(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 …

m6A RNA methylation regulators can contribute to malignant progression and impact the prognosis of bladder cancer

M Chen, Z Nie, X Wen, Y Gao, H Cao… - Bioscience …, 2019 - portlandpress.com
Abstract N6-methyladenosine (m6A) is the most common form of messenger RNA (mRNA)
modification. An increasing number of studies have proven that m6A RNA methylation …

[HTML][HTML] Changes in gene-gene interactions associated with cancer onset and progression are largely independent of changes in gene expression

Z Arshad, JF McDonald - Iscience, 2021 - cell.com
Recent findings indicate that changes underlying cancer onset and progression are not only
attributable to changes in DNA structure and expression of individual genes but to changes …

[HTML][HTML] Upregulation of HOXA11 during the progression of lung adenocarcinoma detected via multiple approaches

X Yang, Y Deng, RQ He, XJ Li… - International …, 2018 - spandidos-publications.com
The altered expression of homeobox (HOX) A11 has been observed in various malignant
tumor types, but it has remained to be determined in human lung adenocarcinoma (LUAD) …

Expressions of m6A RNA methylation regulators and their clinical predictive value in cervical squamous cell carcinoma and endometrial adenocarcinoma

H Wu, H Dong, Y Fu, Y Tang, M Dai… - Clinical and …, 2021 - Wiley Online Library
The mortality caused by cervical squamous cell carcinoma and endocervical
adenocarcinoma (CESC) ranks second among female malignant tumour deaths, but their …

Identification of hub genes distinguishing subtypes in endometrial stromal sarcoma through comprehensive bioinformatics analysis

R Zhang, W Zhao, X Zhu, Y Liu, Q Ding, C Yang… - Scientific Reports, 2024 - nature.com
Diagnosing low-grade and high-grade endometrial stromal sarcoma (LG-ESS and HG-ESS)
is a challenge. This study aimed to identify biomarkers. 22 ESS cases were analyzed using …

Lack of expression of miR-29a/b1 impairs bladder function in male mice

Z Wang, R Spitz, C Vezina, J Hou… - Disease models & …, 2023 - journals.biologists.com
Lower urinary tract symptoms (LUTS) refer to various urological diseases, and incomplete
bladder emptying is common among affected patients. The etiology of LUTS is largely …

[HTML][HTML] A computational approach to generate highly conserved gene co-expression networks with RNA-seq data

Z Arshad, JF McDonald - STAR protocols, 2022 - Elsevier
We describe a consensus approach for network construction based on fully conserved gene-
gene interactions from randomly downsampled data subsets for an unbiased differential …

Changes in Gene Network Interactions in Breast Cancer Onset and Development

Z Arshad, SN Housley, KK Lee, JF McDonald - GEN Biotechnology, 2024 - liebertpub.com
While cancer is generally recognized as a polygenic disease, specific “driver genes” have
been identified as promising candidates for targeted gene therapy. While this precision …

基于SNP 共表达网络肝癌分子分型及预后分析.

张思嘉, 蔡挺, 张顺 - Chinese Journal of Bioinformatics, 2022 - search.ebscohost.com
基于SNP 突变数据与mRNA 表达谱关联分析, 构建一种肝癌分子分型方法并对比不同分型预后
的差异, 并对不同分型肝癌的发生发展机制进一步研究. 首先通过TCGA 数据库收集359 …