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Coexpression cluster:C1588

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Full id: C1588_Eosinophils_CD14CD16_CD14_Neutrophils_Basophils_Whole_embryonic



Phase1 CAGE Peaks

  Short description
Hg19::chr10:60027628..60027641,- p2@IPMK
Hg19::chr5:176730629..176730638,- p5@RAB24
Hg19::chr5:176730640..176730649,- p4@RAB24
Hg19::chr5:176730651..176730666,- p3@RAB24
Hg19::chr5:176730676..176730730,- p1@RAB24


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0050516inositol polyphosphate multikinase activity0.0044742070763476
GO:0046853inositol and derivative phosphorylation0.0044742070763476
GO:0046835carbohydrate phosphorylation0.00760447274511088
GO:0008440inositol trisphosphate 3-kinase activity0.00760447274511088
GO:0006020inositol metabolic process0.00760447274511088
GO:0051766inositol trisphosphate kinase activity0.00760447274511088
GO:0001839neural plate morphogenesis0.00760447274511088
GO:0001841neural tube formation0.00760447274511088
GO:0001840neural plate development0.00760447274511088
GO:0001838embryonic epithelial tube formation0.00760447274511088
GO:0021915neural tube development0.00772624213739308
GO:0016331morphogenesis of embryonic epithelium0.00820029831559406
GO:0006914autophagy0.00894525314623864
GO:0005793ER-Golgi intermediate compartment0.0137339145107121
GO:0005770late endosome0.0152013327330055
GO:0002009morphogenesis of an epithelium0.0173540881453391
GO:0004428inositol or phosphatidylinositol kinase activity0.0173540881453391
GO:0035239tube morphogenesis0.0202127547381958
GO:0048598embryonic morphogenesis0.0202127547381958
GO:0009792embryonic development ending in birth or egg hatching0.0202127547381958
GO:0043009chordate embryonic development0.0202127547381958
GO:0035295tube development0.0237543708322871
GO:0005768endosome0.0374388860274241
GO:0009790embryonic development0.0436597004450281
GO:0019318hexose metabolic process0.046962490367732
GO:0005996monosaccharide metabolic process0.046962490367732



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
myeloid leukocyte2.34e-3072
classical monocyte4.56e-3042
CD14-positive, CD16-negative classical monocyte4.56e-3042
defensive cell6.60e-2748
phagocyte6.60e-2748
granulocyte monocyte progenitor cell7.78e-2767
leukocyte1.49e-26136
macrophage dendritic cell progenitor1.59e-2461
monopoietic cell4.35e-2359
monocyte4.35e-2359
monoblast4.35e-2359
promonocyte4.35e-2359
hematopoietic stem cell1.88e-22168
angioblastic mesenchymal cell1.88e-22168
myeloid lineage restricted progenitor cell2.90e-2266
hematopoietic cell6.18e-22177
myeloid cell1.45e-21108
common myeloid progenitor1.45e-21108
hematopoietic oligopotent progenitor cell3.29e-21161
hematopoietic multipotent progenitor cell3.29e-21161
nongranular leukocyte6.02e-21115
hematopoietic lineage restricted progenitor cell6.74e-21120
stuff accumulating cell2.31e-1087
connective tissue cell1.76e-08361
intermediate monocyte3.03e-089
CD14-positive, CD16-positive monocyte3.03e-089
mesenchymal cell3.59e-08354
motile cell1.49e-07386
granulocyte3.13e-078
multi fate stem cell6.12e-07427
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.08e-2998
blood island1.08e-2998
hemolymphoid system4.40e-28108
bone element6.07e-2482
bone marrow1.39e-2376
skeletal element2.43e-2290
immune system4.35e-2293
skeletal system2.58e-19100
musculoskeletal system9.21e-12167
lateral plate mesoderm5.27e-09203
connective tissue2.54e-08371
blood4.32e-0715
haemolymphatic fluid4.32e-0715
organism substance4.32e-0715


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.12.72292
MA0004.12.5741
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.11.9468
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.17.83726
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.12.41212
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.14.0988
MA0056.10
MA0057.10.189508
MA0058.15.68124
MA0059.12.23433
MA0060.10.321781
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.17.11641
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.15.2144
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.13.28292
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.12.01656
MA0146.12.33916
MA0147.11.77656
MA0148.10.653474
MA0149.10.681935
MA0062.25.97298
MA0035.20.691506
MA0039.21.50246
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.23.24989
MA0047.20.767096
MA0112.20.425004
MA0065.20.880827
MA0150.11.35623
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.11.91168
MA0156.12.09554
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.12.71166
MA0161.10
MA0162.13.53221
MA0163.11.99104
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.24.80311
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#467417.9705396208071.89252338486495e-050.000428841939231742
CCNT2#90556.336201576962639.78880505817628e-050.00138828491508809
CTCF#1066444.288205098460020.005152015588243280.0239195979560142
CTCFL#140690415.79717948717953.15350622350688e-050.000633607226773442
E2F1#186954.907389214879320.0003512818099256460.0035208753307893
E2F6#187655.017155731697390.0003144978599297790.00322397349756637
EGR1#195854.988179094810140.0003237398000590710.00330282904936694
ELF1#199743.406478367046030.01235066105299550.0447211000836873
ELK4#2005412.98854532677446.83810524411663e-050.00109049453899877
ETS1#211347.783008737761870.0005121035947688870.00443884034642441
GABPB1#255345.654147068945740.001776696502096670.0109035377824935
HEY1#2346254.040111043105710.0009288852205177990.00673553034407126
IRF1#365946.109731002851120.001315525264767990.00880605967998362
MAX#414956.452555509007128.93743970843928e-050.00130529613440035
MXI1#460159.96157162875931.01894348670516e-050.000266376567729662
MYC#460955.22228187160940.0002573944848850610.00276223002537103
SIN3A#2594255.408884726815140.0002159522671657270.00247735488032968
SMARCB1#6598310.95162946869440.001511872848343180.00964913764410374
SRF#6722411.03774260973420.0001299255814846750.00170962552660678
TAF1#687253.343046285745290.002394600090870310.0135110555856512
USF1#739156.361499277207969.59569864925045e-050.00136683738574614
USF2#7392410.39375790805570.0001646179728687530.00202598827108646
YY1#752854.911170749853860.00034993140821360.00352425133485247
ZBTB7A#5134157.35190930787594.65425347594289e-050.000814896192412404
ZNF143#7702410.80070124178230.0001415223430863190.00184363876632057



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.