1425837_a_at
type: EFO_0005072
part of: A-AFFY-36

Analysis of 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: MicroarrayDifferentialExpressionAnalysis

Hamp2
type: EnsemblDatabaseReference

Rpl39l
type: EnsemblDatabaseReference

Sectm1a UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 1.9786975041792
p value: 0.0135269308539696
refers to: Sectm1a
refers to: 1425002_at
t statistic: 5.95637881347981

1421771_a_at
type: EFO_0005072
part of: A-AFFY-36

(Factor value) CELL_TYPE/Lineage-c-Kit+Sca-1+CD34+
type: EFO_0000001
property type: CELL_TYPE
property value: Lineage-c-Kit+Sca-1+CD34+

Sgip1 UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 1.81036739700463
p value: 0.0266540952899059
refers to: Sgip1
refers to: 1425180_at
t statistic: 5.04711615463165

(Factor value) GENOTYPE/Dnmt1 fl/fl
type: EFO_0000001
property type: GENOTYPE
property value: Dnmt1 fl/fl

Stag3
type: EnsemblDatabaseReference

Stag3 UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 2.68526935563729
p value: 0.046962546662119
refers to: 1460229_at
refers to: Stag3
t statistic: 4.46690637562399

Nxf2
type: EnsemblDatabaseReference

Tex19.1
type: EnsemblDatabaseReference

Ccrn4l
type: EnsemblDatabaseReference

Clec11a
type: EnsemblDatabaseReference

Sectm1a
type: EnsemblDatabaseReference

Car3 UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 1.36620452235624
p value: 0.0426972630877087
refers to: Car3
refers to: 1449434_at
t statistic: 4.59833484644829

Inadl
type: EnsemblDatabaseReference

1429035_at
type: EFO_0005072
part of: A-AFFY-36

Tex19.2 UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 2.89683241010813
p value: 0.0178469729026837
refers to: Tex19.2
refers to: 1460274_at
t statistic: 5.48433129104569

4930550L24Rik
type: EnsemblDatabaseReference

Dpep3 UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 3.87402636004459
p value: 0.00203354273271859
refers to: Dpep3
refers to: 1429035_at
t statistic: 8.62202579318884

Tnnt1
type: EnsemblDatabaseReference

1425180_at
type: EFO_0005072
part of: A-AFFY-36

(Factor value) CELL_TYPE/Lineage-c-Kit+Sca-1-
type: EFO_0000001
property type: CELL_TYPE
property value: Lineage-c-Kit+Sca-1-

1418984_at
type: EFO_0005072
part of: A-AFFY-36

1449502_at
type: EFO_0005072
part of: A-AFFY-36

1423174_a_at
type: EFO_0005072
part of: A-AFFY-36

(Assay) GSM397908
type: Assay
has participant: A-AFFY-36

Ccrn4l UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 2.10201484450109
p value: 0.0117224465658265
refers to: 1425837_a_at
refers to: Ccrn4l
t statistic: 6.22187128685026

(Assay) GSM397901
type: Assay
has participant: A-AFFY-36

Fkbp6
type: EnsemblDatabaseReference

E-GEOD-15840
type: microarray 1colour mrna differential
RO_0002162: Mus musculus
description: DNA methylation is essential for mammalian development and plays crucial roles in a variety of biological processes. The DNA methyltransferase Dnmt1 serves to maintain parental cell methylation patterns on daughter DNA strands in mitotic cells, however, the precise role of Dnmt1 in regulation of quiescent adult stem cells is not known. To examine the role of Dnmt1 in adult hematopoietic stem cells (HSCs), we conditionally disrupted Dnmt1 in the hematopoietic system. We used microarrays to profile the global gene expression program in hematopoietic stem and progenitor cells following deletion of Dnmt1. Dnmt1 was conditionally deleted in the hematopoietic system by injections of poly(I)poly(C) to induce Cre expression from the Mx-Cre transgene. Control mice were also injected with poly(I)poly(C) but do not carry the Mx-Cre transgene. Four days after completion of poly(I)poly(C) injections, bone marrow was harvested from the mice, antibody-mediated magnetic bead selection was used to remove cells expressing mature lineage markers, and the resulting lineage-depleted cells were stained with fluorochrome-conjugated antibodies against the surface receptors c-Kit, Sca-1 and CD34. Populations of LT-HSCs, MPPs and myeloid progenitors were FACS sorted, RNA was extracted and amplified from these sorted populations and hybridized to Affymetrix microarrays to compare changes in gene expression induced by conditional knockout of Dnmt1 compared to control in each of the three cell populations. There are 2 biological replicates for the LT-HSCs and MPPs and 3 biological replicates for the myeloid progenitors.
uses data from: http://identifiers.org/pubmed/19796624

Inadl UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 1.59630385830843
p value: 0.0258166510182093
refers to: Inadl
refers to: 1418984_at
t statistic: 5.1098620135041

