title: Comprehensive tissue-specific gene set enrichment analysis and transcription factor analysis of breast cancer by integrating 14 gene expression datasets.
abstract: Breast cancer is the most commonly diagnosed malignancy in women. Several key genes and pathways have been proven to correlate with breast cancer pathology. This study sought to explore the differences in key transcription factors (TFs), transcriptional regulation networks and dysregulated pathways in different tissues in breast cancer. We employed 14 breast cancer datasets from NCBI-GEO and performed an integrated analysis in three different tissues including breast, blood and saliva. The results showed that there were eight genes (CEBPD, EGR1, EGR2, EGR3, FOS, FOSB, ID1 and NFIL3) down-regulated in breast tissue but up-regulated in blood tissue. Furthermore, we identified several unreported tissue-specific TFs that may contribute to breast cancer, including ATOH8, DMRT2, TBX15 and ZNF367. The dysregulation of these TFs damaged lipid metabolism, development, cell adhesion, proliferation, differentiation and metastasis processes. Among these pathways, the breast tissue showed the most serious impairment and the blood tissue showed a relatively moderate damage, whereas the saliva tissue was almost unaffected. This study could be helpful for future biomarker discovery, drug design, and therapeutic and predictive applications in breast cancers.
authors.affiliation: Institute of Health Sciences, Anhui University, Hefei 230601, Anhui, China.|State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
authors.forename: Wen-Xing
authors.initials: WX
authors.lastname: Li
authors.affiliation: Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China.|Department of Biostatistics, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China.
authors.forename: Kan
authors.initials: K
authors.lastname: He
authors.affiliation: Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Tang
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.|Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China.
authors.forename: Shao-Xing
authors.initials: SX
authors.lastname: Dai
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.|Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China.
authors.forename: Gong-Hua
authors.initials: GH
authors.lastname: Li
authors.affiliation: Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
authors.forename: Wen-Wen
authors.initials: WW
authors.lastname: Lv
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
authors.forename: Yi-Cheng
authors.initials: YC
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.|Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China.
authors.forename: San-Qi
authors.initials: SQ
authors.lastname: An
authors.affiliation: Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China.
authors.forename: Guo-Ying
authors.initials: GY
authors.lastname: Wu
authors.affiliation: Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China.
authors.forename: Dahai
authors.initials: D
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.|Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China.|KIZ-SU Joint Laboratory of Animal Models and Drug Development, College of Pharmaceutical Sciences, Soochow University, Kunming 650223, Yunnan, China.|Collaborative Innovation Center for Natural Products and Biological Drugs of Yunnan, Kunming 650223, Yunnan, China.|Chinese University of Hong Kong Joint Research Center for Bio-resources and Human Disease Mechanisms, Kunming 650223, Yunnan, China.
authors.forename: Jing-Fei
authors.initials: JF
authors.lastname: Huang
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor / Q000097:blood / Q000235:genetics*; D001943:Breast Neoplasms / Q000097:blood / Q000235:genetics* / Q000473:pathology; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D020022:Genetic Predisposition to Disease; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D012463:Saliva / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics; D014157:Transcription Factors / Q000097:blood / Q000235:genetics*; D059467:Transcriptome
chemical_list: D014408:Biomarkers, Tumor; D014157:Transcription Factors
keywords: GSEA; breast cancer; gene expression; tissue specific; transcription factors