Fig. 2

Identification of breast cancer-associated mRNAs and lncRNAs using published microarray data. a Microarray probes identified by TCGA as identifying differentially expressed genes in breast cancer were re-annotated with human mRNAs and lncRNAs using a hierarchical process [56,57,58]. 3585 out of 3662 probes were aligned to the human genome (hg38) by BLASTn [55]. The targets of the aligned probes were annotated by intersecting probe locations with GENCODE mRNAs, FANTOM CAT lncRNAs and NONCODE lncRNAs in order of descending priority [56,57,58]. 3101 probes were annotated with mRNAs [58]. 79 probes were annotated with lncRNAs from FANTOM CAT [56]. 74 probes were annotated with lncRNAs from NONCODE [57]. Probes that could not be aligned or annotated were discarded from downstream analysis. b Breast cancer-associated genes with putative TE-derived promoters were identified by a hierarchical process. TSSs, indicated by CAGE clusters defined by FANTOM CAT [56] were intersected with breast cancer-associated TFBSs using a 300 bp window, followed by intersecting with TEs and promoters of breast cancer-associated mRNAs and lncRNAs. 41 genes (79 mRNAs) and 8 FANTOM CAT lncRNAs were identified to have putative TE-derived promoters