Slc4a8
type: EnsemblDatabaseReference

A-AFFY-36
type: EFO_0000269

Hamp2 UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 3.46412703413993
p value: 0.0142667635401344
refers to: Hamp2
refers to: 1436643_x_at
t statistic: 5.79369638752658

(Assay) GSM397904
type: Assay
has participant: A-AFFY-36

Fkbp6 UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 2.15774032549137
p value: 0.0426972630877087
refers to: 1425101_a_at
refers to: Fkbp6
t statistic: 4.59459103988495

1435502_a_at
type: EFO_0005072
part of: A-AFFY-36

1450793_at
type: EFO_0005072
part of: A-AFFY-36

Tnnt1 UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 1.76170971505406
p value: 0.0477608273654718
refers to: Tnnt1
refers to: 1419606_a_at
t statistic: 4.44093448636971

Slc4a8 UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 1.40135370620298
p value: 0.0250194323656967
refers to: Slc4a8
refers to: 1423443_at
t statistic: 5.17465025628521

Ipp
type: EnsemblDatabaseReference

1452730_at
type: EFO_0005072
part of: A-AFFY-36

1450178_at
type: EFO_0005072
part of: A-AFFY-36

(Assay) GSM397899
type: Assay
has participant: A-AFFY-36

Dazl UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 5.1694662471001
p value: 3.30872388029582E-4
refers to: Dazl
refers to: 1419542_at
t statistic: 12.284293752847

Ipp
type: EnsemblDatabaseReference

(Assay) GSM397902
type: Assay
has participant: A-AFFY-36

Stag3
type: EnsemblDatabaseReference

(Assay) GSM397905
type: Assay
has participant: A-AFFY-36

2010005H15Rik UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 1.93158403400808
p value: 0.0449266835512893
refers to: 2010005H15Rik
refers to: 1449909_at
t statistic: 4.51299128151263

Mus musculus
type: OBI_0100026

Nxf2
type: EnsemblDatabaseReference

1423443_at
type: EFO_0005072
part of: A-AFFY-36

Nrg4
type: EnsemblDatabaseReference

Ccrn4l
type: EnsemblDatabaseReference

Rpl39l UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 4.96199657184329
p value: 0.00281442059441999
refers to: Rpl39l
refers to: 1423327_at
t statistic: 8.01229922601541

Clec11a
type: EnsemblDatabaseReference

Strc
type: EnsemblDatabaseReference

Nxf2 UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 1.39807594391694
p value: 0.0258166510182093
refers to: Nxf2
refers to: 1420585_a_at
t statistic: 5.11741773295915

Sectm1a
type: EnsemblDatabaseReference

(Sample) genotype/Dnmt1 fl/fl Mx-Cre
type: EFO_0000001
property type: genotype
property value: Dnmt1 fl/fl Mx-Cre

1421183_at
type: EFO_0005072
part of: A-AFFY-36

Inadl
type: EnsemblDatabaseReference

Tnnt1
type: EnsemblDatabaseReference

4930550L24Rik
type: EnsemblDatabaseReference

(Assay) GSM397900
type: Assay
has participant: A-AFFY-36

(Assay) GSM397910
type: Assay
has participant: A-AFFY-36

Tex12 UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 2.54793587078698
p value: 0.0241120328785676
refers to: 1421183_at
refers to: Tex12
t statistic: 5.22458317078075

Dpep3
type: EnsemblDatabaseReference

Tex19.1 UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 4.95158707272381
p value: 4.02701473949597E-4
refers to: Tex19.1
refers to: 1417482_at
t statistic: 11.1923792358472

(Factor value) GENOTYPE/Dnmt1 fl/fl Mx-Cre
type: EFO_0000001
property type: GENOTYPE
property value: Dnmt1 fl/fl Mx-Cre

1460229_at
type: EFO_0005072
part of: A-AFFY-36

(Assay) GSM397898
type: Assay
has participant: A-AFFY-36

Fkbp6
type: EnsemblDatabaseReference

(Sample) cell type/Lineage-c-Kit+Sca-1+CD34+
type: EFO_0000001
property type: cell type
property value: Lineage-c-Kit+Sca-1+CD34+

Pard6b UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 1.70122075659763
p value: 0.0440880331102719
refers to: 1423174_a_at
refers to: Pard6b
t statistic: 4.55607604619192

1421695_at
type: EFO_0005072
part of: A-AFFY-36

Slc4a8
type: EnsemblDatabaseReference

Tex12
type: EnsemblDatabaseReference

Brdt UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 2.33236629652684
p value: 0.035325794836535
refers to: Brdt
refers to: 1450178_at
t statistic: 4.79918415213699

1419542_at
type: EFO_0005072
part of: A-AFFY-36

Clec11a UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 1.91379432081326
p value: 0.0142667635401344
refers to: Clec11a
refers to: 1418796_at
t statistic: 5.8344451593596

Ipp UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 2.35799219789541
p value: 0.0062693508641113
refers to: Ipp
refers to: 1421771_a_at
t statistic: 7.08012286279939

