1,582 results match your criteria weighted co-expression

Co-expression network analysis identifies novel molecular pathways associated with cadmium and pyriproxyfen testicular toxicity in Gammarus fossarum.

Aquat Toxicol 2021 Mar 26;235:105816. Epub 2021 Mar 26.

INRAE, UR RiverLy, Ecotoxicology Team. Centre de Lyon-Grenoble Auvergne Rhône-Alpes, 5 rue de la Doua CS 20244, 69625 Villeurbanne, France. Electronic address:

Omics approaches are continuously providing new clues on the mechanisms of action of contaminants in species of environmental relevance, contributing to the emergence of molecular ecotoxicology. Co-expression network approaches represent a suitable methodological framework for studying the rich content of omics datasets. This study aimed to find evidence of key pathways and proteins related to the testicular toxicity in the sentinel crustacean species Gammarus fossarum exposed to endocrine disruptors using a weighted protein co-expression network analysis. Read More

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Development of a four-gene prognostic model for clear cell renal cell carcinoma based on transcriptome analysis.

Genomics 2021 Apr 7. Epub 2021 Apr 7.

Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan 430022, China. Electronic address:

This study aimed to develop a prognostic model for clear cell renal cell carcinoma (ccRCC) based on transcriptome analysis. We screened Gene Expression Omnibus (GEO) database and the Cancer Genome Atlas (TCGA) database for gene expression data and clinical characteristics of ccRCC. After differentially expression analysis, we identified 533 key genes of the development of ccRCC. Read More

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Identification of transcriptomic signatures and crucial pathways involved in non-alcoholic steatohepatitis.

Endocrine 2021 Apr 10. Epub 2021 Apr 10.

Xiamen Diabetes Institute, The First Affiliated Hospital of Xiamen University, Xiamen, China.

Purpose: Our study aimed to uncover the crucial genes and functional pathways involved in the development of non-alcoholic steatohepatitis (NASH).

Methods: Liver transcriptome datasets were integrated with Robust rank aggregation (RRA) method, and transcriptomic signatures for NASH progression and fibrosis severity in NAFLD were developed. The functions of transcriptomic signatures were explored by multiple bioinformatic analyses, and their diagnostic role was also evaluated. Read More

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Identification of co-expression network correlated with different periods of adipogenic and osteogenic differentiation of BMSCs by weighted gene co-expression network analysis (WGCNA).

BMC Genomics 2021 Apr 10;22(1):254. Epub 2021 Apr 10.

Department of Orthopaedic Surgery, RWTH Aachen University Clinic, Pauwelsstraße 30, 52074, Aachen, Germany.

Background: The differentiation of bone marrow mesenchymal stem cells is a complex and dynamic process. The gene expression pattern and mechanism of different periods of adipogenic and osteogenic differentiation remain unclear. Additionally, the interaction between these two lineage determination requires further exploration. Read More

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Immune-Inhibitory Gene Expression is Positively Correlated with Overall Immune Activity and Predicts Increased Survival Probability of Cervical and Head and Neck Cancer Patients.

Front Mol Biosci 2021 23;8:622643. Epub 2021 Mar 23.

The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia.

Limited immunotherapy options are approved for the treatment of cervical cancer and only 10-25% of patients respond effectively to checkpoint inhibition monotherapy. To aid the development of novel therapeutic immune targets, we aimed to explore survival-associated immune biomarkers and co-expressed immune networks in cervical cancer. Using The Cancer Genome Atlas (TCGA) Cervical Squamous Cell Carcinoma (CESC) data ( = 304), we performed weighted gene co-expression network analysis (WGCNA), and determined which co-expressed immune-related genes and networks are associated with survival probability in CESC patients under conventional therapy. Read More

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Identification and validation of key non-coding RNAs and mRNAs using co-expression network analysis in pre-eclampsia.

Medicine (Baltimore) 2021 Apr;100(14):e25294

Department of Obstetrics and Gynecology, The 2nd Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China.

