Construction of brest cancer cell line BT20-specific interactome

ABSTRACT: Experiment type: Expression profiling by microarray and RNA-seq data, Third-party re-analysis The purpose of our study is to construct breast cancer cell line BT20-specific interactome by aggregating publically available microarray or RNA-seq samples, and identify novel transcriptional regulators that control breast cancer progression. We collected 101 samples of BT20 cell line microarray or RNA-seq from 12 prior studies and our own study data, GSE120919. We performed normalization for Affymetrix microarray platform and Illumina HiSeq and NovaSeq platform datasets. For the normalization, we used SCAN.UPC R package (ver.2.24.0, PMID: 22959562, https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html) on Affymetrix microarray platform datasets. We use Rsubread R package (ver.1.30.5, PMID: 23558742, http://bioconductor.org/packages/Rsubread/), TPM log2 values on Illumina HiSeq and NovaSeq platform datasets. And then, we performed batch effect adjusting to combine the datasets which came from different laboratories. The matrix data we deposited in GEO has normalized log2 signal intensity for 12,360 genes, and the genes were mapped to human Entrez Gene IDs that overlapped across 13 datasets (a total number of 101 samples). BT20-specific interactome was assembled by Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe, PMID: 16723010). Then, we used Master Regulator Analysis-Fisher?s Extact Test (MRA-FET, PMID: 20531406) to infer transcription factors which control a gene signature dysregulated by a fusion gene in BT20 cell line (please refer to GSE120919). We discovered SNAI2 as a master regulator candidate to modulate the gene signature in the fusion gene expressing BT20. Our findings will provide biological insights into the role of the fusion gene in breast cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE123917 | GEO | 2020/03/28

REPOSITORIES: GEO