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Coexpression cluster:C520

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Full id: C520_Natural_CD14_CD8_Basophils_CD4_Peripheral_CD34



Phase1 CAGE Peaks

  Short description
Hg19::chr10:11222326..11222339,- p@chr10:11222326..11222339
-
Hg19::chr10:11222427..11222442,- p@chr10:11222427..11222442
-
Hg19::chr10:17071741..17071777,+ p@chr10:17071741..17071777
+
Hg19::chr13:32889208..32889236,+ p3@BRCA2
Hg19::chr13:33002636..33002647,+ +
p@chr13:33002636..33002647
Hg19::chr15:65282401..65282422,+ p@chr15:65282401..65282422
+
Hg19::chr17:33569466..33569477,+ p@chr17:33569466..33569477
+
Hg19::chr17:65437348..65437360,- p@chr17:65437348..65437360
-
Hg19::chr19:18597484..18597505,+ p@chr19:18597484..18597505
+
Hg19::chr1:160679034..160679048,+ p@chr1:160679034..160679048
+
Hg19::chr1:206751790..206751814,+ p@chr1:206751790..206751814
+
Hg19::chr1:221952092..221952101,+ +
p@chr1:221952092..221952101
Hg19::chr22:36553418..36553428,+ p@chr22:36553418..36553428
+
Hg19::chr4:40201863..40201881,- p@chr4:40201863..40201881
-
Hg19::chr5:43018291..43018327,+ p2@ENST00000509036
Hg19::chr6:37016760..37016773,+ p@chr6:37016760..37016773
+
Hg19::chr6:37139954..37139971,- p@chr6:37139954..37139971
-


