(Differential) co-expression analysis of gene expression: a survey of best practices

HA Chowdhury, DK Bhattacharyya… - IEEE/ACM transactions …, 2019 - ieeexplore.ieee.org
Analysis of gene expression data is widely used in transcriptomic studies to understand
functions of molecules inside a cell and interactions among molecules. Differential co …

Fifteen years of gene set analysis for high-throughput genomic data: a review of statistical approaches and future challenges

S Das, CJ McClain, SN Rai - Entropy, 2020 - mdpi.com
Over the last decade, gene set analysis has become the first choice for gaining insights into
underlying complex biology of diseases through gene expression and gene association …

A network of SLC and ABC transporter and DME genes involved in remote sensing and signaling in the gut-liver-kidney axis

SB Rosenthal, KT Bush, SK Nigam - Scientific reports, 2019 - nature.com
Genes central to drug absorption, distribution, metabolism and elimination (ADME) also
regulate numerous endogenous molecules. The Remote Sensing and Signaling Hypothesis …

Identification of quantitative trait nucleotides and candidate genes for soybean seed weight by multiple models of genome-wide association study

B Karikari, Z Wang, Y Zhou, W Yan, J Feng, T Zhao - BMC plant biology, 2020 - Springer
Background Seed weight is a complex yield-related trait with a lot of quantitative trait loci
(QTL) reported through linkage mapping studies. Integration of QTL from linkage mapping …

Genome-wide association study of soybean (Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield …

R Rani, G Raza, H Ashfaq, M Rizwan… - Frontiers in Plant …, 2023 - frontiersin.org
Soybean (Glycine max [L.] Merr.) is one of the most significant crops in the world in terms of
oil and protein. Owing to the rising demand for soybean products, there is an increasing …

ITGA5 Predicts Dual-Drug Resistance to Temozolomide and Bevacizumab in Glioma

Y Shi, M Wu, Y Liu, L Hu, H Wu, L Xie, Z Liu… - Frontiers in …, 2021 - frontiersin.org
Aims Anti-angiotherapy (Bevacizumab) is currently regarded as a promising option for
glioma patients who are resistant to temozolomide (TMZ) treatment. But ongoing clinical …

Gene co-expression network analysis

JD Montenegro - Plant bioinformatics: methods and protocols, 2022 - Springer
Gene co-expression analysis is a data analysis technique that helps identify groups of
genes with similar expression patterns across several different conditions. By means of …

Multigroup prediction in lung cancer patients and comparative controls using signature of volatile organic compounds in breath samples

SN Rai, S Das, J Pan, DC Mishra, XA Fu - Plos one, 2022 - journals.plos.org
Early detection of lung cancer is a crucial factor for increasing its survival rates among the
detected patients. The presence of carbonyl volatile organic compounds (VOCs) in exhaled …

Identifying cancer targets based on machine learning methods via Chou's 5-steps rule and general pseudo components

R Liang, J Xie, C Zhang, M Zhang… - Current topics in …, 2019 - ingentaconnect.com
In recent years, the successful implementation of human genome project has made people
realize that genetic, environmental and lifestyle factors should be combined together to …

Integrated multiplex network based approach for hub gene identification in oral cancer

S Mahapatra, R Bhuyan, J Das, T Swarnkar - Heliyon, 2021 - cell.com
Abstract Background: The incidence of Oral Cancer (OC) is high in Asian countries, which
goes undetected at its early stage. The study of genetics, especially genetic networks holds …