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Coexpression cluster:C302: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:17, 17 September 2013


Full id: C302_acute_peripheral_Neutrophils_NK_myelodysplastic_CD34_carcinoid



Phase1 CAGE Peaks

Hg19::chr10:134259182..134259198,+p@chr10:134259182..134259198
+
Hg19::chr10:22603976..22603984,-p@chr10:22603976..22603984
-
Hg19::chr11:123351501..123351547,+p@chr11:123351501..123351547
+
Hg19::chr12:125686755..125686767,+p@chr12:125686755..125686767
+
Hg19::chr12:58230871..58230881,+p1@ENST00000549683
Hg19::chr12:9886936..9886942,-p@chr12:9886936..9886942
-
Hg19::chr12:9891753..9891758,-p@chr12:9891753..9891758
-
Hg19::chr13:52303329..52303347,-p@chr13:52303329..52303347
-
Hg19::chr14:21359558..21359580,+p1@RNASE3
Hg19::chr14:21424030..21424062,+p@chr14:21424030..21424062
+
Hg19::chr14:21424359..21424370,+p@chr14:21424359..21424370
+
Hg19::chr15:41794867..41794880,+p@chr15:41794867..41794880
+
Hg19::chr15:57592859..57592869,+p5@LOC283663
Hg19::chr19:29480252..29480261,-p@chr19:29480252..29480261
-
Hg19::chr19:3600549..3600592,-p5@TBXA2R
Hg19::chr1:149157851..149157876,-p@chr1:149157851..149157876
-
Hg19::chr1:165506847..165506853,+p@chr1:165506847..165506853
+
Hg19::chr1:200876945..200876972,+p@chr1:200876945..200876972
+
Hg19::chr1:205899165..205899172,-p8@SLC26A9
Hg19::chr1:205899180..205899197,-p3@SLC26A9
Hg19::chr2:135160470..135160480,+p@chr2:135160470..135160480
+
Hg19::chr3:101504030..101504047,+p12@FAM55C
Hg19::chr3:126207297..126207316,-p@chr3:126207297..126207316
-
Hg19::chr3:32896322..32896332,+p@chr3:32896322..32896332
+
Hg19::chr5:126962527..126962529,-p@chr5:126962527..126962529
-
Hg19::chr5:448728..448747,+p@chr5:448728..448747
+
Hg19::chr5:448759..448770,+p@chr5:448759..448770
+
Hg19::chr5:78011925..78011929,-p1@ENST00000519121
Hg19::chr7:155156870..155156881,+p@chr7:155156870..155156881
+
Hg19::chr7:155156893..155156902,+p@chr7:155156893..155156902
+
Hg19::chr7:155156952..155156963,+p@chr7:155156952..155156963
+
Hg19::chr7:157464010..157464017,-p@chr7:157464010..157464017
-
Hg19::chr7:158330152..158330179,+p1@ENST00000448698
Hg19::chr7:1883150..1883186,-p@chr7:1883150..1883186
-
Hg19::chr8:141370177..141370224,-p@chr8:141370177..141370224
-
Hg19::chr8:141370243..141370257,-p@chr8:141370243..141370257
-
Hg19::chr8:141370262..141370267,-p@chr8:141370262..141370267
-
Hg19::chr8:141370284..141370289,-p@chr8:141370284..141370289
-
Hg19::chrX:64818643..64818666,+p@chrX:64818643..64818666
+
Hg19::chrX:7700640..7700651,+p@chrX:7700640..7700651
+


