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Coexpression cluster:C404: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.

Latest revision as of 11:22, 17 September 2013


Full id: C404_Fibroblast_mesenchymal_Synoviocyte_Smooth_basal_mesodermal_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr3:100468772..100468781,-p@chr3:100468772..100468781
-
Hg19::chr3:100494130..100494141,-p@chr3:100494130..100494141
-
Hg19::chr3:100494155..100494167,-p@chr3:100494155..100494167
-
Hg19::chr3:100497204..100497224,-p5@ABI3BP
Hg19::chr3:100499042..100499055,-p@chr3:100499042..100499055
-
Hg19::chr3:100513811..100513820,-p@chr3:100513811..100513820
-
Hg19::chr3:100513821..100513835,-p@chr3:100513821..100513835
-
Hg19::chr3:100527043..100527076,-p8@ABI3BP
Hg19::chr3:100551141..100551152,-p14@ABI3BP
Hg19::chr3:100551992..100552008,-p@chr3:100551992..100552008
-
Hg19::chr3:100553556..100553602,-p@chr3:100553556..100553602
-
Hg19::chr3:100554469..100554494,-p@chr3:100554469..100554494
-
Hg19::chr3:100557118..100557130,-p@chr3:100557118..100557130
-
Hg19::chr3:100557278..100557294,-p@chr3:100557278..100557294
-
Hg19::chr3:100557300..100557309,-p@chr3:100557300..100557309
-
Hg19::chr3:100558953..100558982,-p6@ABI3BP
Hg19::chr3:100565249..100565269,-p7@ABI3BP
Hg19::chr3:100566492..100566523,-p3@ABI3BP
Hg19::chr3:100567644..100567686,+p@chr3:100567644..100567686
+
Hg19::chr3:100567665..100567691,-p@chr3:100567665..100567691
-
Hg19::chr3:100567697..100567718,-p@chr3:100567697..100567718
-
Hg19::chr3:100568922..100568933,-p@chr3:100568922..100568933
-
Hg19::chr3:100568942..100568975,-p@chr3:100568942..100568975
-
Hg19::chr3:100617652..100617669,-p@chr3:100617652..100617669
-
Hg19::chr3:100712253..100712274,-p1@ABI3BP
Hg19::chr3:100712292..100712338,-p2@ABI3BP


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><br>disease_data<br>

Cell Type
Ontology termp-valuen
fibroblast1.92e-1076
skin fibroblast1.53e-0723
Disease
Ontology termp-valuen
ovarian cancer2.29e-1014


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)
MA0003.19.29921e-06
MA0004.10.122847
MA0006.10.0479067
MA0007.10.112494
MA0009.10.46676
MA0014.11.75925e-06
MA0017.10.0632603
MA0019.10.21677
MA0024.10.378349
MA0025.10.584598
MA0027.12.02165
MA0028.10.0539336
MA0029.11.80508
MA0030.10.384823
MA0031.10.884716
MA0038.10.186009
MA0040.14.80594
MA0041.11.3364
MA0042.10.369454
MA0043.10.467032
MA0046.10.457379
MA0048.10.00223881
MA0050.10.115873
MA0051.10.183217
MA0052.12.74397
MA0055.10.00954983
MA0056.10
MA0057.10.00195484
MA0058.10.257973
MA0059.10.927345
MA0060.10.0152409
MA0061.10.0105788
MA0063.10
MA0066.10.186292
MA0067.10.753856
MA0068.10.0935703
MA0069.10.454067
MA0070.10.44448
MA0071.10.160989
MA0072.10.44064
MA0073.15.5876e-06
MA0074.10.182721
MA0076.10.0815705
MA0077.10.434073
MA0078.12.80624
MA0081.10.256536
MA0083.10.473254
MA0084.10.931415
MA0087.10.438554
MA0088.10.000411213
MA0089.10
MA0090.10.088522
MA0091.10.124326
MA0092.10.338625
MA0093.10.184116
MA0095.10
MA0098.10
MA0100.10.195288
MA0101.10.187837
MA0103.10.170494
MA0105.10.00141689
MA0106.10.214057
MA0107.10.112226
MA0108.20.879282
MA0109.10
MA0111.10.0952636
MA0113.10.640535
MA0114.10.0253615
MA0115.10.682809
MA0116.10.0276251
MA0117.10.499451
MA0119.10.0665855
MA0122.10.522217
MA0124.10.644657
MA0125.10.568516
MA0130.10
MA0131.10.26595
MA0132.10
MA0133.10
MA0135.12.13819
MA0136.10.190708
MA0139.10.00880521
MA0140.10.15932
MA0141.10.0728657
MA0142.11.50055
MA0143.11.19813
MA0144.10.0218306
MA0145.10.0486363
MA0146.11.1744e-05
MA0147.10.118663
MA0148.11.35961
MA0149.10.153304
MA0062.20.00978787
MA0035.20.158878
MA0039.20.000750054
MA0138.20.253407
MA0002.21.17706
MA0137.20.0564642
MA0104.20.0703325
MA0047.21.75719
MA0112.20.00379263
MA0065.20.109893
MA0150.10.605252
MA0151.10
MA0152.10.951379
MA0153.10.553438
MA0154.10.0812436
MA0155.10.0823333
MA0156.10.0573678
MA0157.10.780848
MA0158.10
MA0159.10.0287576
MA0160.10.146326
MA0161.10
MA0162.10.00803817
MA0163.12.97369e-05
MA0164.10.23445
MA0080.20.0490502
MA0018.20.215022
MA0099.20.16368
MA0079.27.42532e-15
MA0102.20.967149
MA0258.10.0196389
MA0259.10.126633
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

No analysis results for this cluster

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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