Abstract: Pre-eclampsia (PE) is a common complication of pregnancy, associated with maternal and fetal morbidity and mortality. In this study, we aimed to explore important long non-coding RNAs (lncRNAs) and their possible mechanisms in PE.GSE60438 expression profile including 25 PE samples and 23 normal samples were obtained from gene expression omnibus (GEO) database. Read More

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Decreased CSTA expression promotes lymphatic metastasis and predicts poor survival in oral squamous cell carcinoma.

Arch Oral Biol 2021 Mar 31;126:105116. Epub 2021 Mar 31.

Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China; National Center for Stomatology, Shanghai, 200011, China; National Clinical Research Center for Oral Diseases, Shanghai, 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China.

Objective: Herein, we aimed to identify biomarkers that affect lymphatic metastasis of oral squamous cell carcinoma (OSCC) through bioinformatic analysis, and clinicopathological and in vitro verifications.

Design: The OSCC-related gene expression dataset was retrieved from The Cancer Genome Atlas (TCGA) and analyzed to identify differentially expressed genes (DEGs), which were subjected to pathway analysis. Weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network analysis were performed to identify hub genes. Read More

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Prognostic alternative splicing regulatory network of RBM25 in hepatocellular carcinoma.

Bioengineered 2021 Dec;12(1):1202-1211

Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.

RNA-binding motif protein 25 (RBM25) is a poorly characterized RNA-binding protein that is involved in several biological processes and regulates the proliferation and metastasis of tumor cells. The regulatory role of RBM25 in hepatocellular carcinoma (HCC) is unknown. Here, RBM25 expression and outcomes in HCC patients were evaluated using The Cancer Genome Atlas database. Read More

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December 2021

Transcriptional changes through menstrual cycle reveal a global transcriptional derepression underlying the molecular mechanism involved in the window of implantation.

Mol Hum Reprod 2021 Apr 8. Epub 2021 Apr 8.

Department of Genomic & Systems Reproductive Medicine, IVI-RMA IVI Foundation - Instituto de Investigación Sanitaria Hospital Universitario y Politécnico La Fe, Av. Fernando Abril Martorell 106, Torre A, Planta 1a, 46026 Valencia, Spain.

The human endometrium is a dynamic tissue that only is receptive to host the embryo during a brief time in the middle secretory phase, called the window of implantation (WOI). Despite its importance, regulation of the menstrual cycle remains incompletely understood. The aim of this study was to characterize the gene cooperation and regulation of menstrual cycle progression, in order to dissect the molecular complexity underlying acquisition of endometrial receptivity for a successful pregnancy; and to provide the scientific community with detailed gene co-expression information throughout the menstrual cycle on a user-friendly web-tool database. Read More

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[Identification of Hub Genes for Ovarian Cancer Stem Cell Properties with Weighted Gene Co-expression Network Analysis].

Sichuan Da Xue Xue Bao Yi Xue Ban 2021 Mar;52(2):248-258

Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.

Objective: To investigate the significance of stemness-related genes in the diagnosis and treatment of ovarian cancer.

Methods: Key modules and genes were identified with weighted gene co-expression network analysis (WGCNA). The signal pathways of high expression of key genes were analyzed by gene set enrichment analysis (GSEA) and single cell sequencing data. Read More

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Identification of key genes associated with secondary metabolites biosynthesis by system network analysis in Valeriana officinalis.

J Plant Res 2021 Apr 7. Epub 2021 Apr 7.

Institute of Biotechnology, Shiraz University, 7144165186, Shiraz, Iran.

Valeriana officinalis is a medicinal plant, a source of bioactive chemical compounds and secondary metabolites which are applied in pharmaceutical industries. The advent of ethnomedicine has provided alternatives for disease treatment and has increased demands for natural products and bioactive compounds. A set of preliminary steps to answers for such demands can include integrative omics for systems metabolic engineering, as an approach that contributes to the understanding of cellular metabolic status. Read More

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High BLM Expression Predicts Poor Clinical Outcome and Contributes to Malignant Progression in Human Cholangiocarcinoma.

Front Oncol 2021 22;11:633899. Epub 2021 Mar 22.

Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

Molecular mechanisms underlying the tumorigenesis of a highly malignant cancer, cholangiocarcinoma (CCA), are still obscure. In our study, the CCA expression profile data were acquired from The Cancer Genome Atlas (TCGA) database, and differentially expressed genes (DEGs) in the TCGA-Cholangiocarcinoma (TCGA-CHOL) data set were utilized to construct a co-expression network weighted gene co-expression network analysis (WGCNA). The blue gene module associated with the histopathologic grade of CCA was screened. Read More

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M2 Macrophage Co-Expression Factors Correlate With Immune Phenotype and Predict Prognosis of Bladder Cancer.

Front Oncol 2021 22;11:609334. Epub 2021 Mar 22.

Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, China.

Purpose: Therapeutic targets of tumor-associated macrophages have been discovered and used clinically as immunotherapy. M2 macrophages are tumor-associated macrophages that promote cancer progression. This article explores the related factors and the effects of type M2 macrophages. Read More

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Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage (Brassica rapa L.) during vernalization.

BMC Genomics 2021 Apr 6;22(1):236. Epub 2021 Apr 6.

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Background: Vernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Although rapid bolting and flowering promote the reproduction of Chinese cabbages (Brassica rapa L. ssp. Read More

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Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations.

BMC Bioinformatics 2021 Apr 6;22(1):178. Epub 2021 Apr 6.

The Leiden Institute of Advanced Computer Science (LIACS), Snellius Gebouw, Niels Bohrweg 1, Leiden, The Netherlands.

Background: The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development and tumourigenesis. However, methods for translating these high-level concepts into data-level associations between hallmarks and genes (for high throughput analysis), vary widely between studies. The examination of different strategies to associate and map cancer hallmarks reveals significant differences, but also consensus. Read More

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Conserved Plasmodium protein (PF3D7_0406000) of unknown function, in-silico analysis and cellular localization.

Infect Genet Evol 2021 Apr 3:104848. Epub 2021 Apr 3.

Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India. Electronic address:

In spite of a decrease in malaria cases, the threat of malaria due to Plasmodium falciparum still prevails. The sequencing of Plasmodium falciparum reveals that approximately 60% of the Plasmodium genes code for hypothetical/putative proteins. Here we report an in silico characterization and localization of one such protein. Read More

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Single-cell RNA-seq reveals dynamic change in tumor microenvironment during pancreatic ductal adenocarcinoma malignant progression.

EBioMedicine 2021 Apr 2;66:103315. Epub 2021 Apr 2.

Department of General Surgery, Peking University First Hospital, Beijing, 100034, China. Electronic address:

Background: Pancreatic ductal adenocarcinoma (PDAC) is most aggressive among all gastrointestinal tumors. The complex intra-tumor heterogeneity and special tumor microenvironment in PDAC bring great challenges for developing effective treatment strategies. We aimed to delineate dynamic changes of tumor microenvironment components during PDAC malignant progression utilizing single-cell RNA sequencing. Read More

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Consensus analysis via weighted gene co-expression network analysis (WGCNA) reveals genes participating in early phase of acute respiratory distress syndrome (ARDS) induced by sepsis.

Bioengineered 2021 Dec;12(1):1161-1172

Department of Pulmonary Medicine, HwaMei Hospital, University of Chinese Academy of Sciences,Ningbo Institute of Life and Health Industry,University of Chinese Academy of Scienc, Ningbo, Zhejiang, China.

The understanding of mechanism during conversion from sepsis to sepsis-related ARDS remains limited. In this study, we collected gene expression matrix from the Gene Expression Omnibus (GEO) database and constructed networks using weighted gene co-expression network analysis (WGCNA) to identify the consensus and opposite modules between sepsis and sepsis-induced ARDS and obtained 27 consensus modules associated with sepsis and sepsis-related ARDS, including one model (160 genes) with opposite correlation and 1 sepsis-ARDS specific model with 34 genes. Differentially expressed genes analysis, functional enrichment and protein-protein interactions analyses of candidate genes were performed; 15 of these genes showed different expressions in sepsis-induced ARDS patients, compared with sepsis patients; genes were enriched in processes associated with ribosome, tissue mechanics and extracellular matrix. Read More

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December 2021

Temporal metabolic and transcriptomic characteristics crossing islets and liver reveal dynamic pathophysiology in diet-induced diabetes.

iScience 2021 Apr 5;24(4):102265. Epub 2021 Mar 5.

Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China.

To investigate the molecular mechanisms underlying islet dysfunction and insulin resistance in diet-induced diabetes, we conducted temporal RNA sequencing of tissues responsible for insulin secretion (islets) and action (liver) every 4 weeks in mice on high-fat (HFD) or chow diet for 24 weeks, linking to longitudinal profile of metabolic characteristics. The diverse responses of α, β, and δ cells to glucose and palmitate indicated HFD-induced dynamic deterioration of islet function from dysregulation to failure. Insulin resistance developed with variable time course in different tissues. Read More

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Identification of Biomarkers Related to CD8 T Cell Infiltration With Gene Co-expression Network in Lung Squamous Cell Carcinoma.

Front Cell Dev Biol 2021 18;9:606106. Epub 2021 Mar 18.

Department of Cardiothoracic Surgery, The Second Affiliated Hospital, University of South China, Hengyang, China.

Lung squamous cell carcinoma (LSCC) is one of the most common types of lung cancer in adults worldwide. With the development of modern medicine, cancer treatment that harnesses the power of the immune system might be particularly effective for treating LSCC. In this research, LSCC expression data, which quantify the cellular composition of immune cells, were analyzed by weighted gene coexpression network analysis (WGCNA) and a deconvolution algorithm based on the Gene Expression Omnibus (GEO) database, and the results indicated a close relationship between LSCC and CD8 T cells. Read More

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Construction of Gene Modules and Analysis of Prognostic Biomarkers for Cervical Cancer by Weighted Gene Co-Expression Network Analysis.

Front Oncol 2021 18;11:542063. Epub 2021 Mar 18.

Department of Pathology, The Shengjing Hospital of China Medical University, Shenyang, China.

Background: Despite advances in the understanding of neoplasm, patients with cervical cancer still have a poor prognosis. Identifying prognostic markers of cervical cancer may enable early detection of recurrence and more effective treatment.

Methods: Gene expression profiling data were acquired from the Gene Expression Omnibus database. Read More

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Molecular Subtypes and CD4 Memory T Cell-Based Signature Associated With Clinical Outcomes in Gastric Cancer.

Front Oncol 2020 17;10:626912. Epub 2021 Mar 17.

Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.

Background: CD4 memory T cells are an important component of the tumor microenvironment (TME) and affect tumor occurrence and progression. Nevertheless, there has been no systematic analysis of the effect of CD4 memory T cells in gastric cancer (GC).

Methods: Three datasets obtained from microarray and the corresponding clinical data of GC patients were retrieved and downloaded from the Gene Expression Omnibus (GEO) database. Read More

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Epigenetic Age Acceleration of Stomach Adenocarcinoma Associated With Tumor Stemness Features, Immunoactivation, and Favorable Prognosis.

Front Genet 2021 18;12:563051. Epub 2021 Mar 18.

Center of Digestive Disease, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.

Abnormal DNA methylation (DNAm) age has been assumed to be an indicator for canceration and all-cause mortality. However, associations between DNAm age and molecular features of stomach adenocarcinoma (STAD), and its prognosis have not been systematically studied. We calculated the DNAm age of 591 STAD samples and 115 normal stomach samples from The Cancer Genome Atlas (TCGA) and gene expression omnibus (GEO) database using the Horvath's clock model. Read More

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, and as Novel Panel for Pancreatic Cancer: A Bioinformatics Analysis and Experiments Validation.

Front Immunol 2021 18;12:649551. Epub 2021 Mar 18.

Laboratory of Molecular Biology, Henan Luoyang Orthopedic Hospital (Henan Provincial Orthopedic Hospital), Zhengzhou, China.

Pancreatic cancer is a lethal malignancy with a poor prognosis. This study aims to identify pancreatic cancer-related genes and develop a robust diagnostic model to detect this disease. Weighted gene co-expression network analysis (WGCNA) was used to determine potential hub genes for pancreatic cancer. Read More

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Age and Sex-Related Changes in Human First-Trimester Placenta Transcriptome and Insights into Adaptative Responses to Increased Oxygen.

Int J Mol Sci 2021 Mar 12;22(6). Epub 2021 Mar 12.

