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Coexpression cluster:C433: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0625128387853364,0,0,0,0,0,0,0,0,0,0.369863631980032,0.21690115973835,0.248641786604834,0.0589565109853561,0.139210117864267,0.0943257785523457,0.0907619220526865,0,0,0,0.0990452042849908,0,0,0,0,0,0.104796384789156,0,0,0,0,0,0.0789870938765965,0,0.110660147363526,0,0,0.097343627213097,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.027549189648299,0,0,0,0,0.185211092929071,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.648070848839897,0.553160249192863,1.02779898412278,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.535607460328699,0.399114709370023,0.492528432668985,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0813768443325499,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0390744040629657,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0593771573651105,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0266094859650764,0,0,0,0,0,0,0,0,0,0,0,0.0699368280688007,0,0,0,0,0.0402022792589852,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0440642112897698,0,0.26208976562482,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.10787168088319,0.0271284845789754,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0839445661171913,0,0,0,0,0,0,0,0,0,0.0300822291072195,0,0,0,0,0,0,0,0,0,0.0796420028184954,0|full_id=C433_Macrophage_Monocytederived_Dendritic_Neutrophils_Urothelial_Eosinophils_immature|gostat_on_coexpression_clusters=GO:0004229!gelatinase B activity!0.024895531419419!4318$GO:0005087!Ran guanyl-nucleotide exchange factor activity!0.024895531419419!1102$GO:0001882!nucleoside binding!0.024895531419419!64078$GO:0008133!collagenase activity!0.024895531419419!4318$GO:0005415!nucleoside:sodium symporter activity!0.024895531419419!64078$GO:0030225!macrophage differentiation!0.0290106079498542!4318$GO:0008329!pattern recognition receptor activity!0.0290106079498542!8685$GO:0005337!nucleoside transmembrane transporter activity!0.0290106079498542!64078$GO:0005518!collagen binding!0.0290106079498542!4318$GO:0005615!extracellular space!0.0290106079498542!4318;6369$GO:0030574!collagen catabolic process!0.0290106079498542!4318$GO:0044259!multicellular organismal macromolecule metabolic process!0.0290106079498542!4318$GO:0044268!multicellular organismal protein metabolic process!0.0290106079498542!4318$GO:0044256!protein digestion!0.0290106079498542!4318$GO:0044254!multicellular organismal protein catabolic process!0.0290106079498542!4318$GO:0044266!multicellular organismal macromolecule catabolic process!0.0290106079498542!4318$GO:0044243!multicellular organismal catabolic process!0.0290106079498542!4318$GO:0032963!collagen metabolic process!0.0290106079498542!4318$GO:0044236!multicellular organismal metabolic process!0.0300968024881436!4318$GO:0015932!nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity!0.031073646407503!64078$GO:0002573!myeloid leukocyte 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0.888488,MA0164.1;1.35976,MA0080.2;0.856804,MA0018.2;0.248141,MA0099.2;1.0711,MA0079.2;0.0105666,MA0102.2;1.01759,MA0258.1;1.64252,MA0259.1;0.0427194,MA0442.1;0}}
|full_id=C433_Macrophage_Monocytederived_Dendritic_Neutrophils_Urothelial_Eosinophils_immature
|id=C433
}}

Latest revision as of 11:22, 17 September 2013


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)
MA0003.10.00427949
MA0004.10.148499
MA0006.10.226525
MA0007.10.840085
MA0009.10.510226
MA0014.10.0167717
MA0017.10.27776
MA0019.10.697462
MA0024.10.419164
MA0025.10.630648
MA0027.12.07466
MA0028.10.0703882
MA0029.10.435662
MA0030.10.425859
MA0031.10.371592
MA0038.10.620638
MA0040.10.440685
MA0041.10.160207
MA0042.10.140252
MA0043.10.510506
MA0046.10.500598
MA0048.11.31646
MA0050.10.14079
MA0051.10.214141
MA0052.10.444013
MA0055.11.21799
MA0056.10
MA0057.10.021569
MA0058.10.312452
MA0059.10.310646
MA0060.10.0981883
MA0061.10.377791
MA0063.10
MA0066.12.56605
MA0067.10.802392
MA0068.10.273749
MA0069.11.24347
MA0070.10.487346
MA0071.11.05953
MA0072.10.483399
MA0073.10.708808
MA0074.10.612288
MA0076.10.102323
MA0077.10.476645
MA0078.10.784228
MA0081.11.58302
MA0083.10.516887
MA0084.10.981601
MA0087.10.481255
MA0088.10.133289
MA0089.10
MA0090.10.355863
MA0091.10.458145
MA0092.11.882
MA0093.10.230362
MA0095.10
MA0098.10
MA0100.10.64405
MA0101.10.234552
MA0103.10.214965
MA0105.10.243344
MA0106.10.247115
MA0107.10.34221
MA0108.20.369058
MA0109.10
MA0111.10.117802
MA0113.10.259368
MA0114.10.600893
MA0115.10.730438
MA0116.10.349495
MA0117.10.543727
MA0119.10.288423
MA0122.10.567011
MA0124.10.691722
MA0125.10.614264
MA0130.10
MA0131.10.302006
MA0132.10
MA0133.10
MA0135.10.537249
MA0136.10.222179
MA0139.10.342778
MA0140.10.188358
MA0141.10.637815
MA0142.10.913702
MA0143.10.7194
MA0144.10.302438
MA0145.10.436464
MA0146.10.08584
MA0147.10.155334
MA0148.10.164295
MA0149.13.06974
MA0062.20.0152768
MA0035.20.18788
MA0039.20.013937
MA0138.20.288795
MA0002.20.691269
MA0137.20.543748
MA0104.20.0975035
MA0047.20.238164
MA0112.20.81173
MA0065.21.16851
MA0150.10.347297
MA0151.10
MA0152.10.192836
MA0153.10.598889
MA0154.11.43666
MA0155.10.232738
MA0156.10.258514
MA0157.10.323429
MA0158.10
MA0159.10.642603
MA0160.10.99551
MA0161.10
MA0162.10.00184932
MA0163.10.888488
MA0164.11.35976
MA0080.20.856804
MA0018.20.248141
MA0099.21.0711
MA0079.20.0105666
MA0102.21.01759
MA0258.11.64252
MA0259.10.0427194
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
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.

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