We have previously shown that glycerol-3P-acyltransferase 2 (GPAT2) is overexpressed in various human cancer cell lines, including breast cancer MDA-MB-231 cells. We also showed that GPAT2 knockdown decreases cell proliferation, anchorage-independent growth, migration, and tumorigenicity, and increases staurosporine-induced apoptosis. GPAT2 is highly expressed in undifferentiated human breast carcinomas showing a significant positive correlation with the histological grade. This gene is also able to modulate the expression level of several small non-coding RNAs, including piRNAs and miRNAs, among others. Here we report a new analysis of a microarray study to assess the impact of GPAT2 silencing on the expression level of long non-coding RNAs (LncRNAs) in MDA-MB-231 cells. After identification, selection, and annotation of differentially expressed LncRNAs in GPAT2-silenced cells versus control cells, we conducted a series of bioinformatics analyses that allowed us to identify three LncRNAs (LINC1085, CTD2066L21.3 and NOVA1.AS1) predictive of overall survival in patients with breast cancer. In addition, we were able to identify specific miRNAs associated with the selected LncRNAs, in order to establish an interaction between both ncRNA groups to be considered for further experimental approaches and eventually therapeutic purposes.