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

Latest revision as of 10:57, 17 September 2013


Full id: C209_acute_myelodysplastic_CD34_granulocyte_CD133_liver_spleen



Phase1 CAGE Peaks

Hg19::chr17:56347341..56347343,-p@chr17:56347341..56347343
-
Hg19::chr17:56347391..56347426,-p@chr17:56347391..56347426
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Hg19::chr17:56347979..56347991,-p@chr17:56347979..56347991
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Hg19::chr17:56348026..56348034,-p@chr17:56348026..56348034
-
Hg19::chr17:56349073..56349082,-p@chr17:56349073..56349082
-
Hg19::chr17:56349229..56349239,-p@chr17:56349229..56349239
-
Hg19::chr17:56350797..56350801,-p@chr17:56350797..56350801
-
Hg19::chr17:56351008..56351018,-p@chr17:56351008..56351018
-
Hg19::chr17:56352942..56352955,-p@chr17:56352942..56352955
-
Hg19::chr17:56352974..56352992,-p@chr17:56352974..56352992
-
Hg19::chr17:56353028..56353052,-p@chr17:56353028..56353052
-
Hg19::chr17:56353056..56353065,-p@chr17:56353056..56353065
-
Hg19::chr17:56355298..56355312,-p@chr17:56355298..56355312
-
Hg19::chr17:56355359..56355366,+p@chr17:56355359..56355366
+
Hg19::chr17:56355384..56355414,-p@chr17:56355384..56355414
-
Hg19::chr17:56355392..56355416,+p@chr17:56355392..56355416
+
Hg19::chr17:56355416..56355433,-p@chr17:56355416..56355433
-
Hg19::chr17:56356430..56356441,-p@chr17:56356430..56356441
-
Hg19::chr17:56356444..56356472,+p@chr17:56356444..56356472
+
Hg19::chr17:56356466..56356479,-p@chr17:56356466..56356479
-
Hg19::chr17:56356480..56356490,-p@chr17:56356480..56356490
-
Hg19::chr17:56356498..56356520,-p@chr17:56356498..56356520
-
Hg19::chr17:56356521..56356550,-p@chr17:56356521..56356550
-
Hg19::chr17:56356555..56356562,-p@chr17:56356555..56356562
-
Hg19::chr17:56356677..56356692,-p@chr17:56356677..56356692
-
Hg19::chr17:56356693..56356700,-p@chr17:56356693..56356700
-
Hg19::chr17:56356703..56356737,-p@chr17:56356703..56356737
-
Hg19::chr17:56356710..56356716,+p@chr17:56356710..56356716
+
Hg19::chr17:56356745..56356760,-p@chr17:56356745..56356760
-
Hg19::chr17:56356761..56356775,-p@chr17:56356761..56356775
-
Hg19::chr17:56356913..56356926,-p@chr17:56356913..56356926
-
Hg19::chr17:56356934..56356952,-p@chr17:56356934..56356952
-
Hg19::chr17:56356957..56356966,-p@chr17:56356957..56356966
-
Hg19::chr17:56356979..56356990,-p@chr17:56356979..56356990
-
Hg19::chr17:56356998..56357013,-p@chr17:56356998..56357013
-
Hg19::chr17:56357123..56357132,-p@chr17:56357123..56357132
-
Hg19::chr17:56357160..56357171,-p@chr17:56357160..56357171
-
Hg19::chr17:56357176..56357192,-p@chr17:56357176..56357192
-
Hg19::chr17:56357207..56357223,-p@chr17:56357207..56357223
-
Hg19::chr17:56357236..56357244,-p@chr17:56357236..56357244
-
Hg19::chr17:56357251..56357269,-p@chr17:56357251..56357269
-
Hg19::chr17:56357272..56357293,-p@chr17:56357272..56357293
-
Hg19::chr17:56357304..56357313,-p@chr17:56357304..56357313
-
Hg19::chr17:56357324..56357333,-p@chr17:56357324..56357333
-
Hg19::chr17:56357337..56357342,-p@chr17:56357337..56357342
-
Hg19::chr17:56357347..56357357,-p@chr17:56357347..56357357
-
Hg19::chr17:56357390..56357401,-p@chr17:56357390..56357401
-
Hg19::chr17:56357785..56357813,-p@chr17:56357785..56357813
-
Hg19::chr17:56358047..56358058,-p3@MPO
Hg19::chr17:56358092..56358104,-p2@MPO
Hg19::chr17:56358287..56358302,-p1@MPO
Hg19::chr17:76122653..76122662,-p@chr17:76122653..76122662
-
Hg19::chr19:840991..841006,+p1@PRTN3
Hg19::chr19:843490..843500,+p5@PRTN3
Hg19::chr19:843540..843551,+p3@PRTN3
Hg19::chr19:843564..843580,+p2@PRTN3
Hg19::chr19:843883..843896,+p@chr19:843883..843896
+
Hg19::chr19:843899..843953,+p@chr19:843899..843953
+
Hg19::chr19:843957..843983,+p@chr19:843957..843983
+
Hg19::chr19:846248..846259,+p@chr19:846248..846259
+
Hg19::chr19:847897..847908,+p@chr19:847897..847908
+
Hg19::chr19:847948..847965,+p@chr19:847948..847965
+
Hg19::chr19:847992..847997,+p@chr19:847992..847997
+
Hg19::chr19:848054..848078,-p@chr19:848054..848078
-
Hg19::chr19:848125..848141,+p@chr19:848125..848141
+
Hg19::chr19:852295..852310,+p1@ELANE
Hg19::chr19:855581..855593,+p4@ELANE
Hg19::chr19:856103..856124,-p@chr19:856103..856124
-
Hg19::chr19:856179..856196,+p@chr19:856179..856196
+
Hg19::chr1:162934104..162934106,-p@chr1:162934104..162934106
-
Hg19::chr22:34197370..34197374,-p@chr22:34197370..34197374
-
Hg19::chr3:74072773..74072775,+p@chr3:74072773..74072775
+


