Integrated analysis of methylomic and transcriptomic profiles in fetal mouse hypothalamus in response to maternal gestational exposure to arsenic by Xuehua Li, Jinzhong Cui, Xinyu Zhang, Yue Wu, Jiajia Xu, Yonggan Zhao, Sajjad Hussain, Leishan Chen

“…Conclusion: This integrative analysis of methylomic and transcriptomic profiles in fetal mouse hypothalamus provides insights into the epigenetic and transcriptional responses to gestational arsenic exposure.…”
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Transcriptomic Analysis for Key Periods of Radicle Development in Contrasting Soybean Varieties HN75 and HN76 by Fengli Yu, Liang Mi, Dawei Xin

“…These findings unravel mechanisms governing leguminous radicle development while establishing molecular blueprints for engineering cultivation protocols that would enhance soybean sustainability in edaphically constrained environments.…”
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Integration of multi-omics transcriptome-wide analysis for the identification of novel therapeutic drug targets in diabetic retinopathy by Guoguo Yi, Zhengran Li, Yuxin Sun, Xinyu Ma, Zijin Wang, Jinken Chen, Dong Cai, Ziran Zhang, Zejun Chen, Fanye Wu, Mingzhe Cao, Min Fu

“…Methods A broad multi-omics exploration of DR was presented to decipher the drug targets of DR and proliferative diabetic retinopathy (PDR). Transcriptome-Wide Association Studies (TWAS), fine-mapping and conditional analysis were applied to unearth potential tissue-specific gene associations with DR. …”
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Integrated transcriptome and metabolome analysis of photoperiod effects on testosterone secretion in ChaHua chicken No.2 Roosters by Mengqian Liu, Lei Tan, Xinlu Li, Haojie Li, Yong Zhang, Xiannian Zi, Changrong Ge, Kun Wang

“…Testicles Transcriptomics analysis revealed 891 differentially expressed genes, including 479 down-regulated and 412 up-regulated genes. …”
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Identification of hub genes regulating seed germination viability in soybean via comparative transcriptome analysis and WGCNA by Long Miao, Lirong Chen, Huihui Gao, Linlin Kong, Mengli Xv, Genhua He, Juan Li, Jinghao Xv, Haowei Zheng, Xv Yang, Pengyu Bai, Jiajia Li, Lijuan Qiu, Xiaobo Wang

“…Comparative transcriptome and WGCNA analysis showed that genes clustered in the mediumpurle2 module may be involved in seed germination viability. …”
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Construction of dynamic ceRNA regulatory networks in osteogenesis during fracture healing based on transcriptomic analysis by Shuhang Guo, Shen Wang, Shaoxun Yuan, Xinyi Gu, Jin Deng, Chen Huang, Xinyi Zeng, Qingguo Lu, Xiaofeng Yin

“…RNA-Seq was used for high-throughput transcriptome sequencing, followed by differential expression analysis to identify differentially expressed genes (DEGs), long non-coding RNA (DELs), and microRNA (DEMs) at different stages. …”
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A comprehensive transcriptome based meta-analysis to unveil the aggression nexus of oral squamous cell carcinoma by Soujanya J. Vastrad, Ganesan Rajalekshmi Saraswathy, Jagadish B. Dasari, Gouri Nair, Ashok Madarakhandi, Dominic Augustine, S.V. Sowmya

“…To address this, an integrative meta-analysis of six publicly available transcriptomic profiles, categorized by lymph nodal status, is conducted. …”
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Integrated metabolome and transcriptome analysis reveals key genes and pathways associated with egg yolk percentage in chicken by Wen Li, Yuxing Luo, Shoujia Zhu, Mengyuan Wang, Xuli Zhao, Zhonghua Ning

“…To elucidate the underlying mechanisms that contribute to variations in egg yolk percentage, we performed integrated transcriptome and metabolome analyses on the liver, ovary, and magnum tissues of Rhode Island Red chickens with high and low yolk percentages. …”
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The effects and mechanisms of Xiaoyao San on nonalcoholic fatty liver disease rat based on transcriptomics and proteomics analysis by Yunxiao Liu, Shuanghu Wang, Ayesha Younas, Jiaojian Lv, Abdullah Al Mamun, Chuxiao Shao