Pathophysiology & Pharmacotoxicology of the Human Placenta, Pre & Postnatal Microbiota, Université de Paris, INSERM, 3PHM, F-75006 Paris, France.

Physiological oxygen tension rises dramatically in the placenta between 8 and 14 weeks of gestation. Abnormalities in this period can lead to gestational diseases, whose underlying mechanisms remain unclear. We explored the changes at mRNA level by comparing the transcriptomes of human placentas at 8-10 gestational weeks and 12-14 gestational weeks. Read More

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NF2 and Canonical Hippo-YAP Pathway Define Distinct Tumor Subsets Characterized by Different Immune Deficiency and Treatment Implications in Human Pleural Mesothelioma.

Cancers (Basel) 2021 Mar 29;13(7). Epub 2021 Mar 29.

Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China.

(1) Inactivation of the tumor suppressor NF2 is believed to play a major role in the pathogenesis of malignant pleural mesothelioma (MPM) by deregulating the Hippo-YAP signaling pathway. However, NF2 has functions beyond regulation of the Hippo pathway, raising the possibility that NF2 contributes to MPM via Hippo-independent mechanisms. (2) We performed weighted gene co-expression analysis (WGCNA) in transcriptomic and proteomic datasets obtained from The Cancer Gene Atlas (TCGA) MPM cohort to identify clusters of co-expressed genes highly correlated with NF2 and phospho (p)-YAP protein, surrogate markers of active Hippo signaling and YAP inactivation. Read More

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Identification of Chlorophyll Metabolism- and Photosynthesis-Related Genes Regulating Green Flower Color in Chrysanthemum by Integrative Transcriptome and Weighted Correlation Network Analyses.

Genes (Basel) 2021 Mar 21;12(3). Epub 2021 Mar 21.

Key Laboratory for Biology of Horticultural Plants, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.

Green chrysanthemums are difficult to breed but have high commercial value. The molecular basis for the green petal color in chrysanthemum is not fully understood. This was investigated in the present study by RNA sequencing analysis of white and green ray florets collected at three stages of flower development from the F progeny of the cross between "Lüdingdang" with green-petaled flowers and with white-petaled flowers. Read More

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Metabolomic Profiling Reveals Sex Specific Associations with Chronic Obstructive Pulmonary Disease and Emphysema.

Metabolites 2021 Mar 11;11(3). Epub 2021 Mar 11.

Division of Medicine, National Jewish Health, Denver, CO 80206, USA.

Susceptibility and progression of lung disease, as well as response to treatment, often differ by sex, yet the metabolic mechanisms driving these sex-specific differences are still poorly understood. Women with chronic obstructive pulmonary disease (COPD) have less emphysema and more small airway disease on average than men, though these differences become less pronounced with more severe airflow limitation. While small studies of targeted metabolites have identified compounds differing by sex and COPD status, the sex-specific effect of COPD on systemic metabolism has yet to be interrogated. Read More

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CARD-Associated Risk Score Features the Immune Landscape and Predicts the Responsiveness to Anti-PD-1 Therapy in IDH Wild-Type Gliomas.

Front Cell Dev Biol 2021 19;9:653240. Epub 2021 Mar 19.

Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, Guangzhou, China.

Background: Proteins containing the caspase recruitment domain (CARD) play critical roles in cell apoptosis and immunity. However, the impact of CARD genes in tumor immune cell infiltration, responsiveness to checkpoint immunotherapy, and clinical outcomes of gliomas remains unclear. Here, we explore using CARD genes to depict the immune microenvironment and predict the responsiveness of gliomas to anti-PD-1 therapy. Read More

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Functional Assessment of Four Novel Immune-Related Biomarkers in the Pathogenesis of Clear Cell Renal Cell Carcinoma.

Front Cell Dev Biol 2021 16;9:621618. Epub 2021 Mar 16.

Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.

Background: Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma whose pathogenesis is not well understood. We aimed at identifying novel immune-related biomarkers that could be valuable in the diagnosis and prognosis of ccRCC.

Methods: The Robust Rank Aggregation (RRA) method was used to integrate differently expressed genes (DEGs) of 7 Gene Expression Omnibus (GEO) datasets and obtain robust DEGs. Read More

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