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Coexpression cluster:C329: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:20, 17 September 2013


Full id: C329_Neutrophils_CD14_Monocytederived_Whole_Peripheral_CD14CD16_Eosinophils



Phase1 CAGE Peaks

Hg19::chr10:43674712..43674716,+p@chr10:43674712..43674716
+
Hg19::chr11:1902698..1902719,+p@chr11:1902698..1902719
+
Hg19::chr11:1905512..1905526,+p8@LSP1
Hg19::chr11:63978537..63978551,+p@chr11:63978537..63978551
+
Hg19::chr14:70180571..70180575,+p@chr14:70180571..70180575
+
Hg19::chr17:4619269..4619294,+p@chr17:4619269..4619294
+
Hg19::chr17:4619437..4619453,+p@chr17:4619437..4619453
+
Hg19::chr17:4637676..4637701,-p@chr17:4637676..4637701
-
Hg19::chr17:4638647..4638678,-p@chr17:4638647..4638678
-
Hg19::chr17:4638695..4638723,-p@chr17:4638695..4638723
-
Hg19::chr17:4642951..4642958,-p11@CXCL16
Hg19::chr19:17212998..17213013,+p3@MYO9B
Hg19::chr19:36398208..36398215,-p@chr19:36398208..36398215
-
Hg19::chr19:46021252..46021263,+p@chr19:46021252..46021263
+
Hg19::chr19:52146610..52146625,-p@chr19:52146610..52146625
-
Hg19::chr1:111441743..111441763,+p@chr1:111441743..111441763
+
Hg19::chr1:12248850..12248869,+p2@TNFRSF1B
Hg19::chr1:12251915..12251946,+p3@TNFRSF1B
Hg19::chr1:12252955..12252987,+p@chr1:12252955..12252987
+
Hg19::chr1:12252996..12253018,+p@chr1:12252996..12253018
+
Hg19::chr1:15755309..15755321,+p11@EFHD2
Hg19::chr1:183532611..183532622,-p@chr1:183532611..183532622
-
Hg19::chr1:183536107..183536129,-p@chr1:183536107..183536129
-
Hg19::chr1:27939407..27939421,-p@chr1:27939407..27939421
-
Hg19::chr1:27943424..27943442,-p@chr1:27943424..27943442
-
Hg19::chr1:31211863..31211872,-p@chr1:31211863..31211872
-
Hg19::chr1:31214479..31214495,+p@chr1:31214479..31214495
+
Hg19::chr21:46313414..46313448,-p8@ITGB2
Hg19::chr21:46320367..46320390,-p@chr21:46320367..46320390
-
Hg19::chr21:46321607..46321655,-p@chr21:46321607..46321655
-
Hg19::chr21:46323401..46323419,-p@chr21:46323401..46323419
-
Hg19::chr2:178121224..178121228,-p1@MIR3128
Hg19::chr2:219252546..219252572,+p@chr2:219252546..219252572
+
Hg19::chr6:44232765..44232778,-p5@NFKBIE
Hg19::chr7:139661798..139661815,+p@chr7:139661798..139661815
+


