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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:23, 17 September 2013


Full id: C440_biphenotypic_acute_immature_splenic_B_myelodysplastic_Eosinophils



Phase1 CAGE Peaks

Hg19::chr10:7454538..7454551,-p@chr10:7454538..7454551
-
Hg19::chr12:120031498..120031508,+p4@TMEM233
Hg19::chr12:66801329..66801341,-p7@GRIP1
Hg19::chr15:28970769..28970773,+p@chr15:28970769..28970773
+
Hg19::chr15:52392705..52392752,-p1@ENST00000558607
Hg19::chr16:2256848..2256864,+p@chr16:2256848..2256864
+
Hg19::chr16:68389531..68389545,+p@chr16:68389531..68389545
+
Hg19::chr19:828296..828310,+p@chr19:828296..828310
+
Hg19::chr19:834404..834417,+p@chr19:834404..834417
+
Hg19::chr19:834523..834536,+p@chr19:834523..834536
+
Hg19::chr1:246257630..246257635,-p@chr1:246257630..246257635
-
Hg19::chr3:18244864..18244870,+p@chr3:18244864..18244870
+
Hg19::chr3:18467290..18467311,-p8@SATB1
Hg19::chr5:134788068..134788078,-p6@TIFAB
Hg19::chr5:134788131..134788156,-p5@TIFAB
Hg19::chr5:49732522..49732546,-p@chr5:49732522..49732546
-
Hg19::chr5:49949931..49949969,-p@chr5:49949931..49949969
-
Hg19::chr6:135501708..135501716,+p@chr6:135501708..135501716
+
Hg19::chr6:135501768..135501779,+p@chr6:135501768..135501779
+
Hg19::chr8:124031213..124031224,-p@chr8:124031213..124031224
-
Hg19::chr8:27456169..27456180,-p@chr8:27456169..27456180
-
Hg19::chr8:38008551..38008585,-p2@STAR


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:0016571histone methylation0.018557891113116
GO:0017127cholesterol transporter activity0.018557891113116
GO:0005720nuclear heterochromatin0.018557891113116
GO:0006700C21-steroid hormone biosynthetic process0.018557891113116
GO:0015248sterol transporter activity0.018557891113116
GO:0008207C21-steroid hormone metabolic process0.018557891113116
GO:0015485cholesterol binding0.018557891113116
GO:0030159receptor signaling complex scaffold activity0.018557891113116
GO:0000792heterochromatin0.018557891113116
GO:0032947protein complex scaffold0.018557891113116
GO:0006479protein amino acid methylation0.018557891113116
GO:0008213protein amino acid alkylation0.018557891113116
GO:0050681androgen receptor binding0.018557891113116
GO:0000790nuclear chromatin0.018557891113116
GO:0032934sterol binding0.0203305991360511
GO:0035258steroid hormone receptor binding0.0211758367765745
GO:0030521androgen receptor signaling pathway0.0225848989214989
GO:0042446hormone biosynthetic process0.0257293510819914
GO:0043414biopolymer methylation0.0257293510819914
GO:0016570histone modification0.0257293510819914
GO:0016569covalent chromatin modification0.0257293510819914
GO:0030518steroid hormone receptor signaling pathway0.0257293510819914
GO:0030522intracellular receptor-mediated signaling pathway0.0257293510819914
GO:0035257nuclear hormone receptor binding0.0257293510819914
GO:0051427hormone receptor binding0.0257293510819914
GO:0044454nuclear chromosome part0.0290715053333163
GO:0032259methylation0.030079515237829
GO:0005496steroid binding0.0334467056568891
GO:0042445hormone metabolic process0.0334467056568891
GO:0006694steroid biosynthetic process0.0334467056568891
GO:0005319lipid transporter activity0.0348691894377747
GO:0000228nuclear chromosome0.0348691894377747
GO:0003690double-stranded DNA binding0.0368766342591346
GO:0006869lipid transport0.0447044467987155
GO:0045211postsynaptic membrane0.0476656236037313
GO:0006730one-carbon compound metabolic process0.0476656236037313
GO:0043566structure-specific DNA binding0.0476656236037313
GO:0044456synapse part0.0476656236037313



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
hemopoietic organ1.68e-097
immune organ1.68e-097
Disease
Ontology termp-valuen
myeloid leukemia3.40e-3931
leukemia4.92e-3139
hematologic cancer1.40e-2351
immune system cancer1.40e-2351
syndrome1.04e-161
hematopoietic system disease5.08e-092
organ system cancer3.29e-08137


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)
MA0003.10.159428
MA0004.10.478761
MA0006.10.0694838
MA0007.11.41691
MA0009.10.526253
MA0014.10.0851404
MA0017.11.53695
MA0019.12.05968
MA0024.11.10823
MA0025.10.647545
MA0027.12.09389
MA0028.10.562332
MA0029.10.450974
MA0030.10.441064
MA0031.10.386141
MA0038.10.22896
MA0040.10.456051
MA0041.10.170492
MA0042.10.894828
MA0043.10.526535
MA0046.10.516541
MA0048.10.537344
MA0050.10.458935
MA0051.10.641247
MA0052.10.459414
MA0055.10.0249719
MA0056.10
MA0057.10.317055
MA0058.10.682118
MA0059.10.101051
MA0060.10.109486
MA0061.10.999163
MA0063.10
MA0066.10.649177
MA0067.10.820123
MA0068.10.302785
MA0069.10.51311
MA0070.10.503171
MA0071.10.583044
MA0072.10.499187
MA0073.10.727057
MA0074.10.225345
MA0076.10.356648
MA0077.10.49237
MA0078.10.30111
MA0081.10.331815
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.10.270219
MA0089.10
MA0090.10.378129
MA0091.11.49791
MA0092.10.4236
MA0093.10.530993
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.11.37711
MA0103.10.501795
MA0105.10.928954
MA0106.10.719625
MA0107.11.45796
MA0108.20.383574
MA0109.10
MA0111.10.794681
MA0113.10.272101
MA0114.10.643657
MA0115.10.747865
MA0116.10.672581
MA0117.10.560027
MA0119.10.0925355
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.846727
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.10.234116
MA0139.10.622109
MA0140.10.578606
MA0141.10.100114
MA0142.10.359701
MA0143.10.272236
MA0144.10.0352516
MA0145.10.0933513
MA0146.10.0152175
MA0147.10.385197
MA0148.10.174705
MA0149.10.192747
MA0062.20.652257
MA0035.20.198962
MA0039.20.371766
MA0138.20.302079
MA0002.21.0893
MA0137.20.0801516
MA0104.20.493759
MA0047.20.250458
MA0112.20.45088
MA0065.20.502939
MA0150.10.115337
MA0151.10
MA0152.10.20405
MA0153.10.615584
MA0154.11.20838
MA0155.10.151875
MA0156.10.58361
MA0157.10.337287
MA0158.10
MA0159.10.0446884
MA0160.10.18494
MA0161.10
MA0162.10.0975101
MA0163.10.472083
MA0164.10.28168
MA0080.20.531199
MA0018.20.260646
MA0099.20.204301
MA0079.20.395262
MA0102.21.03595
MA0258.10.564645
MA0259.10.179817
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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