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 development of better tools for diagnosis and more accurate prognosis of cancer includes the search for biomarkers; molecules whose presence, absence or change in quantity or structure is associated with a particular tumour or prognosis/therapeutic outcome. While biomarkers need not be functionally relevant, if cell survival, then they could also provide new targets for therapeutic drugs. In recent years attention has been applied to a group of proteins known as cancer testis antigens (CT antigens) [1]. These proteins are products of genes whose expression was normally confined to the testis, yet they are expressed in tumour cells. CT genes are bound to serve a wide array of roles in the testes, which have many highly differentiated cel
... Show MoreGas and downhole water sink assisted gravity drainage (GDWS-AGD) is a promising gas-based enhanced oil recovery (EOR) process applicable for reservoirs associated with infinite aquifers. However, it can be costly to implement because it typically involves the drilling of multiple vertical gas-injection wells. The drilling and well-completion costs can be substantially reduced by using additional completions for gas injection in the oil production wells through the annulus positioned at the top of the reservoir. Multi-completion-GDWS-AGD (MC-GDWS-AGD) can be configured to include separate completions for gas injection, oil, and water production in individual wells. This study simulates
The Sebkha of geomorphological aspects of evaporative where climate leads active role, which forms part of the earth's surface in the form of Iraqi Mesopotamia plain who of the most fertile land, and because of natural factors and human Common turned most of the arable land to the territory of Sebkha. It was to determine the exact geomorphological associated of Sebkha formats by field work such as: Alnbaka, lakes, salt flats, and other forms of Small is: bridges salt, mud cracks, salt ponds, Rectangles and polygons salt, Sahaf salt, salt domes, salt gravel, bumps saline (salt points), Ash salt, salt bows, in detail and accurately documented Terrestrial Photogrammetry field and were compared to the levels and standards varieties have been
... Show MoreIdentifying the total number of fruits on trees has long been of interest in agricultural crop estimation work. Yield prediction of fruits in practical environment is one of the hard and significant tasks to obtain better results in crop management system to achieve more productivity with regard to moderate cost. Utilized color vision in machine vision system to identify citrus fruits, and estimated yield information of the citrus grove in-real time. Fruit recognition algorithms based on color features to estimate the number of fruit. In the current research work, some low complexity and efficient image analysis approach was proposed to count yield fruits image in the natural scene. Semi automatic segmentation and yield calculation of fruit
... Show MoreAlzheimer’s disease (AD) is an age-related progressive and neurodegenerative disorder, which is characterized by loss of memory and cognitive decline. It is the main cause of disability among older people. The rapid increase in the number of people living with AD and other forms of dementia due to the aging population represents a major challenge to health and social care systems worldwide. Degeneration of brain cells due to AD starts many years before the clinical manifestations become clear. Early diagnosis of AD will contribute to the development of effective treatments that could slow, stop, or prevent significant cognitive decline. Consequently, early diagnosis of AD may also be valuable in detecting patients with dementia who have n
... Show MoreIn this research, silver nanoparticles (AgNPs) were manufactured using aqueous extract of mushroom Pleurotus ostreatus. Anticancer potential of AgNPs was investigated versus human breast cancer cell line (MCF-7). Cytotoxic response was assessed by MTT assay. AgNPs showed inhibition effect at the following concentrations 12.5, 25, 50, 100 and 200 µg/ml versus MCF-7 cell line, and all treatments had a positive result. The MCF-7 cells were inhibited up to 85.14 % at the concentration 200 μg/ml of AgNPs which reduced cells viability to 14.86%, while 12.5 μg/ml of AgNPs caused 24.23% cells inhibition with reduction of cells viability to 75.77%.