07e-1172
epithelial vesicle1.61e-1178
dense mesenchyme tissue2.22e-1173
epithelium3.93e-11306
cell layer9.17e-11309
anatomical conduit4.74e-10240
epithelial tube open at both ends4.85e-1059
blood vessel4.85e-1059
blood vasculature4.85e-1059
vascular cord4.85e-1059
splanchnic layer of lateral plate mesoderm7.42e-1083
multilaminar epithelium2.36e-0983
epithelial tube3.60e-09117
adult organism3.00e-08114
neural tube7.72e-0856
neural rod7.72e-0856
future spinal cord7.72e-0856
neural keel7.72e-0856
circulatory system7.84e-08112
multi-tissue structure9.92e-08342
vasculature1.21e-0778
vascular system1.21e-0778
trunk mesenchyme1.29e-07122
brain grey matter1.58e-0734
gray matter1.58e-0734
vessel1.58e-0768
structure with developmental contribution from neural crest1.77e-07132
telencephalon2.37e-0734
thoracic segment blood vessel2.48e-075
subclavian artery2.48e-075
primary circulatory organ2.56e-0727
regional part of nervous system2.88e-0753
regional part of brain2.88e-0753
neural plate3.10e-0782
presumptive neural plate3.10e-0782
neural nucleus6.89e-079
nucleus of brain6.89e-079
cardiovascular system8.27e-07109


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
MA0006.11.31813
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
MA0042.12.80052
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
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
MA0078.12.13662
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.12.66951
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
MA0117.11.24497
MA0119.12.44319
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
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.11.75269
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.21.99204
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.10.90014
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
GATA2#2624412.7449317335543.78864877853583e-050.000724030539398909



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.