SHISA5
type: EnsemblDatabaseReference

RUNX2 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.2
p value: 0.0450887179614522
refers to: RUNX2
refers to: A_32_P161762
t statistic: -8.03703464615664

A_23_P386320
type: EFO_0005072
part of: A-AGIL-28

A_23_P23171
type: EFO_0005072
part of: A-AGIL-28

PCSK9 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -2.5
p value: 0.0491642383950286
refers to: PCSK9
refers to: A_32_P142440
t statistic: -7.70911814282234

AKIRIN1 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.1
p value: 0.0432753854411835
refers to: A_23_P256142
refers to: AKIRIN1
t statistic: -8.13637096732468

AGO4
type: EnsemblDatabaseReference

MPHOSPH8
type: EnsemblDatabaseReference

MPHOSPH8
type: EnsemblDatabaseReference

A_23_P331928
type: EFO_0005072
part of: A-AGIL-28

(Assay) GSM880857
type: Assay
has participant: A-AGIL-28

A_23_P335695
type: EFO_0005072
part of: A-AGIL-28

S100A9
type: EnsemblDatabaseReference

TMPRSS13
type: EnsemblDatabaseReference

IRAK3 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.0
p value: 0.0417608580603057
refers to: IRAK3
refers to: A_32_P83256
t statistic: -8.59686282046336

A_23_P64873
type: EFO_0005072
part of: A-AGIL-28

A_23_P356466
type: EFO_0005072
part of: A-AGIL-28

AGO4 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.2
p value: 0.0466314178499691
refers to: A_23_P23171
refers to: AGO4
t statistic: -7.91782320891937

MFI2 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.3
p value: 0.0417608580603057
refers to: MFI2
refers to: A_23_P386320
t statistic: -10.0056270054978

E-GEOD-36082
type: microarray 1colour mrna differential
RO_0002162: Homo sapiens
description: Deficiencies in the ATM gene are the underlying cause for ataxia telangiectasia, a congenital syndrome characterized by neurological, motor and immunological defects, as well as a predisposition to cancer risks. MicroRNAs (miRNAs) are small regulators of post-transcriptional gene expression and a useful tool for cancer diagnosis, staging, and prediction of therapeutic responses to clinical regimens. In particular, miRNAs have been used to develop signatures for breast cancer profiling. We are interested in the consequences of ATM deficiency on miRNA expression in breast epithelial cells and the potential contribution to cancer predisposition. In this study we investigate the effects of ATM loss on the miRNA expression and related gene expression changes in normal human mammary epithelial cells (HME-CC). We have identified 81 significantly differently expressed miRNAs in the ATM-deficient HME-CCs using small RNA sequencing. Many of these differentially expressed miRNAs have been described and implicated in tumorigenesis and proliferation. These changes include down-regulation of tumor suppressor miRNAs, such as hsa-miR-29c and hsa-miR-16, as well as the over-expression of pro-oncogenic miRNAs hsa-miR-93 and hsa-mir-221. All 81 miRNAs were combined with genome wide gene expression profiles to investigate possible targets of miRNA regulation. We identified messenger RNA (mRNA) targets of these miRNAs that were also significantly regulated after the depletion of ATM. Predicted targets included many genes implicated in cancer formation and progression, including SOCS1 and the proto-oncogene MAF. Integrated analysis of miRNA and mRNA expression allows us to build a more complete understanding of the pathways and networks involved in the breast cancer predisposition observed in individuals deficient in ATM. This study highlights miRNA and predicted mRNA target expression changes in ATM-deficient HME-CCs and suggests a mechanism for the breast cancer-prone phenotype seen in…
uses data from: http://identifiers.org/pubmed/23741392

A_32_P161762
type: EFO_0005072
part of: A-AGIL-28

ADAP2
type: EnsemblDatabaseReference

ADAP2
type: EnsemblDatabaseReference

(Sample) genotype/expressing ATM shRNA
type: EFO_0000001
property type: genotype
property value: expressing ATM shRNA

(Sample) genotype/expressing LacZ
type: EFO_0000001
property type: genotype
property value: expressing LacZ