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:0004961thromboxane A2 receptor activity0.00883080183680678
GO:0004960thromboxane receptor activity0.024053182288869
GO:0015116sulfate transmembrane transporter activity0.024053182288869
GO:0008271secondary active sulfate transmembrane transporter activity0.024053182288869
GO:0004522pancreatic ribonuclease activity0.024053182288869
GO:0004953icosanoid receptor activity0.024053182288869
GO:0004954prostanoid receptor activity0.024053182288869
GO:0008272sulfate transport0.024053182288869
GO:0016892endoribonuclease activity, producing 3'-phosphomonoesters0.024053182288869
GO:0007585respiratory gaseous exchange0.024053182288869
GO:0016894endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters0.024053182288869
GO:0006401RNA catabolic process0.0337842027341225
GO:0015103inorganic anion transmembrane transporter activity0.0452733688192364
GO:0004521endoribonuclease activity0.0452733688192364



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><br>disease_data<br>

Disease
Ontology termp-valuen
syndrome6.58e-501
hematopoietic system disease9.18e-262
myeloid leukemia2.73e-1531
cardiovascular system disease1.29e-134
leukemia2.38e-1239
hematologic cancer1.17e-0951
immune system cancer1.17e-0951


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)
MA0003.15.95384e-05
MA0004.11.16915
MA0006.10.170948
MA0007.10.178549
MA0009.10.32421
MA0014.10.00061486
MA0017.11.42708
MA0019.10.375827
MA0024.10.247435
MA0025.11.10005
MA0027.11.83568
MA0028.10.192925
MA0029.10.261061
MA0030.10.252948
MA0031.10.208976
MA0038.10.652865
MA0040.10.265236
MA0041.10.217447
MA0042.10.411484
MA0043.10.324451
MA0046.10.315924
MA0048.10.0869926
MA0050.10.184767
MA0051.10.0935605
MA0052.10.268009
MA0055.10.0914085
MA0056.10
MA0057.10.140426
MA0058.11.15913
MA0059.10.791696
MA0060.10.228733
MA0061.10.0338355
MA0063.10
MA0066.10.0957332
MA0067.10.588512
MA0068.10.00428673
MA0069.10.313005
MA0070.10.30458
MA0071.11.43615
MA0072.10.301215
MA0073.15.88234e-08
MA0074.10.0932113
MA0076.10.122609
MA0077.10.80153
MA0078.10.445005
MA0081.10.792297
MA0083.10.329963
MA0084.10.758508
MA0087.10.810392
MA0088.10.0415543
MA0089.10
MA0090.10.135009
MA0091.10.772511
MA0092.10.370605
MA0093.11.21521
MA0095.10
MA0098.10
MA0100.10.334519
MA0101.10.0685984
MA0103.10.814941
MA0105.10.00316096
MA0106.10.115825
MA0107.10.0057092
MA0108.20.596523
MA0109.10
MA0111.10.340952
MA0113.10.392846
MA0114.10.548876
MA0115.10.52159
MA0116.10.369498
MA0117.10.353309
MA0119.10.23873
MA0122.10.373764
MA0124.10.485991
MA0125.10.415795
MA0130.10
MA0131.10.155349
MA0132.10
MA0133.10
MA0135.10.347651
MA0136.11.63413
MA0139.10.588679
MA0140.10.0770758
MA0141.11.56016
MA0142.11.0528
MA0143.10.393088
MA0144.10.0243423
MA0145.10.101436
MA0146.10.000283793
MA0147.10.864126
MA0148.10.224417
MA0149.10.0730455
MA0062.20.0310062
MA0035.20.561122
MA0039.22.0105e-05
MA0138.20.145586
MA0002.20.523268
MA0137.20.0173938
MA0104.20.811073
MA0047.20.718657
MA0112.20.447862
MA0065.20.265792
MA0150.10.888497
MA0151.10
MA0152.10.27382
MA0153.10.402047
MA0154.10.547086
MA0155.10.00770156
MA0156.10.970246
MA0157.10.171483
MA0158.10
MA0159.10.867498
MA0160.10.518287
MA0161.10
MA0162.10.000120331
MA0163.10.00200041
MA0164.10.131076
MA0080.21.21571
MA0018.20.116537
MA0099.20.0800285
MA0079.21.03823e-11
MA0102.20.793085
MA0258.10.151519
MA0259.10.40428
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

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