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Coexpression cluster:C409: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:22, 17 September 2013


Full id: C409_adipose_mature_breast_lung_skeletal_Melanocyte_left



Phase1 CAGE Peaks

Hg19::chr10:45472158..45472178,-p@chr10:45472158..45472178
-
Hg19::chr10:45472831..45472842,-p@chr10:45472831..45472842
-
Hg19::chr10:45472893..45472939,-p@chr10:45472893..45472939
-
Hg19::chr10:45472995..45473006,-p3@C10orf10
Hg19::chr10:45473374..45473404,-p2@C10orf10
Hg19::chr12:109554288..109554295,+p24@ACACB
Hg19::chr12:12938586..12938600,+p1@APOLD1
Hg19::chr12:76646060..76646067,+p@chr12:76646060..76646067
+
Hg19::chr12:798987..798990,+p@chr12:798987..798990
+
Hg19::chr13:40951436..40951448,-p@chr13:40951436..40951448
-
Hg19::chr17:41924511..41924520,+p2@CD300LG
Hg19::chr17:41924536..41924550,+p1@CD300LG
Hg19::chr17:41926073..41926086,+p@chr17:41926073..41926086
+
Hg19::chr17:62038824..62038843,-p@chr17:62038824..62038843
-
Hg19::chr1:101616154..101616184,+p@chr1:101616154..101616184
+
Hg19::chr3:12189970..12189984,+p4@SYN2
Hg19::chr3:153271174..153271192,-p@chr3:153271174..153271192
-
Hg19::chr3:179457862..179457876,+p@chr3:179457862..179457876
+
Hg19::chr4:190708714..190708723,-p@chr4:190708714..190708723
-
Hg19::chr5:157942095..157942109,-p@chr5:157942095..157942109
-
Hg19::chr5:180257481..180257485,+p3@ENST00000501855
Hg19::chr5:180467219..180467244,+p3@BTNL9
Hg19::chr5:180467259..180467278,+p1@BTNL9
Hg19::chr5:180467283..180467299,+p4@BTNL9
Hg19::chr7:80154162..80154173,+p@chr7:80154162..80154173
+


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

GO IDGO nameFDR corrected p-value
GO:0003989acetyl-CoA carboxylase activity0.0286075869072858
GO:0004075biotin carboxylase activity0.0286075869072858
GO:0016421CoA carboxylase activity0.0333656946030637
GO:0016885ligase activity, forming carbon-carbon bonds0.0333656946030637



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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism9.89e-44114
muscle structure2.22e-082
muscle organ2.22e-082
open tracheal system trachea3.66e-082
compound organ4.06e-0868
throat1.08e-072
primary circulatory organ3.30e-0727
Disease
Ontology termp-valuen
heart disease7.65e-082


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)
MA0003.10.00823048
MA0004.11.31939
MA0006.10.431998
MA0007.10.76566
MA0009.10.480543
MA0014.10.00345799
MA0017.11.33864
MA0019.10.227177
MA0024.10.391254
MA0025.10.599238
MA0027.12.03861
MA0028.10.213776
MA0029.10.407394
MA0030.10.397801
MA0031.10.344829
MA0038.10.569682
MA0040.11.06051
MA0041.10.141769
MA0042.10.123063
MA0043.10.480818
MA0046.11.18753
MA0048.10.243139
MA0050.10.123567
MA0051.10.192868
MA0052.10.41557
MA0055.10.440389
MA0056.10
MA0057.10.118248
MA0058.10.274844
MA0059.10.0796335
MA0060.10.2021
MA0061.10.813491
MA0063.10
MA0066.10.196017
MA0067.10.769322
MA0068.10.0364071
MA0069.10.467738
MA0070.10.458064
MA0071.10.50749
MA0072.10.454189
MA0073.10.00266812
MA0074.10.19236
MA0076.10.0879186
MA0077.10.44756
MA0078.10.72884
MA0081.10.27336
MA0083.10.487092
MA0084.10.947429
MA0087.10.452083
MA0088.10.181337
MA0089.10
MA0090.10.315775
MA0091.10.132307
MA0092.10.357807
MA0093.10.438635
MA0095.10
MA0098.10
MA0100.10.205224
MA0101.10.44587
MA0103.11.11572
MA0105.11.59447
MA0106.13.44515
MA0107.10.539977
MA0108.20.342362
MA0109.10
MA0111.11.13254
MA0113.10.236174
MA0114.10.524336
MA0115.10.697973
MA0116.10.299877
MA0117.10.513502
MA0119.11.37522
MA0122.10.53644
MA0124.10.659634
MA0125.10.583056
MA0130.10
MA0131.10.277285
MA0132.10
MA0133.10
MA0135.10.507125
MA0136.10.581198
MA0139.10.489406
MA0140.10.168354
MA0141.10.96632
MA0142.10.85557
MA0143.10.665621
MA0144.10.48115
MA0145.10.120776
MA0146.10.301569
MA0147.10.561572
MA0148.10.876759
MA0149.10.162171
MA0062.20.150391
MA0035.20.167901
MA0039.20.0064561
MA0138.20.264522
MA0002.20.182759
MA0137.20.481909
MA0104.20.389469
MA0047.21.81274
MA0112.20.671815
MA0065.20.535761
MA0150.10.307678
MA0151.10
MA0152.10.513688
MA0153.11.39352
MA0154.10.31593
MA0155.10.0441847
MA0156.10.840015
MA0157.10.298026
MA0158.10
MA0159.10.307966
MA0160.10.154993
MA0161.10
MA0162.10.155023
MA0163.10.207307
MA0164.10.68636
MA0080.20.766855
MA0018.20.225392
MA0099.20.172833
MA0079.29.04928e-06
MA0102.20.983247
MA0258.10.733928
MA0259.10.587878
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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