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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:23, 17 September 2013


Full id: C462_CD14_Monocytederived_Macrophage_Hepatic_Dendritic_lung_adipose



Phase1 CAGE Peaks

Hg19::chr10:49860525..49860564,-p7@ARHGAP22
Hg19::chr14:61448920..61448942,+p4@SLC38A6
Hg19::chr14:93118883..93118894,+p25@RIN3
Hg19::chr14:93214988..93215002,-p2@LGMN
Hg19::chr17:29281231..29281262,+p3@ADAP2
Hg19::chr17:29290132..29290136,+p@chr17:29290132..29290136
+
Hg19::chr17:29297900..29297936,-p2@AK092436
Hg19::chr17:7462347..7462356,+p10@TNFSF13
Hg19::chr19:11688452..11688486,-p1@ACP5
Hg19::chr19:12992244..12992272,-p2@DNASE2
Hg19::chr19:40872251..40872269,+p25@PLD3
Hg19::chr19:51645742..51645787,+p1@SIGLEC7
Hg19::chr1:159796513..159796524,+p7@SLAMF8
Hg19::chr1:206945673..206945712,-p4@IL10
Hg19::chr1:22965767..22965778,+p@chr1:22965767..22965778
+
Hg19::chr20:43990576..43990596,+p4@SYS1
Hg19::chr20:48884002..48884088,+p1@ENST00000425497
p1@ENST00000445003
p1@uc010zyr.1
Hg19::chr22:27014043..27014073,-p2@CRYBB1
Hg19::chr22:47016102..47016117,+p2@GRAMD4
Hg19::chr2:232106599..232106613,-p@chr2:232106599..232106613
-
Hg19::chr5:76383909..76383944,+p1@ENST00000514288


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

p.valueFDRnGenesnPathwayName
3.25661910109795e-050.020614398909953121Lysosome (KEGG):04142