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:0030595leukocyte chemotaxis0.00186465716784662
GO:0050900leukocyte migration0.00186465716784662
GO:0006928cell motility0.0026585079724821
GO:0051674localization of cell0.0026585079724821
GO:0042330taxis0.0136104827067435
GO:0006935chemotaxis0.0136104827067435
GO:0007626locomotory behavior0.0183273441445966
GO:0051179localization0.0183273441445966
GO:0048247lymphocyte chemotaxis0.0194971231181372
GO:0016477cell migration0.0194971231181372
GO:0007610behavior0.0194971231181372
GO:0015629actin cytoskeleton0.0194971231181372
GO:0005031tumor necrosis factor receptor activity0.0194971231181372
GO:0043531ADP binding0.0194971231181372
GO:0043120tumor necrosis factor binding0.0194971231181372
GO:0042994cytoplasmic sequestering of transcription factor0.0194971231181372
GO:0005515protein binding0.0194971231181372
GO:0005035death receptor activity0.0194971231181372
GO:0031941filamentous actin0.0194971231181372
GO:0051220cytoplasmic sequestering of protein0.0194971231181372
GO:0007159leukocyte adhesion0.0194971231181372
GO:0042308negative regulation of protein import into nucleus0.0194971231181372
GO:0005041low-density lipoprotein receptor activity0.0194971231181372
GO:0042992negative regulation of transcription factor import into nucleus0.0194971231181372
GO:0030228lipoprotein receptor activity0.0194971231181372
GO:0016043cellular component organization and biogenesis0.0194971231181372
GO:0030593neutrophil chemotaxis0.0194971231181372
GO:0046823negative regulation of nucleocytoplasmic transport0.0194971231181372
GO:0051224negative regulation of protein transport0.020391741800133
GO:0000146microfilament motor activity0.0227406185699572
GO:0030048actin filament-based movement0.0230444884246312
GO:0003779actin binding0.0230444884246312
GO:0030169low-density lipoprotein binding0.0234255908084133
GO:0004871signal transducer activity0.0239176684604469
GO:0060089molecular transducer activity0.0239176684604469
GO:0005886plasma membrane0.024999223672671
GO:0042990regulation of transcription factor import into nucleus0.024999223672671
GO:0042991transcription factor import into nucleus0.024999223672671
GO:0042306regulation of protein import into nucleus0.024999223672671
GO:0033157regulation of intracellular protein transport0.024999223672671
GO:0005100Rho GTPase activator activity0.025245053130864
GO:0032507maintenance of cellular protein localization0.025245053130864
GO:0051651maintenance of cellular localization0.025245053130864
GO:0005884actin filament0.025245053130864
GO:0032386regulation of intracellular transport0.025245053130864
GO:0045185maintenance of protein localization0.0253332009963072
GO:0051223regulation of protein transport0.0253332009963072
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.0253332009963072
GO:0006952defense response0.0253332009963072
GO:0042221response to chemical stimulus0.0253332009963072
GO:0046822regulation of nucleocytoplasmic transport0.0253332009963072
GO:0008034lipoprotein binding0.0253332009963072
GO:0008092cytoskeletal protein binding0.0259616498663089
GO:0051051negative regulation of transport0.026072739236562
GO:0009605response to external stimulus0.0274894677450028
GO:0051235maintenance of localization0.031240388662317
GO:0006898receptor-mediated endocytosis0.031240388662317
GO:0018108peptidyl-tyrosine phosphorylation0.031240388662317
GO:0022603regulation of anatomical structure morphogenesis0.031240388662317
GO:0022604regulation of cell morphogenesis0.031240388662317
GO:0008360regulation of cell shape0.031240388662317
GO:0018212peptidyl-tyrosine modification0.032098748068781
GO:0001932regulation of protein amino acid phosphorylation0.032098748068781
GO:0033238regulation of amine metabolic process0.032098748068781
GO:0006521regulation of amino acid metabolic process0.032098748068781
GO:0008305integrin complex0.0377674227227657
GO:0019992diacylglycerol binding0.0397003874994354
GO:0006915apoptosis0.0397003874994354
GO:0012501programmed cell death0.0397411315633756
GO:0042325regulation of phosphorylation0.0402532619818485
GO:0048471perinuclear region of cytoplasm0.0402532619818485
GO:0005938cell cortex0.0402532619818485
GO:0008219cell death0.0405564525700531
GO:0016265death0.0405564525700531
GO:0046907intracellular transport0.0405564525700531
GO:0051174regulation of phosphorus metabolic process0.0405620894408165
GO:0019220regulation of phosphate metabolic process0.0405620894408165
GO:0006968cellular defense response0.041771960764272
GO:0005044scavenger receptor activity0.0418123338046793
GO:0008009chemokine activity0.0429751365009146
GO:0042379chemokine receptor binding0.0429992657534742
GO:0019901protein kinase binding0.0457603802830525
GO:0007229integrin-mediated signaling pathway0.0468307135085685
GO:0006606protein import into nucleus0.0496597971651375
GO:0051649establishment of cellular localization0.0496597971651375
GO:0004872receptor activity0.0496597971651375
GO:0051170nuclear import0.0496597971651375
GO:0019955cytokine binding0.0496597971651375
GO:0007160cell-matrix adhesion0.0496597971651375
GO:0019900kinase binding0.0496597971651375