Trap1a
type: EnsemblDatabaseReference

1436643_x_at
type: EFO_0005072
part of: A-AFFY-36

(Sample) cell type/Lineage-c-Kit+Sca-1+CD34-
type: EFO_0000001
property type: cell type
property value: Lineage-c-Kit+Sca-1+CD34-

Dazl
type: EnsemblDatabaseReference

(Assay) GSM397907
type: Assay
has participant: A-AFFY-36

Rps4l
type: EnsemblDatabaseReference

(Assay) GSM397909
type: Assay
has participant: A-AFFY-36

Strc UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 1.74612538189704
p value: 0.0449266835512893
refers to: 1421695_at
refers to: Strc
t statistic: 4.51546630473475

(Sample) organism part/bone marrow
type: UBERON_0002371
property type: organism part
property value: bone marrow

(Assay) GSM397897
type: Assay
has participant: A-AFFY-36

2010005H15Rik
type: EnsemblDatabaseReference

Tex19.2
type: EnsemblDatabaseReference

(Assay) GSM397906
type: Assay
has participant: A-AFFY-36

Nrg4
type: EnsemblDatabaseReference

1449909_at
type: EFO_0005072
part of: A-AFFY-36

1425101_a_at
type: EFO_0005072
part of: A-AFFY-36

Trap1a UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 6.17566275534961
p value: 3.67430497862136E-4
refers to: 1460226_at
refers to: Trap1a
t statistic: 11.646781130602

Rpl39l
type: EnsemblDatabaseReference

Strc
type: EnsemblDatabaseReference

1420585_a_at
type: EFO_0005072
part of: A-AFFY-36

Brdt
type: EnsemblDatabaseReference

Car3
type: EnsemblDatabaseReference

1417482_at
type: EFO_0005072
part of: A-AFFY-36

Nrg4 UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 2.02321108385825
p value: 0.0322258927338738
refers to: 1421681_at
refers to: Nrg4
t statistic: 4.88529066689541

Brdt
type: EnsemblDatabaseReference

(Sample) cell type/Lineage-c-Kit+Sca-1-
type: EFO_0000001
property type: cell type
property value: Lineage-c-Kit+Sca-1-

Tex19.1
type: EnsemblDatabaseReference

Car3
type: EnsemblDatabaseReference

Dpep3
type: EnsemblDatabaseReference

Pard6b
type: EnsemblDatabaseReference

(Assay) GSM397903
type: Assay
has participant: A-AFFY-36

1425002_at
type: EFO_0005072
part of: A-AFFY-36

Rps4l UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 2.08811838698684
p value: 0.0258946212508624
refers to: 1452730_at
refers to: Rps4l
t statistic: 5.08811503359783

Brdt UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 2.92334994830955
p value: 0.0171784172665304
refers to: Brdt
refers to: 1435502_a_at
t statistic: 5.56770279334368

(Factor value) CELL_TYPE/Lineage-c-Kit+Sca-1+CD34-
type: EFO_0000001
property type: CELL_TYPE
property value: Lineage-c-Kit+Sca-1+CD34-

1418796_at
type: EFO_0005072
part of: A-AFFY-36

1460226_at
type: EFO_0005072
part of: A-AFFY-36

1423327_at
type: EFO_0005072
part of: A-AFFY-36

Pard6b
type: EnsemblDatabaseReference

Tex12
type: EnsemblDatabaseReference

Sgip1
type: EnsemblDatabaseReference

4930550L24Rik UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 2.34339199225804
p value: 0.00956166473967544
refers to: 1450793_at
refers to: 4930550L24Rik
t statistic: 6.63158479134563

1421681_at
type: EFO_0005072
part of: A-AFFY-36

(Sample) organism/Mus musculus
type: Mus musculus
property type: organism
property value: Mus musculus

Trap1a
type: EnsemblDatabaseReference

Dazl
type: EnsemblDatabaseReference

Sgip1
type: EnsemblDatabaseReference

Dazl UP in 'Dnmt1 fl/fl Mx-Cre' vs 'Dnmt1 fl/fl' in 'Lineage-c-Kit+Sca-1-'
type: IncreasedDifferentialExpressionRatio
fold change: 4.64558413399248
p value: 3.30872388029582E-4
refers to: Dazl
refers to: 1449502_at
t statistic: 12.5602549114888

Rps4l
type: EnsemblDatabaseReference

1460274_at
type: EFO_0005072
part of: A-AFFY-36

Hamp2
type: EnsemblDatabaseReference

(Sample) genotype/Dnmt1 fl/fl
type: EFO_0000001
property type: genotype
property value: Dnmt1 fl/fl

2010005H15Rik
type: EnsemblDatabaseReference

1449434_at
type: EFO_0005072
part of: A-AFFY-36

Tex19.2
type: EnsemblDatabaseReference

1419606_a_at
type: EFO_0005072
part of: A-AFFY-36