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Coexpression cluster:C209: Difference between revisions

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|tf_chipseq_enrich=E2F6#1876;31:2.16016427336971:6.84559049924813e-06:0.000198872496843109
|tf_chipseq_enrich=E2F6#1876;31:2.16016427336971:6.84559049924813e-06:0.000198872496843109
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|tfbs_overrepresentation_for_novel_motifs=1.33471,3.17211,4.75534,0.156358,0.0235736,0.0574272,1.51337,2.83666,3.9449,0.159262,0.0439883,0.0327765,3.74047,0.720071,0.226851,1.79274,0.0919548,0.333701,8.75668,0.325637,0.195573,0.0966244,0.0109013,0.0578912,1.26572,0.979612,8.39732,2.78574,0.133224,0.690678,6.32301,1.17384,0.142662,0.283262,0.579018,0.0713397,0.154073,0.804472,0.199079,0.270334,0.0836829,2.7074,1.86972,0.530295,2.3644,1.17189,0.102005,0.113278,1.46472,0.00663081,0.16297,0.267135,0.143583,0.146706,0.238383,0.021945,0.24673,1.29872,7.70222,0.625021,1.30241,1.12164,0.0200245,0.0805564,1.19891,0.0675176,0.29925,0.595848,0.103553,0.458243,0.175704,0.0973128,0.366711,0.237066,0.00607601,1.78074,0.748594,0.0739978,0.102088,1.22702,0.0532057,0.0801309,1.62614,0.00830298,0.204199,0.00042548,0.00323777,0.281867,0.186218,0.683991,0.965009,0.550514,0.116223,0.377918,0.369863,2.21685,0.590356,0.426378,0.190493,0.293671,0.641014,0.11353,0.134627,1.58456,0.063437,0.00813248,0.0868511,0.228655,0.00367727,3.33611,1.36192,0.133206,1.56804,0.272895,0.332386,0.0357824,0.349191,0.00654855,0.236428,0.734032,0.231643,0.0489757,0.151571,0.0302397,0.417826,1.39642,0.097062,0.11863,0.260062,1.2953,0.188175,0.396672,0.26993,0.121765,0.378649,0.911072,0.0335303,0.0530274,0.346199,1.1103,0.731424,0.318453,0.0226719,0.135685,2.97783,0.60281,0.464457,0.957919,0.0870656,0.695458,5.09838,0.00244988,0.188403,0.206683,0.103278,0.483507,0.0449485,0.0515208,0.154026,0.810722,1.53668,0.177454,0.101734,0.0158218,0.0698204,0.0276148,4.08505,0.0232894,5.23388
}}
}}

Revision as of 13:47, 26 November 2012


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
-
Hg19::chr17:56347979..56347991,-p@chr17:56347979..56347991
-
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)

{{{tfbs_overrepresentation_jaspar}}}



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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