E. Kavitha^1,*, R. Tamilarasan², Arunadevi Baladhandapani³, M. K. Jayanthi Kannan⁴

Computer Systems Science and Engineering, Vol.43, No.3, pp. 871-886, 2022, DOI:10.32604/csse.2022.021215

Abstract Gene expression data represents a condition matrix where each row represents the gene and the column shows the condition. Micro array used to detect gene expression in lab for thousands of gene at a time. Genes encode proteins which in turn will dictate the cell function. The production of messenger RNA along with processing the same are the two main stages involved in the process of gene expression. The biological networks complexity added with the volume of data containing imprecision and outliers increases the challenges in dealing with them. Clustering methods are hence essential to identify the patterns present in… More >

MING-AO CAO¹, FEI ZHANG², ELSAYED FATHI ABD_ALLAH³, QIANGSHENG WU^1,*

BIOCELL, Vol.46, No.8, pp. 1959-1966, 2022, DOI:10.32604/biocell.2022.020391

Abstract A potted experiment was carried out to study the effect of an arbuscular mycorrhizal fungus (Diversispora versiformis) and arbuscular mycorrhizal like fungus (Piriformospora indica) on antioxidant enzyme defense system of Satsuma orange (Citrus sinensis cv. Oita 4) grafted on Poncirus trifoliata under favourable temperature (25°C) and cold temperature (0°C) for 12 h. Such short-term treatment of cold temperature did not cause any significant change in root fungal colonization and spore density in soil. Under cold stress, D. versiformis inoculation did not change the activity of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) in leaves and roots, whereas P. indica… More >

IVANA SAMARŽIJA^1,2,*

BIOCELL, Vol.46, No.7, pp. 1747-1750, 2022, DOI:10.32604/biocell.2022.018784

Abstract Comparisons of gene expression profiles between primary tumors and metastasis have revealed genes that are implicated in metastasis formation. However, gene expression studies conducted on metastasis samples from the same primary site usually do not discriminate between different secondary sites. Although the change in the expression of number of genes is expected to be common to metastasis from the same primary but different secondary sites, herein the data that point to substantial differences are presented. Furthermore, the reciprocal communication between metastatic and host cells that is influencing these differences is outlined to emphasize the need for stratification of metastasis samples… More >

Peipei Hong^1,#, Mei Wang^2,#, Liting Zhi², Hongwei Chen^2,3,4,*, Kefeng Liu¹, Hongli Wang²

Phyton-International Journal of Experimental Botany, Vol.91, No.6, pp. 1211-1226, 2022, DOI:10.32604/phyton.2022.018435

Abstract The branching system of higher plants plays a very important role in plant morphogenesis, and the number of branches can directly affect crop yield and the ornamental value of plants. It is a complicated development process involving complex molecular mechanisms. The ‘Cailinghong’ variety of Salvia splendens is characterized by its great branching ability with the ability to grow into a spherical form naturally, without pinching. To gain insight into the molecular events during the branching development of S. splendens, suppressive subtractive hybridization (SSH) technology was used to screen differentially expressed genes between the erect plant type (strain 35) and the… More >

S. Jacophine Susmi^*

Intelligent Automation & Soft Computing, Vol.33, No.2, pp. 1139-1152, 2022, DOI:10.32604/iasc.2022.023865

Abstract The classification of cancer subtypes is substantial for the diagnosis and treatment of cancer. However, the gene expression data used for cancer subtype classification are high dimensional in nature and small in sample size. In this paper, an efficient dimensionality reduction with optimized long short term memory, algorithm (OLSTM) is used for gene expression data classification. The main three stages of the proposed method are explicitly pre-processing, dimensional reduction, and gene expression data classification. In the pre-processing method, the missing values and redundant values are removed for high-quality data. Following, the dimensional reduction is done by orthogonal locality preserving projections… More >

K. Poongodi^1,*, A. Sabari²

Intelligent Automation & Soft Computing, Vol.33, No.2, pp. 939-953, 2022, DOI:10.32604/iasc.2022.023038

Abstract The microarray gene expression data has a large number of genes with different expression levels. Analyzing and classifying datasets with entire gene space is quite difficult because there are only a few genes that are informative. The identification of bio-marker genes is significant because it improves the diagnosis of cancer disease and personalized medicine is suggested accordingly. Initially, the parallelized minimum redundancy and maximum relevance ensemble (mRMRe) is employed to select top m informative genes. The selected genes are then fed into the Genetic Algorithm (GA) that selects the optimal set of genes heuristically, which uses Mahalanobis Distance (MD) as… More >

Ying Liu^1,3,*, Jingye Chen^1,3, Xiaohao Li^1,3, Shaoxia Yang¹, Hanqiao Hu^1,3, Yingbin Xue^2,3,*

Phyton-International Journal of Experimental Botany, Vol.91, No.5, pp. 975-987, 2022, DOI:10.32604/phyton.2022.019057

Abstract In order to investigate the effects of Manganese (Mn) toxicity stress on the growth and gene expression at the seedling stage of soybean, soybean seedlings were treated with normal Mn concentration (5 μmol/L MnSO₄) and excess Mn concentration (100 μmol/L MnSO₄) by the method of hydroponic culture in this study. When soybean was subjected to Mn toxicity stress, excessive Mn could affect seedling growth, root development, the number of Mn oxide spots in leaves, and the Mn accumulation content in different parts of soybean. With the increase of exogenous Mn concentration and the prolongation of culture time, the shoot and… More >

YI HUANG^1,2, CHUNFENG DOU², XUMING HU², HENGMI CUI^2,*

BIOCELL, Vol.46, No.4, pp. 961-967, 2022, DOI:10.32604/biocell.2022.018131

Abstract Metformin is a first-line drug in the fight against type 2 diabetes. In recent years, studies have shown that metformin has some preventive and therapeutic effects on liver cancer, but the effects of metformin on the gene expression of liver cancer cells are not fully known. This study focused on the differences in the gene expression profiles in liver cancer cells treated with or without metformin. A total of 153 differentially expressed genes (DEGs) (FC > 2 and q-values < 0.001) were found, including 77 upregulated genes and 76 downregulated genes. These DEGs are involved in mitogen-activated protein kinase (MAPK),… More >

Hans Christian Correa-Aguado^1,3, Gloria Viviana Cerrillo-Rojas¹, Alejandro Rocha-Uribe², Ruth Elena Soria-Guerra², José Francisco Morales-Domínguez^1,*

Phyton-International Journal of Experimental Botany, Vol.91, No.4, pp. 903-903, 2022, DOI:10.32604/phyton.2022.020625

Abstract This article has no abstract. More >

Huaqiao Ding^*, Lihui Mao, Qingcheng Zou, Wei Hu, Xuerui Cao, Qing Dong^*

Phyton-International Journal of Experimental Botany, Vol.91, No.4, pp. 773-789, 2022, DOI:10.32604/phyton.2022.018075

Abstract Snapdragon (Antirrhinum majus) is one of the most widely cultivated grass flowers in the world. WRKY transcription factors, VQ proteins and their interactions play crucial roles in plant response to abiotic stresses. However, little is known about WRKY and VQ gene families in snapdragon. In the present study, WRKY and VQ genes and their interactions were comprehensively analyzed in snapdragon using bioinformatics approaches, and their expression in response to drought and cold stresses was examined using real-time PCR. A total of 67 AmWRKY genes were identified in snapdragon, which were classified into different groups or subgroups based on phylogenetic analysis.… More >