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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:28, 17 September 2013


Full id: C679_Mesenchymal_Smooth_Cardiac_Hair_Fibroblast_Mesothelial_Skeletal



Phase1 CAGE Peaks

Hg19::chr10:91939935..91939941,+p@chr10:91939935..91939941
+
Hg19::chr20:35695476..35695506,-p@chr20:35695476..35695506
-
Hg19::chr20:35695582..35695602,-p@chr20:35695582..35695602
-
Hg19::chr2:55831402..55831405,-p19@SMEK2
Hg19::chr5:148586717..148586723,+p@chr5:148586717..148586723
+
Hg19::chr5:148600871..148600881,-p@chr5:148600871..148600881
-
Hg19::chr7:136759435..136759447,+p@chr7:136759435..136759447
+
Hg19::chr7:136759451..136759469,+p@chr7:136759451..136759469
+
Hg19::chr9:118701819..118701835,+p@chr9:118701819..118701835
+
Hg19::chr9:118701850..118701882,+p@chr9:118701850..118701882
+
Hg19::chr9:118701892..118701903,+p@chr9:118701892..118701903
+
Hg19::chr9:73094859..73094866,-p@chr9:73094859..73094866
-


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
smooth muscle tissue1.64e-1415
colon5.65e-149
large intestine1.52e-1111
skeletal muscle tissue5.76e-1062
striated muscle tissue5.76e-1062
myotome5.76e-1062
trunk mesenchyme8.59e-10122
muscle tissue1.23e-0964
musculature1.23e-0964
musculature of body1.23e-0964
unilaminar epithelium1.32e-09148
somite1.25e-0871
presomitic mesoderm1.25e-0871
presumptive segmental plate1.25e-0871
dermomyotome1.25e-0871
trunk paraxial mesoderm1.25e-0871
paraxial mesoderm1.68e-0872
presumptive paraxial mesoderm1.68e-0872
dense mesenchyme tissue2.24e-0873
mixed ectoderm/mesoderm/endoderm-derived structure6.58e-082
developing epithelial placode6.58e-082
respiratory system arterial blood vessel6.58e-082
respiratory system blood vessel6.58e-082
respiratory system artery6.58e-082
head blood vessel6.58e-082
pulmonary artery6.58e-082
pulmonary vascular system6.58e-082
pharyngeal vasculature6.58e-082
truncus arteriosus6.58e-082
aortic sac6.58e-082
pharyngeal arch artery6.58e-082
epithelial vesicle8.40e-0878
multilaminar epithelium2.70e-0783
intestine2.92e-0717
mesenchyme3.53e-07160
entire embryonic mesenchyme3.53e-07160
trunk8.98e-07199


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)
MA0003.10.000491243
MA0004.10.32225
MA0006.10.188769
MA0007.10.305951
MA0009.10.756202
MA0014.10.00141144
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.11.6149
MA0030.10.662482
MA0031.10.600685
MA0038.11.06455
MA0040.11.62663
MA0041.10.338572
MA0042.10.835565
MA0043.10.756508
MA0046.10.745626
MA0048.10.155795
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.10.226943
MA0056.10
MA0057.10.0373953
MA0058.10.240796
MA0059.10.239727
MA0060.10.103131
MA0061.10.0856761
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.0633085
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.11.33944e-06
MA0074.10.40963
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.67392
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.397386
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.793019
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.10.181541
MA0105.10.130274
MA0106.10.452066
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.761158
MA0113.10.467266
MA0114.10.134281
MA0115.10.992167
MA0116.10.140463
MA0117.10.792789
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.0781324
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.10.0212759
MA0146.10.00710499
MA0147.10.143012
MA0148.10.910784
MA0149.10.367947
MA0062.20.0823902
MA0035.20.376007
MA0039.27.40554e-05
MA0138.20.503176
MA0002.20.0954816
MA0137.21.76253
MA0104.20.102626
MA0047.20.440861
MA0112.20.0192555
MA0065.20.0221687
MA0150.11.33192
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.30107
MA0155.10.0174879
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.441451
MA0160.10.357736
MA0161.10
MA0162.10.00310762
MA0163.10.0369192
MA0164.10.478818
MA0080.20.191221
MA0018.20.453345
MA0099.20.996203
MA0079.22.21767e-08
MA0102.21.28978
MA0258.10.375
MA0259.10.149181
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
JUN#372544.170943064112110.01196618809532740.0434660795244817



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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