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:0033593BRCA2-MAGE-D1 complex0.00150123631225715
GO:0033595response to genistein0.00150123631225715
GO:0033600negative regulation of mammary gland epithelial cell proliferation0.00150123631225715
GO:0033598mammary gland epithelial cell proliferation0.00150123631225715
GO:0042772DNA damage response, signal transduction resulting in transcription0.00150123631225715
GO:0033599regulation of mammary gland epithelial cell proliferation0.00150123631225715
GO:0006978DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator0.00150123631225715
GO:0048478replication fork protection0.00150123631225715
GO:0007141male meiosis I0.00150123631225715
GO:0001556oocyte maturation0.00150123631225715
GO:0010225response to UV-C0.00150123631225715
GO:0010332response to gamma radiation0.00150123631225715
GO:0033205cytokinesis during cell cycle0.0017156986425796
GO:0001833inner cell mass cell proliferation0.0017156986425796
GO:0031573intra-S DNA damage checkpoint0.00187654539032144
GO:0045931positive regulation of progression through mitotic cell cycle0.00187654539032144
GO:0001832blastocyst growth0.00191066439741819
GO:0048599oocyte development0.00191066439741819
GO:0009994oocyte differentiation0.00191066439741819
GO:0010165response to X-ray0.00191066439741819
GO:0007140male meiosis0.00191066439741819
GO:0051298centrosome duplication0.00191066439741819
GO:0043015gamma-tubulin binding0.00200164841634287
GO:0042771DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis0.00200164841634287
GO:0007090regulation of S phase of mitotic cell cycle0.0024726245143059
GO:0014070response to organic cyclic substance0.0024726245143059
GO:0000724double-strand break repair via homologous recombination0.0024726245143059
GO:0050680negative regulation of epithelial cell proliferation0.0024726245143059
GO:0000725recombinational repair0.0024726245143059
GO:0007569cell aging0.0024726245143059
GO:0010212response to ionizing radiation0.0024726245143059
GO:0030879mammary gland development0.0024726245143059
GO:0007098centrosome cycle0.0024726245143059
GO:0001824blastocyst development0.0024726245143059
GO:0033261regulation of progression through S phase0.00257354796386941
GO:0030330DNA damage response, signal transduction by p53 class mediator0.00259304453935326
GO:0008156negative regulation of DNA replication0.00259304453935326
GO:0048477oogenesis0.00259304453935326
GO:0000084S phase of mitotic cell cycle0.00259304453935326
GO:0051297centrosome organization and biogenesis0.00259304453935326
GO:0031023microtubule organizing center organization and biogenesis0.00259304453935326
GO:0051053negative regulation of DNA metabolic process0.00259304453935326
GO:0008630DNA damage response, signal transduction resulting in induction of apoptosis0.00259304453935326
GO:0007281germ cell development0.00259304453935326
GO:0051320S phase0.00280230778288002
GO:0043627response to estrogen stimulus0.00287193033649194
GO:0035264multicellular organism growth0.0030024726245143
GO:0045787positive regulation of progression through cell cycle0.0030024726245143
GO:0000077DNA damage checkpoint0.00306374757603501
GO:0007568aging0.00312257152949488
GO:0008585female gonad development0.00316624385857872
GO:0031570DNA integrity checkpoint0.00316624385857872
GO:0006275regulation of DNA replication0.00316624385857872
GO:0046545development of primary female sexual characteristics0.00316624385857872
GO:0046660female sex differentiation0.00316624385857872
GO:0050678regulation of epithelial cell proliferation0.00321693495483676
GO:0007346regulation of progression through mitotic cell cycle0.00335869819013464
GO:0009411response to UV0.00335869819013464
GO:0050673epithelial cell proliferation0.00335869819013464
GO:0000910cytokinesis0.00336640870021301
GO:0007292female gamete generation0.00336640870021301
GO:0006302double-strand break repair0.00336640870021301
GO:0008629induction of apoptosis by intracellular signals0.00336640870021301
GO:0048589developmental growth0.00336640870021301
GO:0030141secretory granule0.00336640870021301
GO:0048545response to steroid hormone stimulus0.00336640870021301
GO:0007584response to nutrient0.00374221225664102
GO:0006289nucleotide-excision repair0.00374221225664102
GO:0042770DNA damage response, signal transduction0.00374221225664102
GO:0048469cell maturation0.00386032194580411
GO:0048732gland development0.00389052790782135
GO:0051052regulation of DNA metabolic process0.00408669885003336
GO:0001701in utero embryonic development0.0041129761979648
GO:0008406gonad development0.00416342870599317
GO:0048608reproductive structure development0.00416342870599317
GO:0021700developmental maturation0.00418765918682259
GO:0000075cell cycle checkpoint0.00436723290838445
GO:0031667response to nutrient levels0.00456071791065464
GO:0045137development of primary sexual characteristics0.00456071791065464
GO:0003697single-stranded DNA binding0.00457877075238432
GO:0010033response to organic substance0.00459637784493548
GO:0009991response to extracellular stimulus0.00483324861507181
GO:0015631tubulin binding0.00484736544198695
GO:0051327M phase of meiotic cell cycle0.00487460261391734
GO:0007126meiosis0.00487460261391734
GO:0051321meiotic cell cycle0.00495757107768641
GO:0009725response to hormone stimulus0.005245699298002
GO:0009416response to light stimulus0.00546517488956537
GO:0007548sex differentiation0.00546517488956537
GO:0051329interphase of mitotic cell cycle0.00567133717963813
GO:0003006reproductive developmental process0.00574099161170867
GO:0051325interphase0.00587440296100625
GO:0009792embryonic development ending in birth or egg hatching0.00606882764529487
GO:0043009chordate embryonic development0.00606882764529487
GO:0009314response to radiation0.00638420494896726
GO:0005813centrosome0.00806914517838219
GO:0007420brain development0.00860502463520594
GO:0005815microtubule organizing center0.00900741787354291
GO:0043566structure-specific DNA binding0.00964430600601564
GO:0006261DNA-dependent DNA replication0.00981005907019525
GO:0009628response to abiotic stimulus0.00981005907019525
GO:0006310DNA recombination0.0115977864123396
GO:0007283spermatogenesis0.0120665409249349
GO:0006917induction of apoptosis0.0120665409249349
GO:0048232male gamete generation0.0120665409249349
GO:0012502induction of programmed cell death0.0120665409249349
GO:0008285negative regulation of cell proliferation0.0126272213180508
GO:0007417central nervous system development0.0129464415919424
GO:0009790embryonic development0.0129464415919424
GO:0051301cell division0.0133746507819274
GO:0043065positive regulation of apoptosis0.013832820305798
GO:0043068positive regulation of programmed cell death0.013832820305798
GO:0007276gamete generation0.0140292526171996
GO:0022414reproductive process0.015978376053937
GO:0000279M phase0.015978376053937
GO:0016563transcription activator activity0.0159959317409469
GO:0019953sexual reproduction0.0161671602858463
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0162337079189841
GO:0000278mitotic cell cycle0.0164505222788515
GO:0016023cytoplasmic membrane-bound vesicle0.0173313460439444
GO:0031988membrane-bound vesicle0.0173313460439444
GO:0000074regulation of progression through cell cycle0.0173313460439444
GO:0006260DNA replication0.0173313460439444
GO:0051726regulation of cell cycle0.0173852850354941
GO:0022403cell cycle phase0.0177265983751325
GO:0031324negative regulation of cellular metabolic process0.0181578106339675
GO:0006281DNA repair0.0185349491151119
GO:0031410cytoplasmic vesicle0.0199382947721653
GO:0031982vesicle0.0201095840897702
GO:0009892negative regulation of metabolic process0.0201396625275113
GO:0006974response to DNA damage stimulus0.0205359959661436
GO:0042127regulation of cell proliferation0.0213357524378365
GO:0015630microtubule cytoskeleton0.0233425315319383
GO:0009719response to endogenous stimulus0.0237060898263891
GO:0042981regulation of apoptosis0.0253542132736764
GO:0043067regulation of programmed cell death0.0254327092900035
GO:0042221response to chemical stimulus0.0258168813991084
GO:0008092cytoskeletal protein binding0.0262389998924946
GO:0022402cell cycle process0.0270006530981502
GO:0009605response to external stimulus0.0271509310188222
GO:0007399nervous system development0.0304931971510956
GO:0008283cell proliferation0.0315048183839881
GO:0007049cell cycle0.0352318116359091
GO:0006915apoptosis0.0356543624161074
GO:0012501programmed cell death0.0356983641700873
GO:0008219cell death0.0370917706538638
GO:0016265death0.0370917706538638
GO:0044430cytoskeletal part0.0372468901257315
GO:0048522positive regulation of cellular process0.0384477702521698
GO:0048518positive regulation of biological process0.0425150123631226
GO:0048523negative regulation of cellular process0.0450765955864582
GO:0048513organ development0.0450765955864582
GO:0048519negative regulation of biological process0.0463911456493583
GO:0006950response to stress0.0476496304825517
GO:0048468cell development0.0480780552310047
GO:0006259DNA metabolic process0.0480780552310047



