Cancer is in general not a result of an abnormality of a single gene but a consequence of changes in many genes, it is therefore of great importance to understand the roles of different oncogenic and tumor suppressor pathways in tumorigenesis. In recent years, there have been many computational models developed to study the genetic alterations of different pathways in the evolutionary process of cancer. However, most of the methods are knowledge-based enrichment analyses and inflexible to analyze user-defined pathways or gene sets. In this paper, we develop a nonparametric and data-driven approach to testing for the dynamic changes of pathways over the cancer progression. Our method is based on an expansion and refinement of the pathway being studied, followed by a graph-based multivariate test, which is very easy to implement in practice. The new test is applied to the rich Cancer Genome Atlas data to study the (epi)genetic alterations of 186 KEGG pathways in the development of serous ovarian cancer. To make use of the comprehensive data, we incorporate three data types in the analysis representing gene expression level, copy number and DNA methylation level. Our analysis suggests a list of nine pathways that are closely associated with serous ovarian cancer progression, including cell cycle, ERBB, JAK-STAT signaling and p53 signaling pathways. By pairwise tests, we found that most of the identified pathways contribute only to a particular transition step. For instance, the cell cycle and ERBB pathways play key roles in the early-stage transition, while the ECM receptor and apoptosis pathways contribute to the progression from stage III to stage IV. The proposed computational pipeline is powerful in detecting important pathways and gene sets that drive cancers at certain stage(s). It offers new insights into the understanding of molecular mechanism of cancer initiation and progression. © 2020 Elsevier Ltd
The qualified subjects for this study included 33 patients with benign and malignant oral tumors aged 15-75 years and 31 matched age and gender healthy subjects used as control. Proteins measurements included total protein, albumin, globulines in sera and saliva samples, and immunoglobulins (IgG, IgM, IgA) in sera samples of control and patients. Meanwhile, polyacrylamide gel electrophoresis (PAGE) was used to differentiate between protein patterns in both serum and saliva samples among the studied groups. The gel was also stained for glycoprotein to evaluate as well the changes in glycoprotein contents. For total protein, the results revealed a signifigant increase (P?0.01) in both samples (serum and saliva) of patient group. Albumin conce
... Show MoreThe educational sector is one of the important sectors in the world, and it is considered one of the means of community development. In addition, it is one of the means of making the country’s renaissance and devel-opment because it represents the factory of thinking minds that make change. There is no doubt that this sector is the same as any other sector. The deficit in the studied scientific planning has been prolonged, which led to its deterioration, and the problems of education remain diverse and inherited from previous time periods, where the hierarchical cluster analysis was used on postgraduate students in universities in Iraq, except for Kurdistan region, and the number of universities that were included in the study was
... Show MoreNonlinear time series analysis is one of the most complex problems ; especially the nonlinear autoregressive with exogenous variable (NARX) .Then ; the problem of model identification and the correct orders determination considered the most important problem in the analysis of time series . In this paper , we proposed splines estimation method for model identification , then we used three criterions for the correct orders determination. Where ; proposed method used to estimate the additive splines for model identification , And the rank determination depends on the additive property to avoid the problem of curse dimensionally . The proposed method is one of the nonparametric methods , and the simulation results give a
... Show MoreThree cultivars of the crop Almash (Green Indian VC6089A10, Green Indian VC6173B1319, and Black Indian Gold Star) were tested in a field experiment during the 2022 growing season in Ramadi, Anbar province, to determine the impact of spraying levels of zinc (0, 25, and 50) mg Zn L-1 and manganese (0, 30, and 60) mg Mn L-1 on some growth characteristics. The experiment was conducted using a randomized complete block design (RCBD) with three replicates, with each treatment being tested in a separate split plot. The study found that there were statistically significant differences between zinc levels, with the level giving 50 mg Zn L-1
The possibility of using activated carbon developed from date palm seeds wastes as a permeable reactive barrier (PRB) to remove copper from polluted shallow groundwater was investigated. The activated carbon has been developed from date palm seeds by dehydrating methods using concentrated sulfuric acid. Batch tests were performed to characterize the equilibrium sorption properties of new activated carbon in copper-containing aqueous solutions, while the sandy soil (aquifer) was assumed to be inert. Under the studied conditions, the Langmuir isotherm model gives a better fit for the sorption data of copper by activated carbon than other models. At a pilot scale, One-dimensional column experiments were performed, and an integrated model ba
... Show MoreIn this paper, a procedure to establish the different performance measures in terms of crisp value is proposed for two classes of arrivals and multiple channel queueing models, where both arrival and service rate are fuzzy numbers. The main idea is to convert the arrival rates and service rates under fuzzy queues into crisp queues by using graded mean integration approach, which can be represented as median rule number. Hence, we apply the crisp values obtained to establish the performance measure of conventional multiple queueing models. This procedure has shown its effectiveness when incorporated with many types of membership functions in solving queuing problems. Two numerical illustrations are presented to determine the validity of the
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