Shail Rakesh Modi, Terrick Andey^*, George Acquaah-Mensah^*

Oncology Research, Vol.34, No.2, 2026, DOI:10.32604/or.2025.070793 - 19 January 2026

Abstract Objectives: The current treatment options and therapeutic targets for triple-negative breast cancer (TNBC), an aggressive subtype of breast cancer (BrCA), are limited. This study aimed to identify novel biomarkers and transcriptional regulatory networks (TRN) inherent in TNBC samples. Methods: We analyzed pan-cancer BrCA datasets from The Cancer Genome Atlas (TCGA) to compare triple-positive breast cancer (TPBC) with TNBC. TRN algorithms and virtual inference of protein-enriched regulon (VIPER) were used to identify master regulators and their target genes. Utilizing TNBC cells (MDA-MB-231 and MDA-MB-468), we validated the relationship of nuclear factor erythroid 2-like 3 (NFE2L3) and… More > Graphic Abstract

Jiawei Shi^1,2,3,#, Zhen Wang^1,2,3,#, Ying Bai^1,2,3, Shiying Li^1,2,3, Xin Zhang^1,2,3, Tianshu Liu^1,2,3, Liu Hong^1,2,3, Li Cui^1,2,3, Yi Zhang^1,2,3, Jing Ma^1,2,3, Juanjuan Liu^1,2,3, Jing Zhang^1,2,3, Haiyan Cao^1,2,3,*, Jing Wang^1,2,3,*

Congenital Heart Disease, Vol.20, No.2, pp. 213-229, 2025, DOI:10.32604/chd.2025.064950 - 30 April 2025

Abstract Background: Tetralogy of Fallot (TOF), the predominant cyanotic congenital heart defect, arises from multifactorial gene-environment interactions disrupting cardiac developmental networks. This study investigated TOF-specific transcriptional alterations and identified high-confidence candidate genes. Methods: Based on GSE36761 transcriptome data, a weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network were conducted to identify TOF-related sub-network and Hub genes. The potential biological functions among these genes were revealed by enrichment analysis. Genetic, epigenetic and transcriptional alteration in the Hub genes were analyzed with leveraged public resources: a methylation dataset (GSE62629) and two single-cell datasets (EGAS00001003996 and GSE126128). Results:… More >

VAN THI TUONG NGUYEN^1,2, KHUONG DUY PHAM^1,2,3, HUONG THI QUE CAO^1,2, PHUC VAN PHAM^1,2,*

BIOCELL, Vol.48, No.2, pp. 173-189, 2024, DOI:10.32604/biocell.2023.043664 - 23 February 2024

Abstract Mesenchymal stem cells (MSCs) have been proposed in regenerative medicine, especially for angiogenic purposes, due to their potential to self-renew, differentiate, and regulate the microenvironment. Peripheral vascular diseases, which are associated with reduced blood supply, have been treated but not cured. An effective therapy is to recover blood supply via vessel regeneration in the affected area, and MSCs appear to be promising for such conditions. Several studies aimed to explore the role of MSCs in performing angiogenesis and have revealed numerous potential methods to enhance MSC capacity in vessel formation. Efforts have been made to More > Graphic Abstract

CHUYAO WANG^1,2,#, CHUAN LU^2,#, LUXIANG ZOU^2,*, DONGMEI HE^2,*

BIOCELL, Vol.47, No.6, pp. 1293-1306, 2023, DOI:10.32604/biocell.2023.028199 - 19 May 2023

Abstract Background: Temporomandibular joint osteoarthritis (TMJOA) is an end-stage disease that seriously affects the patients’ quality of life. Molecular insights in advancing our understanding of TMJOA are the need of the hour. Methods: We performed RNA high-throughput sequencing and bioinformatics analysis of differentially expressed (DE) long non-coding RNA (lncRNAs), microRNAs (miRNAs), and messenger RNA (mRNAs) in human synovial TMJOA tissues. Firstly, synovium samples of TMJOA patients and non-TMJOA controls were collected for highthroughput sequencing of lncRNAs, miRNAs, and mRNAs. We then performed biological function analysis of the top 100 mRNAs with more than 2-fold differential expression, and… More >