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:0042744hydrogen peroxide catabolic process0.00926961244116411
GO:0042743hydrogen peroxide metabolic process0.00926961244116411
GO:0009056catabolic process0.00926961244116411
GO:0030574collagen catabolic process0.00926961244116411
GO:0044256protein digestion0.00926961244116411
GO:0044254multicellular organismal protein catabolic process0.00926961244116411
GO:0044266multicellular organismal macromolecule catabolic process0.00926961244116411
GO:0044259multicellular organismal macromolecule metabolic process0.00926961244116411
GO:0042542response to hydrogen peroxide0.00926961244116411
GO:0044268multicellular organismal protein metabolic process0.00926961244116411
GO:0044243multicellular organismal catabolic process0.00926961244116411
GO:0032963collagen metabolic process0.00926961244116411
GO:0044236multicellular organismal metabolic process0.00937120036595884
GO:0000302response to reactive oxygen species0.0102145888597069
GO:0006800oxygen and reactive oxygen species metabolic process0.0158851492391733
GO:0004601peroxidase activity0.0208619636819112
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.0208619636819112
GO:0007586digestion0.0279255164146127
GO:0003682chromatin binding0.0317352050678504
GO:0006979response to oxidative stress0.0317352050678504
GO:0006916anti-apoptosis0.0427857746694047
GO:0005764lysosome0.0455677970498542
GO:0000323lytic vacuole0.0455677970498542
GO:0043066negative regulation of apoptosis0.0455677970498542
GO:0043069negative regulation of programmed cell death0.0455677970498542
GO:0005773vacuole0.0455677970498542
GO:0008284positive regulation of cell proliferation0.0455677970498542