A_23_P23048
type: EFO_0005072
part of: A-AGIL-28

DCN
type: EnsemblDatabaseReference

A_23_P76480
type: EFO_0005072
part of: A-AGIL-28

ENOX1
type: EnsemblDatabaseReference

GPR64
type: EnsemblDatabaseReference

DCN
type: EnsemblDatabaseReference

GPR64
type: EnsemblDatabaseReference

PRMT8
type: EnsemblDatabaseReference

PRMT8
type: EnsemblDatabaseReference

(Assay) GSM880858
type: Assay
has participant: A-AGIL-28

A_23_P213620
type: EFO_0005072
part of: A-AGIL-28

SNX22
type: EnsemblDatabaseReference

CD109
type: EnsemblDatabaseReference

SNX22
type: EnsemblDatabaseReference

(Assay) GSM880855
type: Assay
has participant: A-AGIL-28

CD109
type: EnsemblDatabaseReference

A_23_P212475
type: EFO_0005072
part of: A-AGIL-28

SLIT2 UP in 'expressing ATM shRNA' vs 'expressing LacZ'
type: IncreasedDifferentialExpressionRatio
fold change: 1.6
p value: 0.0417608580603057
refers to: SLIT2
refers to: A_23_P144348
t statistic: 9.43057398096781

(Factor value) GENOTYPE/expressing LacZ
type: EFO_0000001
property type: GENOTYPE
property value: expressing LacZ

SNX22 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.0
p value: 0.0398293085065498
refers to: SNX22
refers to: A_24_P375421
t statistic: -12.3431711817591

AGO4
type: EnsemblDatabaseReference

A_32_P83256
type: EFO_0005072
part of: A-AGIL-28

A_24_P234871
type: EFO_0005072
part of: A-AGIL-28

A_23_P406025
type: EFO_0005072
part of: A-AGIL-28

TFPI
type: EnsemblDatabaseReference

TFPI
type: EnsemblDatabaseReference

TMPRSS13
type: EnsemblDatabaseReference

CLEC2B
type: EnsemblDatabaseReference

CLEC2B
type: EnsemblDatabaseReference

RHOV UP in 'expressing ATM shRNA' vs 'expressing LacZ'
type: IncreasedDifferentialExpressionRatio
fold change: 2.2
p value: 0.0417608580603057
refers to: RHOV
refers to: A_23_P117912
t statistic: 8.39379793508709

CD109 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.0
p value: 0.0417608580603057
refers to: CD109
refers to: A_23_P331928
t statistic: -8.73216029232268

TFPI DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.0
p value: 0.0417608580603057
refers to: TFPI
refers to: A_23_P17095
t statistic: -10.304811680634

ADAP2 UP in 'expressing ATM shRNA' vs 'expressing LacZ'
type: IncreasedDifferentialExpressionRatio
fold change: 1.3
p value: 0.0417608580603057
refers to: ADAP2
refers to: A_24_P373562
t statistic: 9.26539275447631

MPHOSPH8 UP in 'expressing ATM shRNA' vs 'expressing LacZ'
type: IncreasedDifferentialExpressionRatio
fold change: 2.1
p value: 0.0417608580603057
refers to: MPHOSPH8
refers to: A_23_P204967
t statistic: 9.3297262995041

A_23_P424561
type: EFO_0005072
part of: A-AGIL-28

ENOX1
type: EnsemblDatabaseReference

GDA
type: EnsemblDatabaseReference

GDA
type: EnsemblDatabaseReference

A_24_P393571
type: EFO_0005072
part of: A-AGIL-28

Homo sapiens
type: OBI_0100026

CLEC2B DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.1
p value: 0.0466314178499691
refers to: A_23_P76480
refers to: CLEC2B
t statistic: -7.81800420025484

MFI2
type: EnsemblDatabaseReference

(Assay) GSM880854
type: Assay
has participant: A-AGIL-28

PPP2R2B
type: EnsemblDatabaseReference

PPP2R2B
type: EnsemblDatabaseReference

RHOV UP in 'expressing ATM shRNA' vs 'expressing LacZ'
type: IncreasedDifferentialExpressionRatio
fold change: 2.2
p value: 0.0417608580603057
refers to: A_23_P424561
refers to: RHOV
t statistic: 8.98424462589261

