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
AA wahid, journal mustansiriyah of sports science, 2023
Absence or hypoplasia of the internal carotid artery (ICA) is a rare congenital anomaly that is mostly unilateral and highly associated with other intracranial vascular anomalies, of which saccular aneurysm is the most common. Blood flow to the circulation of the affected side is maintained by collateral pathways, some of which include the anterior communicating artery (Acom) as part of their anatomy. Therefore, temporary clipping during microsurgery on Acom aneurysms in patients with unilateral ICA anomalies could jeopardize these collaterals and place the patient at risk of ischemic damage. In this paper, we review the literature on cases with a unilaterally absent ICA associa
In the presence of deep submicron noise, providing reliable and energy‐efficient network on‐chip operation is becoming a challenging objective. In this study, the authors propose a hybrid automatic repeat request (HARQ)‐based coding scheme that simultaneously reduces the crosstalk induced bus delay and provides multi‐bit error protection while achieving high‐energy savings. This is achieved by calculating two‐dimensional parities and duplicating all the bits, which provide single error correction and six errors detection. The error correction reduces the performance degradation caused by retransmissions, which when combined with voltage swing reduction, due to its high error detection, high‐energy savings are achieved. The res
... Show MoreA three-stage learning algorithm for deep multilayer perceptron (DMLP) with effective weight initialisation based on sparse auto-encoder is proposed in this paper, which aims to overcome difficulties in training deep neural networks with limited training data in high-dimensional feature space. At the first stage, unsupervised learning is adopted using sparse auto-encoder to obtain the initial weights of the feature extraction layers of the DMLP. At the second stage, error back-propagation is used to train the DMLP by fixing the weights obtained at the first stage for its feature extraction layers. At the third stage, all the weights of the DMLP obtained at the second stage are refined by error back-propagation. Network structures an
... Show MoreThis paper is concerned with introducing and studying the o-space by using out degree system (resp. i-space by using in degree system) which are the core concept in this paper. In addition, the m-lower approximations, the m-upper approximations and ospace and i-space. Furthermore, we introduce near supraopen (near supraclosed) d. g.'s. Finally, the supra-lower approximation, supraupper approximation, supra-accuracy are defined and some of its properties are investigated.