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
myeloid leukocyte1.22e-7772
monopoietic cell1.29e-7359
monocyte1.29e-7359
monoblast1.29e-7359
promonocyte1.29e-7359
defensive cell3.29e-7348
phagocyte3.29e-7348
macrophage dendritic cell progenitor3.32e-7361
leukocyte3.43e-67136
granulocyte monocyte progenitor cell3.51e-6767
myeloid lineage restricted progenitor cell4.72e-6666
classical monocyte2.16e-6442
CD14-positive, CD16-negative classical monocyte2.16e-6442
myeloid cell6.65e-62108
common myeloid progenitor6.65e-62108
nongranular leukocyte3.29e-59115
hematopoietic stem cell5.67e-58168
angioblastic mesenchymal cell5.67e-58168
hematopoietic oligopotent progenitor cell1.04e-56161
hematopoietic multipotent progenitor cell1.04e-56161
hematopoietic cell1.35e-53177
hematopoietic lineage restricted progenitor cell1.39e-53120
stuff accumulating cell1.53e-3287
mesenchymal cell1.68e-13354
intermediate monocyte1.92e-139
CD14-positive, CD16-positive monocyte1.92e-139
connective tissue cell9.05e-13361
motile cell3.09e-10386
macrophage7.15e-106
granulocyte1.50e-098
conventional dendritic cell9.77e-098
multi fate stem cell2.84e-07427
somatic stem cell7.01e-07433
dendritic cell7.13e-0710
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.61e-6698
blood island3.61e-6698
hemolymphoid system1.65e-61108
bone marrow6.16e-5776
immune system4.36e-5393
bone element2.33e-5182
skeletal element4.40e-4590
skeletal system1.15e-38100
lateral plate mesoderm4.49e-22203
musculoskeletal system1.23e-16167
connective tissue2.57e-12371
mesoderm7.67e-09315
mesoderm-derived structure7.67e-09315
presumptive mesoderm7.67e-09315
blood1.64e-0815
haemolymphatic fluid1.64e-0815
organism substance1.64e-0815


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)
MA0003.10.145782
MA0004.10.250106
MA0006.10.0931752
MA0007.11.2868
MA0009.10.366503
MA0014.10.157527
MA0017.11.25224
MA0019.10.145319
MA0024.10.77938
MA0025.10.47683
MA0027.11.89328
MA0028.10.483716
MA0029.10.812088
MA0030.10.291553
MA0031.10.24472
MA0038.10.120244
MA0040.10.304553
MA0041.10.970425
MA0042.10.867824
MA0043.10.366755
MA0046.10.357837
MA0048.10.547696
MA0050.10.507351
MA0051.10.376278
MA0052.10.828653
MA0055.11.64945
MA0056.10
MA0057.10.0701724
MA0058.10.148161
MA0059.10.340565
MA0060.10.0046941
MA0061.10.0571069
MA0063.10
MA0066.11.82484
MA0067.10.638784
MA0068.10.0795413
MA0069.10.354782
MA0070.10.345954
MA0071.10.675927
MA0072.10.342425
MA0073.10.405206
MA0074.10.754649
MA0076.10.16355
MA0077.10.336397
MA0078.10.520188
MA0081.10.147095
MA0083.10.372513
MA0084.10.811454
MA0087.10.340509
MA0088.10.335716
MA0089.10
MA0090.11.09175
MA0091.10.539562
MA0092.10.209949
MA0093.10.236964
MA0095.10
MA0098.10
MA0100.10.40142
MA0101.10.0226238
MA0103.11.39112
MA0105.10.18719
MA0106.12.01161
MA0107.10.0495017
MA0108.20.242565
MA0109.10
MA0111.12.14027
MA0113.10.152632
MA0114.11.01377
MA0115.10.570409
MA0116.10.286939
MA0117.10.396851
MA0119.10.569091
MA0122.10.418111
MA0124.10.533912
MA0125.10.461632
MA0130.10
MA0131.10.548008
MA0132.10
MA0133.10
MA0135.10.390959
MA0136.10.391883
MA0139.10.79031
MA0140.10.326417
MA0141.10.609947
MA0142.10.222682
MA0143.11.45411
MA0144.10.932046
MA0145.10.180161
MA0146.10.487922
MA0147.10.145252
MA0148.10.280213
MA0149.10.0944562
MA0062.20.236276
MA0035.20.325494
MA0039.20.0240301
MA0138.21.59073
MA0002.20.472005
MA0137.20.50116
MA0104.20.176968
MA0047.20.422993
MA0112.20.67359
MA0065.20.760568
MA0150.10.172115
MA0151.10
MA0152.10.102351
MA0153.10.447419
MA0154.10.17951
MA0155.11.01122
MA0156.10.507342
MA0157.10.204296
MA0158.10
MA0159.11.08772
MA0160.10.621983
MA0161.10
MA0162.10.00480139
MA0163.10.667329
MA0164.10.482782
MA0080.21.07037
MA0018.20.143876
MA0099.20.335524
MA0079.20.00143571
MA0102.20.846442
MA0258.10.387384
MA0259.10.531383
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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