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Coexpression cluster:C433: Difference between revisions

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|tf_chipseq_enrich=SIRT6#51548;2:13.3598612165239:0.00978099051106676:0.0367782850759784
|tf_chipseq_enrich=SIRT6#51548;2:13.3598612165239:0.00978099051106676:0.0367782850759784
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|tfbs_overrepresentation_for_novel_motifs=0.610853,0.198841,0.283006,0.495534,0.228802,0.492946,0.21518,1.50388,0.740314,0.0813672,0.145297,0.68884,0.0638208,0.596995,0.491982,0.928857,0.386278,0.0425957,0.369861,1.07304,0.99876,0.681145,0.480786,0.834629,0.704829,0.263074,0.739216,0.477404,0.502201,0.657924,0.412868,1.07066,0.30708,0.172492,0.0500279,0.382604,0.0488212,0.16489,1.43277,0.082891,0.185583,0.122756,0.135175,0.0628082,0.227268,0.0986693,0.617815,0.429484,0.341215,0.502497,0.273745,0.637443,0.0697815,0.482679,0.61862,0.209199,0.238182,0.186863,0.657353,0.18619,0.451758,0.217609,0.742416,0.363534,0.230363,0.33576,0.699678,1.04962,0.408258,0.893579,0.11533,0.10522,0.0215101,0.616804,0.0606565,0.290509,0.690177,0.349828,0.405538,1.14044,0.943285,0.362659,0.230109,0.473278,0.570388,0.00360896,0.788233,0.633576,0.293613,1.14619,1.84966,0.546282,0.43117,0.0341616,0.0643605,0.348406,0.607922,0.467605,0.297172,0.808817,0.36371,0.426385,0.462798,0.389311,0.326595,0.439104,0.376249,0.204779,0.106511,0.057369,0.620092,0.460417,0.275626,0.151086,0.741849,1.1061,0.0459163,0.131498,3.3311,0.0350599,0.60929,0.291743,0.162396,1.24577,0.846043,0.350442,0.210743,0.435409,0.648109,0.984026,0.546896,0.826452,0.66129,1.23665,0.798972,0.215,0.803835,0.929703,0.759101,1.59408,1.19737,0.724259,0.608353,0.464565,0.874666,0.181235,0.84518,1.43649,0.7692,0.1339,0.132286,0.000779656,3.4027,0.433859,0.217268,0.922839,0.281215,0.463478,0.106679,0.30612,0.723128,0.530809,1.04432,0.310552,0.340824,0.649817,0.536442,0.214247,0.0515206
}}
}}

Revision as of 14:12, 26 November 2012


Full id: C433_Macrophage_Monocytederived_Dendritic_Neutrophils_Urothelial_Eosinophils_immature



Phase1 CAGE Peaks

Hg19::chr13:49110026..49110037,-p15@RCBTB2
Hg19::chr13:77338767..77338773,+p@chr13:77338767..77338773
+
Hg19::chr1:161059154..161059172,-p6@PVRL4
Hg19::chr20:44637526..44637554,+p1@MMP9
Hg19::chr20:44638538..44638547,-p@chr20:44638538..44638547
-
Hg19::chr20:44638625..44638633,-p@chr20:44638625..44638633
-
Hg19::chr20:44638633..44638646,+p@chr20:44638633..44638646
+
Hg19::chr20:44640866..44640875,-p@chr20:44640866..44640875
-
Hg19::chr20:48914162..48914165,+p@chr20:48914162..48914165
+
Hg19::chr2:119699764..119699777,+p2@MARCO
Hg19::chr2:119699790..119699805,+p3@MARCO
Hg19::chr2:119699824..119699835,+p4@MARCO
Hg19::chr2:119699884..119699905,+p1@MARCO
Hg19::chr2:119731986..119731993,+p@chr2:119731986..119731993
+
Hg19::chr2:119735453..119735460,-p@chr2:119735453..119735460
-
Hg19::chr2:119735483..119735502,-p@chr2:119735483..119735502
-
Hg19::chr2:119739008..119739032,-p@chr2:119739008..119739032
-
Hg19::chr2:119748190..119748210,-p@chr2:119748190..119748210
-
Hg19::chr2:119750034..119750055,-p@chr2:119750034..119750055
-
Hg19::chr2:38368798..38368805,-p@chr2:38368798..38368805
-
Hg19::chr7:75443066..75443080,-p2@CCL24
Hg19::chr7:75443118..75443130,-p1@CCL24
Hg19::chr9:86983573..86983587,-p6@SLC28A3


