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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:31, 17 September 2013


Full id: C821_migratory_CD14_immature_CD14CD16_Dendritic_Macrophage_Monocytederived



Phase1 CAGE Peaks

Hg19::chr12:69719024..69719043,-p@chr12:69719024..69719043
-
Hg19::chr17:4643087..4643113,+p2@ZMYND15
Hg19::chr17:4643118..4643145,+p1@ZMYND15
Hg19::chr18:56203944..56203982,-p17@ALPK2
Hg19::chr3:121774202..121774222,+p1@CD86
Hg19::chr3:121774295..121774306,+p3@CD86
Hg19::chr3:121821281..121821283,+p@chr3:121821281..121821283
+
Hg19::chr7:6414211..6414222,+p2@RAC1
Hg19::chr8:39771339..39771352,+p4@IDO1
Hg19::chr8:623777..623823,-p2@ERICH1


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
0.0001878784920775180.03964236182835632102Toll-like receptor signaling pathway (KEGG):04620
9.34899905302393e-050.0396423618283563272Viral myocarditis (KEGG):05416
0.0001878784920775180.03964236182835632102Toll-like receptor signaling pathway (Wikipathways):WP75



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:0043016regulation of lymphotoxin A biosynthetic process0.00753461939402311
GO:0043017positive regulation of lymphotoxin A biosynthetic process0.00753461939402311
GO:0048261negative regulation of receptor-mediated endocytosis0.00753461939402311
GO:0045630positive regulation of T-helper 2 cell differentiation0.00753461939402311
GO:0035025positive regulation of Rho protein signal transduction0.00753461939402311
GO:0045404positive regulation of interleukin-4 biosynthetic process0.00753461939402311
GO:0045402regulation of interleukin-4 biosynthetic process0.00753461939402311
GO:0032641lymphotoxin A production0.00753461939402311
GO:0042109lymphotoxin A biosynthetic process0.00753461939402311
GO:0042097interleukin-4 biosynthetic process0.00753461939402311
GO:0045624positive regulation of T-helper cell differentiation0.00753461939402311
GO:0045628regulation of T-helper 2 cell differentiation0.00753461939402311
GO:0045806negative regulation of endocytosis0.00753461939402311
GO:0032633interleukin-4 production0.00753461939402311
GO:0045064T-helper 2 cell differentiation0.0082406260734007
GO:0031529ruffle organization and biogenesis0.0082406260734007
GO:0045622regulation of T-helper cell differentiation0.00852921161836958
GO:0048259regulation of receptor-mediated endocytosis0.00852921161836958
GO:0030032lamellipodium biogenesis0.00852921161836958
GO:0051057positive regulation of small GTPase mediated signal transduction0.00852921161836958
GO:0002294CD4-positive, alpha-beta T cell differentiation during immune response0.00852921161836958
GO:0002292T cell differentiation during immune response0.00852921161836958
GO:0042093T-helper cell differentiation0.00852921161836958
GO:0002366leukocyte activation during immune response0.00852921161836958
GO:0042092T-helper 2 type immune response0.00852921161836958
GO:0002285lymphocyte activation during immune response0.00852921161836958
GO:0002293alpha-beta T cell differentiation during immune response0.00852921161836958
GO:0002286T cell activation during immune response0.00852921161836958
GO:0002263cell activation during immune response0.00852921161836958
GO:0030742GTP-dependent protein binding0.00852921161836958
GO:0005041low-density lipoprotein receptor activity0.00852921161836958
GO:0043367CD4-positive, alpha beta T cell differentiation0.00852921161836958
GO:0045086positive regulation of interleukin-2 biosynthetic process0.00852921161836958
GO:0030228lipoprotein receptor activity0.00852921161836958
GO:0045076regulation of interleukin-2 biosynthetic process0.0110977673958521
GO:0015026coreceptor activity0.0110977673958521
GO:0042094interleukin-2 biosynthetic process0.0110977673958521
GO:0046632alpha-beta T cell differentiation0.0110977673958521
GO:0030169low-density lipoprotein binding0.0114885274969046
GO:0046631alpha-beta T cell activation0.0125180103570752
GO:0032623interleukin-2 production0.0134970475465134
GO:0008034lipoprotein binding0.0181885724770088
GO:0051051negative regulation of transport0.0185575468569413
GO:0030041actin filament polymerization0.0185575468569413
GO:0030100regulation of endocytosis0.0198985033483514
GO:0042108positive regulation of cytokine biosynthetic process0.0224885972698191
GO:0030217T cell differentiation0.0224885972698191
GO:0006898receptor-mediated endocytosis0.0224885972698191
GO:0030031cell projection biogenesis0.0268547456505492
GO:0045727positive regulation of translation0.0278930136771611
GO:0042035regulation of cytokine biosynthetic process0.0302754135134063
GO:0031328positive regulation of cellular biosynthetic process0.0302754135134063
GO:0008154actin polymerization and/or depolymerization0.0302754135134063
GO:0030098lymphocyte differentiation0.0311720084080662
GO:0042089cytokine biosynthetic process0.0319317503155234
GO:0042107cytokine metabolic process0.0319317503155234
GO:0009891positive regulation of biosynthetic process0.0322913838427321
GO:0005044scavenger receptor activity0.0326458682279682
GO:0002250adaptive immune response0.0326458682279682
GO:0008009chemokine activity0.0326458682279682
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0326458682279682
GO:0042379chemokine receptor binding0.0326458682279682
GO:0048770pigment granule0.0340809899234666
GO:0042470melanosome0.0340809899234666
GO:0051247positive regulation of protein metabolic process0.0343622254130415
GO:0002521leukocyte differentiation0.0358243535923532
GO:0051258protein polymerization0.0378480464406347
GO:0042110T cell activation0.0378480464406347
GO:0001664G-protein-coupled receptor binding0.0395726775772995
GO:0051049regulation of transport0.0412468429366429
GO:0001816cytokine production0.0417694350402286
GO:0044267cellular protein metabolic process0.0484331498350187
GO:0044260cellular macromolecule metabolic process0.0495517687458814



