1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Weighted gene coexpression network analysis of DEGs detected in breast cancer cell response to soy isoflavones
Paper ID : 1148-ICB10
Authors:
Elham Ashrafi-Dehkordi *1, Ahmad Tahmasebi2, Habil Zare3, Mohammad Mazloomi1
1Nutrition Research Center, Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, 71348-14336, Iran
2Biotechnology Institute, College of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
3Department of Computer Science, Texas State University, San Marcos, Texas, 78666, USA 4 Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, Texas, 78229, USA
Abstract:
Soy foods are rich in isoflavones, which belong to the phytoestrogen family that could reduce breast cancer risk [1]. To define the biological networks affected by isoflavones in breast cancer cells, a WGCNA was performed to identify modules by analyzing 283 microarray samples from 7 different experiments. The results showed, genes were grouped into five discrete modules, each of which was coded by a unique color. The size of these modules ranged from 101 to 2,257 genes. The two major modules were named turquoise (2,257 genes), and blue (1,013genes). We performed an enrichment of GO to gain insight into the biological functions of the genes within these modules. The turquoise module was highly enriched for cell division and mitotic nuclear division. The blue module was associated with DNA replication. The majority of genes in blue module were up-regulated by isoflavones. The blue module also included 39 genes that were related to pathways in cancer (e.g., BAD, HSP90B1, and E2F3). BAD regulates cell growth. Role of Hsp90B1 in ovarian cell survival and cell apoptosis has been highlighted [2]. E2F3 controls cell cycle progression. The brown module was highly enriched for genes involved in embryonic digit morphogenesis. Moreover, we observed this module was annotated in response to estrogen. This module was enriched for hippo signaling pathway. Hippo pathway plays an important role in cell proliferation and breast cancer metastasis [3]. The GATA3 gene was found in the brown module. GATA3 requires normal development of the mammary gland and shows a relatively high sensitivity to breast carcinomas. The yellow module was observed to be enriched with terms such as cell-cell adhesion, translation, and protein folding. Finally, the green module was not enriched for any significant biological process term. In the blue module, DEGs were significantly enriched in the cell cycle and cancer pathways.
Keywords:
Breast cancer, Isoflavones, Weighted gene coexpression network analysis, Meta-analysis
Status : Paper Accepted (Poster Presentation)