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).<br><b>Background</b><br>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.<br><br><b>Methods and sample size</b><br>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 <b>Supplementary Data Sonnenblick.pdf.xlsx</b><br><br><b>Data sources</b><br>The dataset name, relevant DOI, accession number or access requirements are listed alongside the file type and repository name or other source where applicable.<br>GEO=Gene Expression OmnibusEGA=European Genome-phenome Archive<br>This data table is available to download as <b>NPJBCANCER-00304R1-data-sources.xlsx </b>including more detailed information and web urls to each data source. <b>data_db.tab</b> contains more detailed technical metadata for each data source.<br><br> Dataset Data location Permanent identifier/url NKI CCB NKI http://ccb.nki.nl/data/van-t-Veer_Nature_2002/<br><br> 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<br> 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