Identification of key differentially expressed genes and gene mutations in breast ductal carcinoma in situ using RNA-seq analysis

World Journal of Surgical Oncology
Congyuan ZhuJingqiu Sun

Abstract

The aim of this study was to identify the key differentially expressed genes (DEGs) and high-risk gene mutations in breast ductal carcinoma in situ (DCIS). Raw data (GSE36863) were downloaded from the database of Gene Expression Omnibus (GEO), including three DCIS samples (DCIS cell lines MCF10.DCIS, Sum102, and Sum225) and one normal control sample (normal mammary epithelial cell line MCF10A). The DEGs were analyzed using NOIseq and annotated via DAVID. Motif scanning in the promoter region of DEGs was performed via SeqPos. Additionally, single nucleotide variations (SNVs) were identified via GenomeAnalysisTK and SNV risk was assessed via VarioWatch. Mutant genes with a high frequency and risk were validated by RT-PCR analyses. Finally, 5391, 7073, and 7944 DEGs were identified in DCIS, Sum102, and Sum22 cell lines, respectively, when compared with MCF10A. VENN analysis of the three cell lines revealed 603 upregulated and 1043 downregulated DEGs, including 16 upregulated and 36 downregulated transcription factor (TF) genes. In addition, six TFs each (e.g., E2F1 and CREB1) were found to regulate the core up- and downregulated DEGs, respectively. Furthermore, SNV detection results revealed 1104 (MCF10.DCIS), 2833 (Sum102), and 1...Continue Reading

References

Jul 15, 1994·Biochemical and Biophysical Research Communications·S NakatsuruY Nakamura
Dec 11, 2003·Proceedings of the National Academy of Sciences of the United States of America·Frederique ZindyCharles J Sherr
Aug 10, 2005·Proceedings of the National Academy of Sciences of the United States of America·John R TimmerLee Niswander
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Mar 3, 2009·Breast Cancer Research : BCR·Stella TommasiGerd P Pfeifer
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Jan 15, 2010·Journal of the National Cancer Institute·Beth A VirnigRobert L Kane
Mar 9, 2010·Nature Genetics·Housheng Hansen HeX Shirley Liu
Jul 16, 2010·Molecular Oncology·Jovana JovanovicVessela Kristensen
Jul 16, 2010·Genes, Chromosomes & Cancer·George W WoodfieldRonald J Weigel
Sep 10, 2011·Genome Research·Sonia TarazonaAna Conesa
Oct 23, 2012·The Journal of Urology·Christopher J RickettsW Marston Linehan
Nov 28, 2012·Breast Cancer Research and Treatment·Emanuele MazzolaGiovanni Parmigiani
Jul 28, 2013·SpringerPlus·Sewha KimJa Seung Koo
Oct 12, 2013·Histopathology·Yun-Bi NiGary M Tse
Dec 4, 2013·The Journal of Biological Chemistry·Qinglin LiQun Zhou
Oct 29, 2014·Nature Reviews. Endocrinology·Lara P FernándezPilar Santisteban
Dec 30, 2014·Science Translational Medicine·J Keith KillianPaul S Meltzer
May 13, 2015·Chinese Journal of Cancer·Danila CoradiniFederico Ambrogi
Aug 8, 2015·Cancer Research·Martin C AbbaC Marcelo Aldaz
Nov 22, 2015·Nucleic Acids Research·Min ZhaoZhongming Zhao
Mar 28, 2017·Cancer Biology & Therapy·Xun TianDing Ma
Oct 4, 2017·CA: a Cancer Journal for Clinicians·Carol E DeSantisAhmedin Jemal

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Methods Mentioned

BETA
RNA-Seq

Software Mentioned

Database for Annotation , Visualization and Integrated Discove...
VarioWatch
VENN
Seqpos
Cufflinks
GenomeAnalysisTK
TopHat
NOISeq
Cuffdiff

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