4.8 Article

Improved biomarker discovery through a plot twist in transcriptomic data analysis

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Cell Biology

Weighted gene co-expression network analysis can sort cancer-associated fibroblast-specific markers promoting bladder cancer progression

Bitian Liu et al.

Summary: The study found that the cell fraction of cancer-associated fibroblasts (CAFs) gradually increased with the progression of bladder urothelial carcinoma (BLCA), and these CAFs have a specific gene expression module that is relevant to cancer progression and survival status. 15 key genes act as BLCA-specific CAF markers and can predict CAF changes in BLCA.

JOURNAL OF CELLULAR PHYSIOLOGY (2021)

Article Respiratory System

Transcriptome analysis of IPF fibroblastic foci identifies key pathways involved in fibrogenesis

Delphine Guillotin et al.

Summary: This study aimed to identify major transcriptional programs in idiopathic pulmonary fibrosis (IPF) by profiling myofibroblasts in fibrotic foci using novel data mining strategies and weighted gene co-expression network analysis (WGCNA). The findings revealed clusters of genes associated with cell cycle, inflammation/differentiation, translation, and cytoskeleton/cell adhesion, with key signaling pathways like TGF-beta 1, RhoA kinase, and the TSC2/RHEB axis influencing collagen gene expression. Functional studies using CRISPR-Cas9 gene-edited cells demonstrated the potential role of the TSC2/RHEB axis in regulating excessive matrix deposition in IPF and other fibrotic conditions.

THORAX (2021)

Article Multidisciplinary Sciences

Unraveling the genotype by environment interaction in a thermosensitive fish with a polygenic sex determination system

Benjamin Geffroy et al.

Summary: The study used the European sea bass as a model to investigate a polygenic sex determination system and its interaction with temperature. Findings suggest that energetic pathways play a role in sex determination, and early exposure to high temperature may affect sex development by regulating specific gene expressions.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Multidisciplinary Sciences

Transcriptome analysis of the procession from chronic pancreatitis to pancreatic cancer and metastatic pancreatic cancer

Jihao Tu et al.

Summary: This study analyzed transcriptome data and constructed co-expression networks to reveal gradually activated gene networks during the progression of pancreatic diseases. The number of differentially expressed genes increases as the pancreatic disease worsens, with upregulation of gene networks involving T cells and interferon.

SCIENTIFIC REPORTS (2021)

Article Genetics & Heredity

Transcriptome Characterization of Short Distance Transport Stress in Beef Cattle Blood

Haidong Zhao et al.

Summary: The study revealed that short distance transportation increased white blood cell count significantly, indicating a resilience to oxidative stress. It also showed that energy expenditure was increased after transportation, but not enough to activate fatty decomposition. Moreover, short distance transportation may affect cattle health by disrupting B cell differentiation, proliferation, survival, and apoptosis mechanisms.

FRONTIERS IN GENETICS (2021)

Review Genetics & Heredity

Diverse Regulation but Conserved Function: SOX9 in Vertebrate Sex Determination

Brittany Vining et al.

Summary: Sex determination is a crucial process early in vertebrate embryogenesis, involving a variety of molecular switches and genes. SOX9 plays a central role in male gonadal differentiation, being positively regulated in males and negatively regulated in females. Despite diversity among vertebrates, the protein sequence and function of SOX9 remains highly conserved.
Review Physiology

SEX DETERMINATION, GONADAL SEX DIFFERENTIATION, AND PLASTICITY IN VERTEBRATE SPECIES

Yoshitaka Nagahama et al.

Summary: A diverse array of sex determination mechanisms exist among vertebrates, with the major milestone being the discovery of the SRY gene in mammals. Significant progress has been made in understanding the molecular and cellular mechanisms involved in vertebrate sex determination and gonadal sex differentiation over the past three decades. The discovery of a large diversity of sex determination genes suggests the complexity and evolutionary implications of this biological event.

PHYSIOLOGICAL REVIEWS (2021)

Review Genetics & Heredity

Comparative Analyses of Gene Co-expression Networks: Implementations and Applications in the Study of Evolution

Katie Ovens et al.

Summary: Comparing gene co-expression networks across species can provide insights into evolutionary relationships, identifying evidence of conservation or adaptation. However, challenges such as the lack of comparative datasets and limitations of protein-protein interaction methods hinder the study of evolution using these networks.

FRONTIERS IN GENETICS (2021)

Article Biochemistry & Molecular Biology

Transcriptome analysis and weighted gene co-expression network reveals potential genes responses to heat stress in turbot Scophthalmus maximus

Zhihui Huang et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS (2020)

Article Biochemistry & Molecular Biology

Co-Expression Network Analysis of Spleen Transcriptome in Rock Bream (Oplegnathus fasciatus) Naturally Infected with Rock Bream Iridovirus (RBIV)

Ahran Kim et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Review Reproductive Biology

Gonadal development and sex determination in mouse

Ecem Yildirim et al.

REPRODUCTIVE BIOLOGY (2020)

Article Obstetrics & Gynecology

Dynamics of the transcriptional landscape during human fetal testis and ovary development

Estelle Lecluze et al.

HUMAN REPRODUCTION (2020)

Review Computer Science, Software Engineering

Use of Big Data Tools and Industrial Internet of Things: An Overview

Yingzi Wang et al.

SCIENTIFIC PROGRAMMING (2020)

Article Biochemistry & Molecular Biology

A comprehensive analysis of WGCNA and serum metabolomics manifests the lung cancer-associated disordered glucose metabolism

Mingchao Ding et al.