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>

Cell Type
Ontology termp-valuen
CD34-positive, CD38-negative hematopoietic stem cell6.23e-181
Uber Anatomy
Ontology termp-valuen
hemopoietic organ2.83e-107
immune organ2.83e-107
spleen9.12e-073
gastrointestinal system mesentery9.12e-073
stomach region9.12e-073
mesentery9.12e-073
gastrointestinal system serosa9.12e-073
mesentery of stomach9.12e-073
gut mesentery9.12e-073
dorsal mesentery9.12e-073
dorsal mesogastrium9.12e-073
peritoneal cavity9.12e-073
spleen primordium9.12e-073
Disease
Ontology termp-valuen
myeloid leukemia3.85e-1931
syndrome4.44e-181
leukemia3.43e-1539
hematologic cancer1.41e-1151
immune system cancer1.41e-1151
hematopoietic system disease1.03e-092


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)
MA0003.16.09403
MA0004.11.7451
MA0006.10.534685
MA0007.10.00731907
MA0009.10.492707
MA0014.11.06232
MA0017.10.188582
MA0019.10.0339835
MA0024.10.109512
MA0025.10.247157
MA0027.11.58296
MA0028.10.0736698
MA0029.10.118774
MA0030.10.113235
MA0031.10.0845223
MA0038.10.0240784
MA0040.10.385745
MA0041.10.0110777
MA0042.10.0406692
MA0043.10.164234
MA0046.10.157912
MA0048.15.38492
MA0050.10.00786771
MA0051.10.0232608
MA0052.10.123572
MA0055.11.33586
MA0056.10
MA0057.10.274724
MA0058.12.60402
MA0059.15.67599
MA0060.10.00208911
MA0061.10.0511789
MA0063.10
MA0066.10.253463
MA0067.10.381464
MA0068.10.498926
MA0069.10.472186
MA0070.10.149597
MA0071.10.389753
MA0072.10.147151
MA0073.10.132423
MA0074.11.50148
MA0076.10.00328923
MA0077.13.45185
MA0078.10.179358
MA0081.11.10893
MA0083.10.503276
MA0084.10.535037
MA0087.10.145828
MA0088.10.137132
MA0089.10
MA0090.10.00404125
MA0091.15.51467
MA0092.10.206829
MA0093.11.94844
MA0095.10
MA0098.10
MA0100.13.16572
MA0101.10.00678306
MA0103.11.19548
MA0105.10.484712
MA0106.10.033045
MA0107.10.0214511
MA0108.20.593514
MA0109.10
MA0111.10.0273966
MA0113.10.340357
MA0114.12.45809
MA0115.10.32333
MA0116.11.88768
MA0117.13.10813
MA0119.10.10402
MA0122.10.20187
MA0124.10.293105
MA0125.10.235228
MA0130.10
MA0131.10.196353
MA0132.10
MA0133.10
MA0135.10.18172
MA0136.10.491451
MA0139.10.193796
MA0140.10.197637
MA0141.10.120131
MA0142.10.0719821
MA0143.10.0371635
MA0144.10.225632
MA0145.14.45314
MA0146.13.00365
MA0147.16.2974
MA0148.10.0118327
MA0149.10.0153848
MA0062.20.00303792
MA0035.20.0167284
MA0039.20.443708
MA0138.27.71943
MA0002.20.415672
MA0137.20.0794914
MA0104.26.19543
MA0047.20.0302178
MA0112.22.4544
MA0065.21.34995
MA0150.10.00372043
MA0151.10
MA0152.10.0178744
MA0153.10.224199
MA0154.13.86297
MA0155.12.03955
MA0156.10.0325469
MA0157.10.0620533
MA0158.10
MA0159.10.308664
MA0160.10.571609
MA0161.10
MA0162.10.241972
MA0163.11.16273
MA0164.10.0403976
MA0080.21.60496
MA0018.20.909577
MA0099.20.017932
MA0079.20.00123363
MA0102.20.567066
MA0258.10.598804
MA0259.12.75994
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
E2F6#1876312.160164273369716.84559049924813e-060.000198872496843109



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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