Gene expression data sources for in silico approach to assessing activation of AKT/mTOR signalling pathway in ER-positive early Breast Cancer

This dataset contains data files and identifiers for original data sources for 39 gene expression datasets from over 7,000 individuals with estrogen receptor positive (ER-positive) Breast Cancer (BC).
Background
The related study developed a novel in silico approach to assess activation of different signalling pathways. The phosphatidylinositol 3-kinase (PI3K)/AKT/mTOR signalling pathway mediates key cellular functions, including growth, proliferation and survival and is frequently involved in carcinogenesis, tumor progression and metastases. This research seeks to target relative contribution of AKT and mTOR (downstream of PI3K) in BC outcomes using the in silico approach via integrated reverse phase protein array (RPPA) and matched gene expression.

Methods and sample size
The methodology includes the development of gene signatures that reflect level of expression of pAKT and p-mTOR separately. Pooled analysis of gene expression data from over 7,000 patients with ER-positive BC was then performed. This data record holds links to the repositories holding these data, as well as the R-data files for each data record used in the analysis. All gene signatures developed are captured in Supplementary Data Sonnenblick.pdf.xlsx

Data sources
The dataset name, relevant DOI, accession number or access requirements are listed alongside the file type and repository name or other source where applicable.
GEO=Gene Expression OmnibusEGA=European Genome-phenome Archive
This data table is available to download as NPJBCANCER-00304R1-data-sources.xlsx including more detailed information and web urls to each data source. data_db.tab contains more detailed technical metadata for each data source.

Dataset
Data location
Permanent identifier/url

NKI
CCB NKI
http://ccb.nki.nl/data/van-t-Veer_Nature_2002/

UCSF
GEO
GSE123833

STNO2
GEO
GSE4335

NCI
Research Article (Supplementary files)
10.1073/pnas.1732912100

UNC4
GEO
GSE18229

CAL
Array Express
E-TABM-158

MDA4
GEO
GSE123832

KOO
GEO
GSE123831

HLP
Array Express
E-TABM-543

EXPO
GEO
GSE2109

VDX
GEO
GSE2034/GSE5327

MSK
GEO
GSE2603

UPP
GEO
GSE3494

STK
GEO
GSE1456

UNT
GEO
GSE2990

DUKE
GEO
GSE3143

TRANSBIG
GEO
GSE7390

DUKE2
GEO
GSE6961

MAINZ
GEO
GSE11121

LUND2
GEO
GSE5325

LUND
GEO
GSE5325

FNCLCC
GEO
GSE7017

EMC2
GEO
GSE12276

MUG
GEO
GSE10510

NCCS
GEO
GSE5364

MCCC
GEO
GSE19177

EORTC10994
GEO
GSE1561

DFHCC
GEO
GSE19615

DFHCC2
GEO
GSE18864

DFHCC3
GEO
GSE3744

DFHCC4
GEO
GSE5460

MAQC2
GEO
GSE20194

TAM
GEO
GSE6532/GSE9195

MDA5
GEO
GSE17705

VDX3
GEO
GSE12093

METABRIC
EGA
EGAS00000000083

TCGA
TCGA
https://tcga-data.nci.nih.gov/docs/publications/brca_2012/

DNA methylation (Dedeurwaerder et al.
2011)
GEO
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20713