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
macrophage dendritic cell progenitor1.40e-6261
defensive cell2.50e-6248
phagocyte2.50e-6248
monopoietic cell4.76e-6059
monocyte4.76e-6059
monoblast4.76e-6059
promonocyte4.76e-6059
granulocyte monocyte progenitor cell1.06e-5867
classical monocyte9.60e-5642
CD14-positive, CD16-negative classical monocyte9.60e-5642
myeloid leukocyte3.37e-5572
myeloid lineage restricted progenitor cell4.83e-5566
leukocyte1.76e-40136
myeloid cell6.89e-40108
common myeloid progenitor6.89e-40108
nongranular leukocyte1.88e-35115
hematopoietic lineage restricted progenitor cell7.73e-34120
hematopoietic stem cell1.46e-29168
angioblastic mesenchymal cell1.46e-29168
hematopoietic oligopotent progenitor cell1.48e-27161
hematopoietic multipotent progenitor cell1.48e-27161
stuff accumulating cell3.54e-2787
hematopoietic cell9.52e-27177
intermediate monocyte1.73e-129
CD14-positive, CD16-positive monocyte1.73e-129
conventional dendritic cell1.12e-098
dendritic cell3.14e-0910
Langerhans cell3.78e-085
macrophage8.40e-086
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.12e-5898
blood island4.12e-5898
hemolymphoid system9.40e-54108
bone marrow3.26e-4976
immune system1.09e-4793
bone element4.67e-4482
skeletal element2.85e-3890
skeletal system8.21e-35100
adult organism7.83e-31114
lateral plate mesoderm1.90e-20203
musculoskeletal system3.02e-14167
neural tube1.57e-1056
neural rod1.57e-1056
future spinal cord1.57e-1056
neural keel1.57e-1056
regional part of nervous system1.70e-0953
regional part of brain1.70e-0953
organ2.13e-09503
mesoderm2.77e-09315
mesoderm-derived structure2.77e-09315
presumptive mesoderm2.77e-09315
germ layer1.57e-08560
germ layer / neural crest1.57e-08560
embryonic tissue1.57e-08560
presumptive structure1.57e-08560
germ layer / neural crest derived structure1.57e-08560
epiblast (generic)1.57e-08560
embryonic structure3.11e-08564
developing anatomical structure1.04e-07581
brain grey matter1.68e-0734
gray matter1.68e-0734
embryo2.72e-07592
brainstem3.32e-076
neural nucleus4.60e-079
nucleus of brain4.60e-079
tissue5.57e-07773
regional part of forebrain6.18e-0741
forebrain6.18e-0741
anterior neural tube6.18e-0741
future forebrain6.18e-0741


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)
MA0003.10.312279
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.462516
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.480635
MA0050.14.58274
MA0051.12.0713
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.631708
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.000749839
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.11.44489
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.126492
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.918839
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.646502
MA0105.10.0508589
MA0106.10.516528
MA0107.10.529721
MA0108.20.666881
MA0109.10
MA0111.10.885497
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.11.21476
MA0139.10.109245
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.332712
MA0146.10.0169564
MA0147.10.184931
MA0148.11.04145
MA0149.10.428597
MA0062.20.366815
MA0035.21.11424
MA0039.20.0317541
MA0138.20.569505
MA0002.20.407187
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.20.0329985
MA0065.20.0371828
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.0494985
MA0155.10.030416
MA0156.10.715501
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.11.23231
MA0163.10.0235237
MA0164.10.544294
MA0080.21.24809
MA0018.20.517858
MA0099.20.444294
MA0079.20.00464855
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
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
BATF#1053837.307340537691090.006678517386486440.0284147829603315
BDP1#558141105.0153409090910.00948194717338890.0357245700159294
IRF4#366236.574353806023240.008949141806857310.033936292115986
PAX5#507953.334782765588910.009853624493675830.0370314029685142
SPI1#668864.922594105113640.0004434197902305250.00412931961407809



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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