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{{Coexpression_clusters
{
|full_id=C4206_Smooth_Keratinocyte_mesenchymal_Fibroblast_Bronchial_mucinous_Tracheal

Latest revision as of 12:41, 17 September 2013


Full id: C4206_Smooth_Keratinocyte_mesenchymal_Fibroblast_Bronchial_mucinous_Tracheal



Phase1 CAGE Peaks

Hg19::chr2:239335353..239335391,+p4@ASB1
Hg19::chr2:239335396..239335448,+p3@ASB1
Hg19::chr2:239335449..239335460,+p7@ASB1


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>

Cell Type
Ontology termp-valuen
animal cell1.55e-20679
eukaryotic cell1.55e-20679
somatic cell5.08e-18588
mesodermal cell3.23e-16121
native cell6.51e-16722
muscle precursor cell2.46e-1358
myoblast2.46e-1358
multi-potent skeletal muscle stem cell2.46e-1358
embryonic cell6.45e-13250
vascular associated smooth muscle cell6.54e-1332
muscle cell1.51e-1255
smooth muscle cell2.03e-1143
smooth muscle myoblast2.03e-1143
fibroblast2.06e-1176
contractile cell7.48e-1159
somatic stem cell7.79e-11433
multi fate stem cell7.66e-10427
stem cell1.86e-09441
electrically responsive cell1.93e-0961
electrically active cell1.93e-0961
cardiocyte1.94e-0716
defensive cell2.38e-0748
phagocyte2.38e-0748
aortic smooth muscle cell4.83e-0710
respiratory epithelial cell6.26e-0713
classical monocyte9.89e-0742
CD14-positive, CD16-negative classical monocyte9.89e-0742
Uber Anatomy
Ontology termp-valuen
artery7.98e-2242
arterial blood vessel7.98e-2242
arterial system7.98e-2242
systemic artery2.23e-1833
systemic arterial system2.23e-1833
epithelial tube open at both ends1.88e-1759
blood vessel1.88e-1759
blood vasculature1.88e-1759
vascular cord1.88e-1759
splanchnic layer of lateral plate mesoderm1.01e-1683
vessel1.40e-1668
vasculature2.06e-1678
vascular system2.06e-1678
epithelial tube3.41e-15117
unilaminar epithelium5.48e-14148
mesoderm3.70e-13315
mesoderm-derived structure3.70e-13315
presumptive mesoderm3.70e-13315
epithelial vesicle1.50e-1278
somite1.71e-1271
presomitic mesoderm1.71e-1271
presumptive segmental plate1.71e-1271
dermomyotome1.71e-1271
trunk paraxial mesoderm1.71e-1271
cardiovascular system2.14e-12109
paraxial mesoderm4.30e-1272
presumptive paraxial mesoderm4.30e-1272
dense mesenchyme tissue6.22e-1273
lateral plate mesoderm9.18e-12203
anatomical system9.35e-12624
musculoskeletal system1.31e-11167
anatomical group1.37e-11625
skeletal muscle tissue1.50e-1162
striated muscle tissue1.50e-1162
myotome1.50e-1162
circulatory system1.82e-11112
multilaminar epithelium2.32e-1183
aorta3.20e-1121
aortic system3.20e-1121
trunk mesenchyme6.11e-11122
muscle tissue1.40e-1064
musculature1.40e-1064
musculature of body1.40e-1064
multi-cellular organism4.85e-10656
germ layer5.50e-10560
germ layer / neural crest5.50e-10560
embryonic tissue5.50e-10560
presumptive structure5.50e-10560
germ layer / neural crest derived structure5.50e-10560
epiblast (generic)5.50e-10560
embryonic structure9.80e-10564
trunk4.94e-09199
epithelium2.03e-08306
cell layer6.29e-08309
developing anatomical structure8.61e-08581
organism subdivision1.22e-07264
blood vessel smooth muscle4.83e-0710
arterial system smooth muscle4.83e-0710
artery smooth muscle tissue4.83e-0710
aorta smooth muscle tissue4.83e-0710
embryo7.47e-07592


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)
MA0003.13.22681
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0048.10.904546
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
MA0061.11.15625
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
MA0083.12.96495
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.11.84783
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.12.63873
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.13.44314
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.13.00132
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.25.35871
MA0137.21.60005
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
MA0162.12.05956
MA0163.11.2663
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
E2F1#186934.907389214879320.008460985347239390.0326301410095763
EGR1#195834.988179094810140.008056488137383440.0321456185130922
ELF1#199734.258097958807540.01295179875054610.0463529884760566
ELK4#2005316.2356816584680.0002336043955745990.00256033261301454
ETS1#211339.728760922202340.001085840092584840.00763715088083155
GABPB1#255337.067683836182170.002832212825417420.0154461344790481
NFKB1#479035.488063424193840.006049381815655430.0270169505001171
PAX5#507936.669565531177830.003370290999677260.0173283031415987
REST#597839.650028716128020.001112636247114590.00769349953736763
RFX5#5993312.04791082719510.0005717246050312580.00485528915472919
TFAP2A#7020316.5186343730450.0002218033880766340.00248790935961074
TFAP2C#7022310.80922860986020.0007916746575753130.00617165854762321



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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