POLS Algorithm to Find a Local Bicluster on Interactions between HIV-1 Proteins and Human Proteins
PROCEEDINGS OF THE SYMPOSIUM ON BIOMATHEMATICS (SYMOMATH) 2018
Authors: Kaloka, Tesdiq Prigel; Bustaman, Alhadi; Lestari, Dian; Mangunwardoyo, Wibowo
Abstract
Protein is an important part of the organism. Proteins must interact with others to perform its functions properly. One of the interactions between proteins is the interactions between HIV-1 proteins and human proteins. Although HIV-1 and human proteins interact, we need to do depth analysis because some of the HIV-1 proteins do not interact with human proteins. Bicluster is the method which used to observe this interaction. Bicluster can groups interactions by rows and columns, so we can analyze it easier. The local search framework based on pairs operation algorithm called POLS algorithm. POLS algorithm is one of many algorithms to find a bicluster, it uses a balanced biclique approach. The algorithm is good for binary data because the initial step of the algorithm is to find local bicluster. The purpose of finding local bicluster is to make sure whether a bicluster can be found or not. In this paper, we use the POLS algorithm to find local bicluster on data interactions protein between HIV-1 and human. We divided the data into two types. The first data is HIV positive and the second is HIV negative. In HIV positive, the local bicluster consists of protein asp, envelope surface glycoprotein gp120, BECN1, and IFNG. In HIV negative, we found the local bicluster consist of protein envelope surface glycoprotein gp120, envelope surface glycoprotein gp160, ICAM1, and ICAM3.
Autoantibody biomarkers for the detection of serous ovarian cancer
GYNECOLOGIC ONCOLOGY
Authors: Katchman, Benjamin A.; Chowell, Diego; Wallstrom, Garrick; Vitonis, Allison F.; LaBaer, Joshua; Cramer, Daniel W.; Anderson, Karen S.
Abstract
Objective The purpose of this study was to identify a panel of novel serum tumor antigen-associated autoantibody (TAAb) biomarkers for the diagnosis of high-grade serous ovarian cancer. Methods. To detect TAAb we probed high-density programmable protein microarrays (NAPPA) containing 10,247 antigens with sera from patients with serous ovarian cancer (n = 30 cases/30 healthy controls) and measured bound IgG. We identified 735 promising tumor antigens and evaluated these with an independent set of serous ovarian cancer sera (n = 30 cases/30 benign disease controls/30 healthy controls). Thirty-nine potential tumor autoantigens were identified and evaluated using an orthogonal programmable ELISA platform against a total of 153 sera samples (n = 63 cases/30 benign disease controls/60 healthy controls). Sensitivities at 95% specificity were calculated and a classifier for the detection of high-grade serous ovarian cancer was constructed. Results. We identified 11-TAAbs (ICAM3, CTAG2, p53, STYXLI, PVR, POMC, NUDT11, TRIM39, UHMK1, KSR1, and NXF3) that distinguished high-grade serous ovarian cancer cases from healthy controls with a combined 45% sensitivity at 98% specificity. Conclusion. These are potential circulating biomarkers for the detection of serous ovarian cancer, and warrant confirmation in larger clinical cohorts. (C) 2017 Elsevier Inc. All rights reserved.