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:0005764lysosome0.00929741119260226
GO:0000323lytic vacuole0.00929741119260226
GO:0005773vacuole0.00946609524320958
GO:0030886negative regulation of myeloid dendritic cell activation0.0179307328724496
GO:0045355negative regulation of interferon-alpha biosynthetic process0.0179307328724496
GO:0005141interleukin-10 receptor binding0.0179307328724496
GO:0032695negative regulation of interleukin-12 production0.0179307328724496
GO:0045347negative regulation of MHC class II biosynthetic process0.0228169020854112
GO:0016889endodeoxyribonuclease activity, producing 3'-phosphomonoesters0.0228169020854112
GO:0004531deoxyribonuclease II activity0.0228169020854112
GO:0030885regulation of myeloid dendritic cell activation0.0228169020854112
GO:0032655regulation of interleukin-12 production0.0313510836916462
GO:0007253cytoplasmic sequestering of NF-kappaB0.0313510836916462
GO:0001773myeloid dendritic cell activation0.0313510836916462
GO:0042347negative regulation of NF-kappaB import into nucleus0.0313510836916462
GO:0045348positive regulation of MHC class II biosynthetic process0.0313510836916462
GO:0045354regulation of interferon-alpha biosynthetic process0.0313510836916462
GO:0032607interferon-alpha production0.0313510836916462
GO:0045349interferon-alpha biosynthetic process0.0313510836916462
GO:0045342MHC class II biosynthetic process0.0313510836916462
GO:0045346regulation of MHC class II biosynthetic process0.0313510836916462
GO:0004630phospholipase D activity0.0313510836916462
GO:0032615interleukin-12 production0.0313510836916462
GO:0001509legumain activity0.0313510836916462
GO:0042130negative regulation of T cell proliferation0.0328150059188141
GO:0045351interferon type I biosynthetic process0.0328150059188141
GO:0032606interferon type I production0.0328150059188141
GO:0042994cytoplasmic sequestering of transcription factor0.0328150059188141
GO:0045191regulation of isotype switching0.0328150059188141
GO:0042092T-helper 2 type immune response0.0328150059188141
GO:0051220cytoplasmic sequestering of protein0.0328150059188141
GO:0002237response to molecule of bacterial origin0.0328150059188141
GO:0001818negative regulation of cytokine production0.0328150059188141
GO:0002208somatic diversification of immunoglobulins during immune response0.0328150059188141
GO:0002381immunoglobulin production during immune response0.0328150059188141
GO:0050868negative regulation of T cell activation0.0328150059188141
GO:0042308negative regulation of protein import into nucleus0.0328150059188141
GO:0042992negative regulation of transcription factor import into nucleus0.0328150059188141
GO:0050672negative regulation of lymphocyte proliferation0.0328150059188141
GO:0002204somatic recombination of immunoglobulin genes during immune response0.0328150059188141
GO:0045190isotype switching0.0328150059188141
GO:0032945negative regulation of mononuclear cell proliferation0.0328150059188141
GO:0042348NF-kappaB import into nucleus0.033405743502606
GO:0046823negative regulation of nucleocytoplasmic transport0.033405743502606
GO:0042345regulation of NF-kappaB import into nucleus0.033405743502606
GO:0016447somatic recombination of immunoglobulin gene segments0.0346434571716005
GO:0051224negative regulation of protein transport0.0346434571716005
GO:0016444somatic cell DNA recombination0.0375615612892389
GO:0016445somatic diversification of immunoglobulins0.0375615612892389
GO:0002562somatic diversification of immune receptors via germline recombination within a single locus0.0375615612892389
GO:0002200somatic diversification of immune receptors0.0385178777119114
GO:0042036negative regulation of cytokine biosynthetic process0.0385178777119114
GO:0002377immunoglobulin production0.0417129711359742
GO:0042100B cell proliferation0.0417129711359742
GO:0051250negative regulation of lymphocyte activation0.0432221762489413
GO:0005096GTPase activator activity0.0443656361163416
GO:0042990regulation of transcription factor import into nucleus0.0445173893930843
GO:0042991transcription factor import into nucleus0.0445173893930843
GO:0005212structural constituent of eye lens0.0445173893930843
GO:0042306regulation of protein import into nucleus0.0451002136213308
GO:0033157regulation of intracellular protein transport0.0451002136213308
GO:0016788hydrolase activity, acting on ester bonds0.0453904386158153
GO:0030595leukocyte chemotaxis0.0456453341420361
GO:0032507maintenance of cellular protein localization0.046635970718298
GO:0051651maintenance of cellular localization0.046635970718298
GO:0050864regulation of B cell activation0.046635970718298
GO:0032386regulation of intracellular transport0.046635970718298
GO:0045185maintenance of protein localization0.047779721085016
GO:0002440production of molecular mediator of immune response0.0481912578546151
GO:0002274myeloid leukocyte activation0.0481912578546151
GO:0051223regulation of protein transport0.0492635366268128
GO:0046822regulation of nucleocytoplasmic transport0.0496163041105543
GO:0030183B cell differentiation0.0496163041105543



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
monopoietic cell3.26e-5559
monocyte3.26e-5559
monoblast3.26e-5559
promonocyte3.26e-5559
macrophage dendritic cell progenitor6.13e-5361
defensive cell6.44e-5248
phagocyte6.44e-5248
myeloid lineage restricted progenitor cell7.48e-4866
myeloid leukocyte3.17e-4772
granulocyte monocyte progenitor cell6.32e-4767
classical monocyte6.61e-4142
CD14-positive, CD16-negative classical monocyte6.61e-4142
myeloid cell1.38e-26108
common myeloid progenitor1.38e-26108
nongranular leukocyte7.06e-24115
stuff accumulating cell6.76e-2387
leukocyte3.09e-20136
hematopoietic lineage restricted progenitor cell4.80e-20120
hematopoietic stem cell1.03e-13168
angioblastic mesenchymal cell1.03e-13168
hematopoietic oligopotent progenitor cell2.64e-13161
hematopoietic multipotent progenitor cell2.64e-13161
macrophage4.36e-136
hematopoietic cell2.45e-12177
adult endothelial progenitor cell2.47e-073
Uber Anatomy
Ontology termp-valuen
immune system3.85e-4093
bone marrow1.10e-3976
hematopoietic system4.36e-3798
blood island4.36e-3798
bone element9.63e-3682
hemolymphoid system2.20e-35108
adult organism1.42e-31114
skeletal element2.60e-3190
skeletal system8.75e-27100
lateral plate mesoderm1.16e-14203
organ3.20e-14503
musculoskeletal system3.57e-12167
germ layer1.61e-09560
germ layer / neural crest1.61e-09560
embryonic tissue1.61e-09560
presumptive structure1.61e-09560
germ layer / neural crest derived structure1.61e-09560
epiblast (generic)1.61e-09560
anatomical system1.71e-09624
anatomical group1.95e-09625
embryonic structure2.82e-09564
developing anatomical structure2.90e-09581
multi-cellular organism7.47e-09656
embryo1.27e-08592
mesoderm3.25e-08315
mesoderm-derived structure3.25e-08315
presumptive mesoderm3.25e-08315
neural tube2.08e-0756
neural rod2.08e-0756
future spinal cord2.08e-0756
neural keel2.08e-0756