A_23_P93032
type: EFO_0005072
part of: A-AGIL-28

A_23_P143331
type: EFO_0005072
part of: A-AGIL-28

A_32_P142440
type: EFO_0005072
part of: A-AGIL-28

PCSK9
type: EnsemblDatabaseReference

PCSK9
type: EnsemblDatabaseReference

(Factor value) GENOTYPE/expressing ATM shRNA
type: EFO_0000001
property type: GENOTYPE
property value: expressing ATM shRNA

VGLL1
type: EnsemblDatabaseReference

VGLL1
type: EnsemblDatabaseReference

AGPAT3
type: EnsemblDatabaseReference

AGPAT3
type: EnsemblDatabaseReference

A_23_P139740
type: EFO_0005072
part of: A-AGIL-28

ZBED3 UP in 'expressing ATM shRNA' vs 'expressing LacZ'
type: IncreasedDifferentialExpressionRatio
fold change: 1.2
p value: 0.0466314178499691
refers to: ZBED3
refers to: A_23_P93032
t statistic: 7.84925877724589

ENOX1 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.5
p value: 0.0417608580603057
refers to: ENOX1
refers to: A_23_P128574
t statistic: -8.75993519852504

SLIT2
type: EnsemblDatabaseReference

A_23_P128574
type: EFO_0005072
part of: A-AGIL-28

SLIT2
type: EnsemblDatabaseReference

PRUNE2 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.4
p value: 0.0417608580603057
refers to: A_23_P406025
refers to: PRUNE2
t statistic: -10.3729326069049

A_24_P375421
type: EFO_0005072
part of: A-AGIL-28

RUNX2
type: EnsemblDatabaseReference

RUNX2
type: EnsemblDatabaseReference

SHISA5 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.0
p value: 0.0422140198495297
refers to: A_23_P212475
refers to: SHISA5
t statistic: -8.26176662518112

BMP2 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.5
p value: 0.0417608580603057
refers to: BMP2
refers to: A_23_P143331
t statistic: -8.72989647529317

GALNT10
type: EnsemblDatabaseReference

A_23_P144348
type: EFO_0005072
part of: A-AGIL-28

MFI2
type: EnsemblDatabaseReference

DCN DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -2.1
p value: 0.0417608580603057
refers to: DCN
refers to: A_23_P64873
t statistic: -9.97401601161676

GPR64 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.8
p value: 0.0417608580603057
refers to: A_23_P253692
refers to: GPR64
t statistic: -8.8599345465446

PRUNE2
type: EnsemblDatabaseReference

SHISA5
type: EnsemblDatabaseReference

OBSL1 UP in 'expressing ATM shRNA' vs 'expressing LacZ'
type: IncreasedDifferentialExpressionRatio
fold change: 1.2
p value: 0.0417608580603057
refers to: OBSL1
refers to: A_23_P335695
t statistic: 8.83054507998369

MPHOSPH8 UP in 'expressing ATM shRNA' vs 'expressing LacZ'
type: IncreasedDifferentialExpressionRatio
fold change: 2.0
p value: 0.0417608580603057
refers to: MPHOSPH8
refers to: A_24_P287403
t statistic: 8.44724328978419

AKIRIN1
type: EnsemblDatabaseReference

(Assay) GSM880856
type: Assay
has participant: A-AGIL-28

AKIRIN1
type: EnsemblDatabaseReference

A-AGIL-28
type: EFO_0000269

EFHD2
type: EnsemblDatabaseReference

EFHD2
type: EnsemblDatabaseReference

GALNT10 UP in 'expressing ATM shRNA' vs 'expressing LacZ'
type: IncreasedDifferentialExpressionRatio
fold change: 1.2
p value: 0.0398293085065498
refers to: GALNT10
refers to: A_24_P234871
t statistic: 12.373606130087

