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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.996064937064487,0

Latest revision as of 11:27, 17 September 2013


Full id: C628_Adipocyte_Preadipocyte_Fibroblast_tenocyte_Smooth_Placental_chorionic



Phase1 CAGE Peaks

Hg19::chr12:8798930..8798945,-p@chr12:8798930..8798945
-
Hg19::chr12:8798958..8798980,-p@chr12:8798958..8798980
-
Hg19::chr12:8799724..8799753,-p9@MFAP5
Hg19::chr12:8800547..8800576,-p8@MFAP5
Hg19::chr12:8800599..8800615,-p10@MFAP5
Hg19::chr12:8800619..8800651,-p6@MFAP5
Hg19::chr12:8800745..8800781,-p@chr12:8800745..8800781
-
Hg19::chr12:8803128..8803164,-p7@MFAP5
Hg19::chr12:8815259..8815298,-p2@MFAP5
Hg19::chr12:8815299..8815331,-p3@MFAP5
Hg19::chr12:8815363..8815398,-p4@MFAP5
Hg19::chr12:8815404..8815438,-p1@MFAP5
Hg19::chr12:8815477..8815490,-p5@MFAP5
Hg19::chr3:112321809..112321819,-p@chr3:112321809..112321819
-


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
fat cell1.58e-1115
preadipocyte3.30e-1112
fibroblast3.65e-1076
vascular associated smooth muscle cell2.23e-0932
Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm9.70e-1283
systemic artery1.34e-1133
systemic arterial system1.34e-1133
artery7.03e-1142
arterial blood vessel7.03e-1142
arterial system7.03e-1142
extraembryonic membrane7.33e-0914
membranous layer7.33e-0914
omentum8.54e-086
peritoneum8.54e-086
abdominal cavity8.54e-086
visceral peritoneum8.54e-086
muscle tissue1.38e-0764
musculature1.38e-0764
musculature of body1.38e-0764
chorion1.80e-077
epithelial tube open at both ends1.82e-0759
blood vessel1.82e-0759
blood vasculature1.82e-0759
vascular cord1.82e-0759
adipose tissue2.96e-0714
skeletal muscle tissue4.47e-0762
striated muscle tissue4.47e-0762
myotome4.47e-0762
primary circulatory organ6.25e-0727
larynx6.69e-079


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)
MA0003.11.06747e-05
MA0004.10.275994
MA0006.10.152601
MA0007.10.260673
MA0009.10.695988
MA0014.10.000542531
MA0017.10.534321
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.0262025
MA0050.10.265714
MA0051.10.359609
MA0052.10.623986
MA0055.10.00349085
MA0056.10
MA0057.10.10396
MA0058.10.200063
MA0059.10.199079
MA0060.10.0773489
MA0061.10.0626878
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.0444239
MA0069.10.681911
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.11.61602e-07
MA0074.10.358953
MA0076.10.212295
MA0077.10.65962
MA0078.10.447828
MA0081.11.09529
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.14098
MA0089.10
MA0090.11.85461
MA0091.10.762163
MA0092.10.247341
MA0093.10.154754
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.146091
MA0105.10.0203556
MA0106.10.399649
MA0107.10.708233
MA0108.21.33623
MA0109.10
MA0111.11.91175
MA0113.10.414278
MA0114.10.104181
MA0115.10.929032
MA0116.10.10959
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.0564547
MA0140.10.327488
MA0141.10.197753
MA0142.10.514195
MA0143.10.414436
MA0144.13.54218
MA0145.10.0126924
MA0146.10.000361686
MA0147.10.111828
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.20.872194
MA0039.20.00108873
MA0138.20.44894
MA0002.20.0708857
MA0137.23.74944
MA0104.20.0769208
MA0047.20.388882
MA0112.20.0113102
MA0065.20.0133095
MA0150.10.218956
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.0872435
MA0155.10.0505475
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.112236
MA0160.10.30953
MA0161.10
MA0162.10.00136062
MA0163.10.000620686
MA0164.10.425415
MA0080.20.915505
MA0018.20.400879
MA0099.20.333432
MA0079.26.46027e-09
MA0102.21.22472
MA0258.10.089643
MA0259.10.117259
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
GTF2F1#296254.54987888455630.003260749591375690.0168873066832136
STAT3#677453.756951784697940.007450706951958610.0307360423176366



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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