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)
MA0003.10.00457877
MA0004.10.505176
MA0006.10.0763783
MA0007.10.924144
MA0009.10.543169
MA0014.10.173658
MA0017.10.657001
MA0019.10.275941
MA0024.10.450307
MA0025.12.69758
MA0027.12.11401
MA0028.10.286192
MA0029.10.467171
MA0030.10.457153
MA0031.10.401568
MA0038.10.24162
MA0040.10.472301
MA0041.10.535574
MA0042.10.938412
MA0043.11.34186
MA0046.10.533373
MA0048.10.211102
MA0050.10.484906
MA0051.10.670696
MA0052.10.475699
MA0055.10.710409
MA0056.10
MA0057.10.0306551
MA0058.10.721539
MA0059.10.718209
MA0060.10.122116
MA0061.10.237238
MA0063.10
MA0066.10.678752
MA0067.10.83875
MA0068.10.0636439
MA0069.10.529912
MA0070.10.519883
MA0071.11.79891
MA0072.11.28327
MA0073.10.0320155
MA0074.10.23792
MA0076.10.379988
MA0077.10.508982
MA0078.10.846104
MA0081.10.354412
MA0083.10.549943
MA0084.11.01907
MA0087.10.513678
MA0088.10.179504
MA0089.10
MA0090.10.402075
MA0091.10.170864
MA0092.10.879964
MA0093.10.268179
MA0095.10
MA0098.10
MA0100.10.252028
MA0101.10.272702
MA0103.10.0719484
MA0105.10.168486
MA0106.10.272934
MA0107.10.177872
MA0108.21.03141
MA0109.10
MA0111.11.35328
MA0113.11.42179
MA0114.10.388646
MA0115.10.766188
MA0116.10.40798
MA0117.10.577217
MA0119.11.12202
MA0122.10.600851
MA0124.10.727093
MA0125.10.648747
MA0130.10
MA0131.10.329895
MA0132.10
MA0133.10
MA0135.10.570637
MA0136.10.690268
MA0139.10.0845536
MA0140.10.211376
MA0141.11.72159
MA0142.10.978356
MA0143.10.779645
MA0144.11.42189
MA0145.10.772194
MA0146.10.0432698
MA0147.10.415954
MA0148.10.185927
MA0149.10.204488
MA0062.20.0907669
MA0035.20.210872
MA0039.20.0287691
MA0138.20.316226
MA0002.20.799796
MA0137.21.03083
MA0104.20.121334
MA0047.20.263601
MA0112.20.979121
MA0065.20.368601
MA0150.10.785204
MA0151.10
MA0152.10.618168
MA0153.10.633172
MA0154.10.484177
MA0155.10.303035
MA0156.11.03924
MA0157.10.352016
MA0158.10
MA0159.10.417407
MA0160.11.08448
MA0161.10
MA0162.10.0305571
MA0163.10.0144385
MA0164.10.295453
MA0080.21.43309
MA0018.20.274004
MA0099.20.618776
MA0079.20.00158455
MA0102.21.05522
MA0258.10.953225
MA0259.10.435255
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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