PPP2R2B UP in 'expressing ATM shRNA' vs 'expressing LacZ'
type: IncreasedDifferentialExpressionRatio
fold change: 1.4
p value: 0.0423092175136854
refers to: PPP2R2B
refers to: A_23_P213620
t statistic: 8.20911384842003

A_23_P253692
type: EFO_0005072
part of: A-AGIL-28

ZBED3
type: EnsemblDatabaseReference

ZBED3
type: EnsemblDatabaseReference

EFHD2 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.7
p value: 0.0405240131984994
refers to: A_23_P23443
refers to: EFHD2
t statistic: -11.4183127693908

BMP2
type: EnsemblDatabaseReference

(Assay) GSM880859
type: Assay
has participant: A-AGIL-28

BMP2
type: EnsemblDatabaseReference

GDA DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.3
p value: 0.0417608580603057
refers to: A_24_P393571
refers to: GDA
t statistic: -9.28244581298236

A_24_P924484
type: EFO_0005072
part of: A-AGIL-28

A_24_P373562
type: EFO_0005072
part of: A-AGIL-28

A_23_P117912
type: EFO_0005072
part of: A-AGIL-28

A_24_P287403
type: EFO_0005072
part of: A-AGIL-28

AGPAT3 UP in 'expressing ATM shRNA' vs 'expressing LacZ'
type: IncreasedDifferentialExpressionRatio
fold change: 1.0
p value: 0.0466314178499691
refers to: AGPAT3
refers to: A_23_P356466
t statistic: 7.88432327480277

OBSL1
type: EnsemblDatabaseReference

OBSL1
type: EnsemblDatabaseReference

S100A9
type: EnsemblDatabaseReference

IRAK3
type: EnsemblDatabaseReference

IRAK3
type: EnsemblDatabaseReference

(Sample) organism/Homo sapiens
type: Homo sapiens
property type: organism
property value: Homo sapiens

A_23_P256142
type: EFO_0005072
part of: A-AGIL-28

PRMT8 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.1
p value: 0.0417608580603057
refers to: A_23_P139740
refers to: PRMT8
t statistic: -9.6496015898098

RHOV
type: EnsemblDatabaseReference

RHOV
type: EnsemblDatabaseReference

Analysis of 'expressing ATM shRNA' vs 'expressing LacZ'
type: MicroarrayDifferentialExpressionAnalysis

A_23_P204967
type: EFO_0005072
part of: A-AGIL-28

MFI2 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.2
p value: 0.0417608580603057
refers to: MFI2
refers to: A_24_P924484
t statistic: -10.0607819265594

VGLL1 UP in 'expressing ATM shRNA' vs 'expressing LacZ'
type: IncreasedDifferentialExpressionRatio
fold change: 1.5
p value: 0.0398293085065498
refers to: VGLL1
refers to: A_23_P253123
t statistic: 13.3220794312961

A_23_P17095
type: EFO_0005072
part of: A-AGIL-28

GALNT10
type: EnsemblDatabaseReference

TMPRSS13 UP in 'expressing ATM shRNA' vs 'expressing LacZ'
type: IncreasedDifferentialExpressionRatio
fold change: 1.8
p value: 0.0417608580603057
refers to: TMPRSS13
refers to: A_23_P203150
t statistic: 8.75590526631708

A_23_P23443
type: EFO_0005072
part of: A-AGIL-28

S100A9 DOWN in 'expressing ATM shRNA' vs 'expressing LacZ'
type: DecreasedDifferentialExpressionRatio
fold change: -1.2
p value: 0.0405240131984994
refers to: S100A9
refers to: A_23_P23048
t statistic: -11.445315782109

(Sample) cell type/isogenic hTERT-immortalized normal human mammary epithelial cell
type: EFO_0000001
property type: cell type
property value: isogenic hTERT-immortalized normal human mammary epithelial cell

A_23_P253123
type: EFO_0005072
part of: A-AGIL-28

A_23_P203150
type: EFO_0005072
part of: A-AGIL-28

PRUNE2
type: EnsemblDatabaseReference