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:0004229gelatinase B activity0.024895531419419
GO:0005087Ran guanyl-nucleotide exchange factor activity0.024895531419419
GO:0001882nucleoside binding0.024895531419419
GO:0008133collagenase activity0.024895531419419
GO:0005415nucleoside:sodium symporter activity0.024895531419419
GO:0030225macrophage differentiation0.0290106079498542
GO:0008329pattern recognition receptor activity0.0290106079498542
GO:0005337nucleoside transmembrane transporter activity0.0290106079498542
GO:0005518collagen binding0.0290106079498542
GO:0005615extracellular space0.0290106079498542
GO:0030574collagen catabolic process0.0290106079498542
GO:0044259multicellular organismal macromolecule metabolic process0.0290106079498542
GO:0044268multicellular organismal protein metabolic process0.0290106079498542
GO:0044256protein digestion0.0290106079498542
GO:0044254multicellular organismal protein catabolic process0.0290106079498542
GO:0044266multicellular organismal macromolecule catabolic process0.0290106079498542
GO:0044243multicellular organismal catabolic process0.0290106079498542
GO:0032963collagen metabolic process0.0290106079498542
GO:0044236multicellular organismal metabolic process0.0300968024881436
GO:0015932nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity0.031073646407503
GO:0002573myeloid leukocyte differentiation0.0354996750478198



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><br>


Cell Type
Ontology termp-valuen
macrophage2.41e-376
monopoietic cell1.65e-3259
monocyte1.65e-3259
monoblast1.65e-3259
promonocyte1.65e-3259
macrophage dendritic cell progenitor2.50e-3161
myeloid leukocyte5.95e-2972
myeloid lineage restricted progenitor cell1.10e-2866
granulocyte monocyte progenitor cell3.32e-2867
defensive cell2.90e-2548
phagocyte2.90e-2548
adult endothelial progenitor cell3.67e-193
myeloid cell5.57e-18108
common myeloid progenitor5.57e-18108
nongranular leukocyte7.48e-15115
hematopoietic lineage restricted progenitor cell4.51e-14120
leukocyte1.94e-13136
stuff accumulating cell1.57e-1287
hematopoietic oligopotent progenitor cell1.03e-10161
hematopoietic multipotent progenitor cell1.03e-10161
hematopoietic stem cell4.27e-10168
angioblastic mesenchymal cell4.27e-10168
classical monocyte5.87e-1042
CD14-positive, CD16-negative classical monocyte5.87e-1042
hematopoietic cell2.25e-09177
Uber Anatomy
Ontology termp-valuen
bone marrow1.97e-2476
immune system6.19e-2493
hematopoietic system1.68e-2298
blood island1.68e-2298
bone element2.26e-2282
skeletal element4.77e-2090
hemolymphoid system5.00e-20108
skeletal system1.16e-17100
lateral plate mesoderm7.74e-11203
musculoskeletal system5.11e-09167
spleen1.10e-083
gastrointestinal system mesentery1.10e-083
stomach region1.10e-083
mesentery1.10e-083
gastrointestinal system serosa1.10e-083
mesentery of stomach1.10e-083
gut mesentery1.10e-083
dorsal mesentery1.10e-083
dorsal mesogastrium1.10e-083
peritoneal cavity1.10e-083
spleen primordium1.10e-083
lower lobe of right lung1.54e-071
right lung lobe1.54e-071
lower lobe of lung1.54e-071
lobe of lung1.54e-071
right lung1.54e-071
epididymis4.08e-071
dura mater7.40e-071
future meninx7.40e-071
ectomeninx7.40e-071
future dura mater7.40e-071


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
SIRT6#51548213.35986121652390.009780990511066760.0367782850759784



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.