Yanyan Pu^1,#, Liwen Wang^2,#, Leilei Li³, Yujun Si⁴, Shubin Xie², Yunzhe Cong¹, Dong Wang¹, Yongchao Gong¹, Rumei Tian¹, Xue Chen³, Xiaoyan Zhang¹, Min Liu¹, Hanfeng Ding^1,3,*, Nana Li^1,3,*

Phyton-International Journal of Experimental Botany, Vol.92, No.6, pp. 1793-1812, 2023, DOI:10.32604/phyton.2023.026822 - 11 April 2023

Abstract During the life cycle of a plant, seed germination is crucial. Upon ingestion of water, the dry seeds resumed energy metabolism and cellular repair. To dissect the complex mechanisms at the very beginning of seed germination, two approaches including transcriptome and small RNA sequencing were conducted during the water imbibition process of mung bean seeds compared with dry seed. The transcriptome sequencing analysis identified 10,108 differentially expressed genes (DEGs) between dry and imbibed mung bean seeds. KEGG enrichment analyses demonstrated numerous DEGs involved in hormone signaling pathways, carbohydrate, and energy metabolism. Out of the total… More >

Yan Li^1,2, Dayou Liu^1,2, Yungang Zhu^1,2, Jie Liu^1,2,*

CMES-Computer Modeling in Engineering & Sciences, Vol.124, No.1, pp. 303-313, 2020, DOI:10.32604/cmes.2020.09353 - 19 June 2020

Abstract Under different conditions, gene regulatory networks (GRNs) of the same gene set could be similar but different. The differential analysis of GRNs under different conditions is important for understanding condition-specific gene regulatory relationships. In a naive approach, existing GRN inference algorithms can be used to separately estimate two GRNs under different conditions and identify the differences between them. However, in this way, the similarities between the pairwise GRNs are not taken into account. Several joint differential analysis algorithms have been proposed recently, which were proved to outperform the naive approach apparently. In this paper, we… More >

Mian LIU¹, Xumeng ZHANG^{2, *}

BIOCELL, Vol.41, No.1, pp. 19-26, 2017, DOI:10.32604/biocell.2017.41.019

Abstract Bladder, kidney, prostate and testicular carcinoma are the top four genitourinary cancers in China. Here we analyzed mRNA and miRNA expression profiles of carcinomas of the bladder (TCC), kidney (ccRCC) and testis (TGCT) to uncover their specific regulatory mechanisms. The gene expression profiles of GSE31617 were downloaded from GEO database, which contained 27 samples, including 10 TCC, 7 TGCT and 10 ccRCC. Specific up- and downregulated differentially expressed genes (DEGs) and differentially expressed microRNAs (DEmiRNAs) of each cancer were selected and target genes of DEmiRNAs were predicted. Gene interaction network of the shared genes and… More >

Thomas Werner^1,2, Susan M. Dombrowski^3,4, Carlos Zgheib⁵, Fouad A. Zouein⁵, Henry L. Keen⁶, Mazen Kurdi^5,7, George W. Booz⁵

European Cytokine Network, Vol.24, No.2, pp. 75-90, 2013, DOI:10.1684/ecn.2013.0336

Abstract Microarrays do not yield direct evidence for functional connections between genes. However, transcription factors (TFs) and their binding sites (TFBSs) in promoters are important for inducing and coordinating changes in RNA levels, and thus represent the first layer of functional interaction. Similar to genes, TFs act only in context, which is why a TF/TFBS-based promoter analysis of genes needs to be done in the form of gene(TF)-gene networks, not individual TFs or TFBSs. In addition, integration of the literature and various databases (e.g. GO, MeSH, etc) allows the adding of genes relevant for the functional… More >