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
classical monocyte3.03e-8842
CD14-positive, CD16-negative classical monocyte3.03e-8842
defensive cell1.00e-7548
phagocyte1.00e-7548
leukocyte1.02e-73136
nongranular leukocyte6.26e-73115
hematopoietic lineage restricted progenitor cell5.51e-69120
myeloid leukocyte9.27e-6672
myeloid lineage restricted progenitor cell1.89e-6266
granulocyte monocyte progenitor cell2.40e-6167
monopoietic cell2.89e-6159
monocyte2.89e-6159
monoblast2.89e-6159
promonocyte2.89e-6159
hematopoietic stem cell2.16e-60168
angioblastic mesenchymal cell2.16e-60168
macrophage dendritic cell progenitor6.69e-5961
hematopoietic cell1.80e-56177
hematopoietic oligopotent progenitor cell2.11e-55161
hematopoietic multipotent progenitor cell2.11e-55161
myeloid cell1.59e-41108
common myeloid progenitor1.59e-41108
stuff accumulating cell1.57e-3687
mesenchymal cell9.33e-20354
connective tissue cell4.81e-19361
intermediate monocyte1.15e-169
CD14-positive, CD16-positive monocyte1.15e-169
motile cell1.55e-16386
CD4-positive, alpha-beta T cell1.38e-146
multi fate stem cell1.76e-13427
stem cell3.01e-13441
somatic stem cell4.62e-13433
lymphoid lineage restricted progenitor cell1.59e-1252
lymphocyte3.40e-1253
common lymphoid progenitor3.40e-1253
nucleate cell1.42e-1155
mature alpha-beta T cell4.12e-1018
alpha-beta T cell4.12e-1018
immature T cell4.12e-1018
mature T cell4.12e-1018
immature alpha-beta T cell4.12e-1018
natural killer cell1.62e-093
pro-NK cell1.62e-093
basophil5.52e-093
T cell2.94e-0825
pro-T cell2.94e-0825
single nucleate cell3.14e-083
mononuclear cell3.14e-083
naive T cell8.18e-083
Uber Anatomy
Ontology termp-valuen
bone marrow2.65e-5576
hematopoietic system1.75e-5398
blood island1.75e-5398
bone element2.24e-5082
immune system1.47e-4993
hemolymphoid system2.76e-47108
skeletal element8.02e-4590
skeletal system4.00e-39100
lateral plate mesoderm6.69e-19203
musculoskeletal system1.32e-18167
connective tissue4.51e-18371
mesoderm8.95e-08315
mesoderm-derived structure8.95e-08315
presumptive mesoderm8.95e-08315