JOURNAL OF CELLULAR BIOCHEMISTRY (2019)

Article Biotechnology & Applied Microbiology

Characterization of the European Sea Bass (Dicentrarchus labrax) Gonadal Transcriptome During Sexual Development

L. Ribas et al.

MARINE BIOTECHNOLOGY (2019)

Review Biology

Comparison of Methods for Differential Co-expression Analysis for Disease Biomarker Prediction

Tulika Kakati et al.

COMPUTERS IN BIOLOGY AND MEDICINE (2019)

Article Multidisciplinary Sciences

Identification of crucial genes in abdominal aortic aneurysm by WGCNA

Siliang Chen et al.

Article Biochemistry & Molecular Biology

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

Huaiyu Mi et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Urology & Nephrology

Regulation of masculinization: androgen signalling for external genitalia development

Shoko Matsushita et al.

NATURE REVIEWS UROLOGY (2018)

Article Multidisciplinary Sciences

Transcriptome and epigenome landscape of human cortical development modeled in organoids

Anahita Amiri et al.

SCIENCE (2018)

Review Genetics & Heredity

Vertebrate sex determination: evolutionary plasticity of a fundamental switch

Blanche Capel

NATURE REVIEWS GENETICS (2017)

Article Multidisciplinary Sciences

Heat-induced masculinization in domesticated zebrafish is family-specific and yields a set of different gonadal transcriptomes

Laia Ribas et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Review Biochemical Research Methods

Transcriptomics technologies

Rohan Lowe et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Multidisciplinary Sciences

Expansion by whole genome duplication and evolution of the sox gene family in teleost fish

Emilien Voldoire et al.

PLOS ONE (2017)

Article Biochemical Research Methods

Glimma: interactive graphics for gene expression analysis

Shian Su et al.

BIOINFORMATICS (2017)

Article Endocrinology & Metabolism

Integrative Analysis of Genomics and Transcriptome Data to Identify Potential Functional Genes of BMDs in Females

Yuan-Cheng Chen et al.

JOURNAL OF BONE AND MINERAL RESEARCH (2016)

Article Biotechnology & Applied Microbiology

Effect of BMP-6 on development and maturation of mouse preantral follicles in vitro

Xiyan Wang et al.

BIOTECHNOLOGY & BIOTECHNOLOGICAL EQUIPMENT (2015)

Article Biotechnology & Applied Microbiology

Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq

Katie L. Ayers et al.

BMC GENOMICS (2015)

Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

Article Biochemistry & Molecular Biology

limma powers differential expression analyses for RNA-sequencing and microarray studies

Matthew E. Ritchie et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

Transcriptome analyses reveal molecular mechanisms underlying functional recovery after spinal cord injury

Hongmei Duan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Genetics & Heredity

Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations

Ovidiu D. Iancu et al.

FRONTIERS IN GENETICS (2015)

Article Statistics & Probability

FastRFunctions for Robust Correlations and Hierarchical Clustering

Peter Langfelder et al.

Journal of Statistical Software (2015)

Article Biochemistry & Molecular Biology

Epigenetic modification and inheritance in sexual reversal of fish

Changwei Shao et al.

GENOME RESEARCH (2014)

Article Biochemical Research Methods

Topological analysis and interactive visualization of biological networks and protein structures

Nadezhda T. Doncheva et al.

NATURE PROTOCOLS (2012)

Article Biochemistry & Molecular Biology

Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress

Charu Lata et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2010)

Article Biochemical Research Methods

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules

Bruno M. Tesson et al.

BMC BIOINFORMATICS (2010)

Article Multidisciplinary Sciences

Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways

Jeremy A. Miller et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Evolutionary Biology

Expression Profiles of Sex Differentiation-Related Genes During Ontogenesis in the European Sea Bass Acclimated to Two Different Temperatures

Mercedes Blazquez et al.

JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION (2009)

Review Genetics & Heredity

RNA-Seq: a revolutionary tool for transcriptomics

Zhong Wang et al.

NATURE REVIEWS GENETICS (2009)

Article Biochemical Research Methods

WGCNA: an R package for weighted correlation network analysis

Peter Langfelder et al.

BMC BIOINFORMATICS (2008)

Article Neurosciences

Functional organization of the transcriptome in human brain

Michael C. Oldham et al.

NATURE NEUROSCIENCE (2008)

Article Biochemical Research Methods

Geometric Interpretation of Gene Coexpression Network Analysis

Steve Horvath et al.

PLOS COMPUTATIONAL BIOLOGY (2008)

Article Biochemistry & Molecular Biology

Foxl2 is required for commitment to ovary differentiation

C Ottolenghi et al.

HUMAN MOLECULAR GENETICS (2005)

Article Biochemistry & Molecular Biology

A general framework for weighted gene co-expression network analysis

Bin Zhang et al.

STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY (2005)

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)

Article Biochemistry & Molecular Biology

Regulation of follicle-stimulating hormone (FSH) and luteinizing hormone (LH) gene expression by gonadotropin-releasing hormone (GnRH) and sexual steroids in the Mediterranean Sea bass

J Mateos et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY (2002)

Article Biochemistry & Molecular Biology

Characterization of neuropeptide Y expression in the brain of a perciform fish, the sea bass (Dicentrarchus labrax)

JM Cerdá-Reverter et al.

JOURNAL OF CHEMICAL NEUROANATOMY (2000)