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)
MA0003.10.00176401
MA0004.10.631966
MA0006.10.731819
MA0007.10.599001
MA0009.10.621697
MA0014.10.249137
MA0017.10.425352
MA0019.10.901513
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.776012
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.817744
MA0040.10.548121
MA0041.10.236024
MA0042.10.211928
MA0043.10.621991
MA0046.10.611559
MA0048.10.0663643
MA0050.11.14756
MA0051.11.47078
MA0052.10.551663
MA0055.10.0085634
MA0056.10
MA0057.10.164004
MA0058.11.46022
MA0059.10.907445
MA0060.10.0509127
MA0061.10.640118
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.111262
MA0069.10.607975
MA0070.10.597583
MA0071.11.36955
MA0072.10.593415
MA0073.10.102168
MA0074.10.808577
MA0076.10.493997
MA0077.10.586275
MA0078.10.995054
MA0081.10.907903
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.320704
MA0089.10
MA0090.10.174619
MA0091.10.223914
MA0092.11.08245
MA0093.11.21412
MA0095.10
MA0098.10
MA0100.11.52405
MA0101.10.372085
MA0103.10.34743
MA0105.10.492971
MA0106.10.33677
MA0107.10.259598
MA0108.20.471286
MA0109.10
MA0111.10.541878
MA0113.10.350573
MA0114.10.072201
MA0115.10.850405
MA0116.10.264652
MA0117.11.58019
MA0119.11.39041
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.11.02939
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.10.140313
MA0140.10.74193
MA0141.10.151722
MA0142.10.445733
MA0143.10.350722
MA0144.11.2999
MA0145.10.838342
MA0146.10.0313344
MA0147.10.569428
MA0148.10.240905
MA0149.10.261654
MA0062.20.148712
MA0035.20.268747
MA0039.20.243085
MA0138.20.38342
MA0002.20.393994
MA0137.21.29199
MA0104.20.420925
MA0047.20.326636
MA0112.20.00512484
MA0065.20.098884
MA0150.10.170499
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.10.280624
MA0155.10.0782503
MA0156.10.4018
MA0157.10.421609
MA0158.10
MA0159.10.0787617
MA0160.10.252705
MA0161.10
MA0162.10.0369674
MA0163.10.0193966
MA0164.10.948242
MA0080.21.21447
MA0018.20.337929
MA0099.20.754549
MA0079.20.0198059
MA0102.21.14323
MA0258.10.0605489
MA0259.10.28219
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
EBF1#187963.143458887024350.00825567983850420.0325327301306848
FOS#235363.175748932550970.007855105611196470.0322577608889489
FOSL2#235565.975364919257070.0002974595145965480.00310446429948525
MEF2A#420544.410171978739780.01100701972061150.040493223875478
NFKB1#479082.582618081973570.006129620732625820.0271029407152713
POLR2A#5430151.894811626374770.000454121370826330.00422032228579205
SPI1#668862.895643591243320.01225321287858110.0444190662903897
STAT1#677256.090172793293880.0009955417570414920.00714348234721102
WRNIP1#56897212.9199958058090.01029231209724920.0382329284412098
YY1#752882.311139176401810.01219218250456880.0442054972607069



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.