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Transcriptome sequencing and Mendelian randomization analysis identified biomarkers related to neutrophil extracellular traps in diabetic retinopathy by Linlin Hao, Songhong Wang, Lian Zhang, Lian Zhang, Jie Huang, Yue Zhang, Xuejiao Qin

“…To explore the mechanism of NETs-related genes in DR, the transcriptome of NETs from normal and DR individuals were analyzed with gene sequencing and mendelian randomization (MR) analysis. …”
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Transcriptome analysis of insecticide resistance mechanisms in field populations of the bean flower thrips, Megalurothrips usitatus (Bagnall) by Hongyi Cao, Jiangjiang Yuan, Yanran Wan, Yingxi Tang, Xiaobin Zheng, Jing Wang, Kanghua Qian, Jiuming Feng, Sirui Chen, Youjun Zhang, Qingjun Wu

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Comparative transcriptome analysis reveals molecular mechanisms of resistance in Chinese cabbage to Plasmodiophora brassicae pathotype 11 by Yue Qiu, Yue Qiu, Yue Qiu, Jinhao Zhang, Jinhao Zhang, Chunju Deng, Chunju Deng, Jiasheng Yuan, Jiasheng Yuan, Bowen Wang, Bowen Wang, Han Meng, Han Meng, Mohamed Mohany, Liting Zeng, Liting Zeng, Lanfang Wei, Lanfang Wei, Waqar Ahmed, Guanghai Ji, Guanghai Ji

“…Comparative transcriptome analysis revealed substantial differences in the number and types of differentially expressed genes (DEGs) between the two cultivars, highlighting the key pathways involved in the resistance response. …”
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Transcriptomic comparison analysis across seven developmental stages of the Triatoma rubrofasciata, a vector of Chagas disease by Lei Duan, Yunjia Tian, Ziyi Wang, Limin Yang, Yunhai Guo, Yuanyuan Li, Zhengbin Zhou, Yong Shen, Yi Zhang, Qin Liu

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Transcriptomic profiling reveals response mechanisms of Lactuca indica seedlings to seawater irrigation stress by Dingding Cao, Lirong Xiang, Ziling Li, Neng Wei, Neng Wei, Qingfeng Wang, Qingfeng Wang

“…Tissue-specific -plant transcriptome analysis identified key metabolic pathways and regulatory genes in roots, stems, and leaves.ResultsDifferential gene expression analysis showed tissue-specific enrichment patterns: leaves predominantly enriched light-harvesting complex (LHC) genes in photosynthesis pathways; stems exhibited upregulation in cutin, suberin, and wax biosynthesis pathways; while roots showed activation of nitrogen metabolism pathways.DiscussionBased on the data from transcriptomics, we infered that the key salt-tolerant candidate genes include: (1) leaf-specific LHC genes enhancing photosynthetic efficiency; (2) stem-expressed wax biosynthesis gene aldehyde decarbonylase CER1, and cytochrome P450 family members fatty acid omega-hydroxylase CYP86A4S and cytochrome P450 family 77 subfamily A (CYP77A); and (3) root-specific nitrogen metabolism regulators (nitrate reductase (NR), nitrate/nitrite transporter 2 (NRT2), and nitrite reductase (NirA). …”
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Proinflammatory transcriptomic and kinomic alterations in astrocytes derived from patients with familial Alzheimer's disease by Benjamin Siciliano, Nicholas D. Henkel, William G. Ryan V, Ali Sajid Imami, John M. Vergis, Chongchong Xu, Taylen O. Arvay, Smita Sahay, Priyanka Pulvender, Abdul-rizaq Hamoud, Chadwick Hales, Robert E. McCullumsmith, Zhexing Wen

“…In this study, we employed a multiomic integrative analysis combining transcriptomic and kinomic profiling of human induced pluripotent stem cell (hiPSC)-derived astrocytes from patients with familial AD (fAD) compared to healthy controls (HCs). …”
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Biological mechanism of sex differences in mental rotation: Evidence from multimodal MRI, transcriptomic and receptor/transporter data by Haixia Long, Hao Wu, Chaoliang Sun, Xinli Xu, Xu-Hua Yang, Jie Xiao, Mingqi Lv, Qiuju Chen, Ming Fan

“…In addition, transcriptome-neuroimaging association analysis and correlation analysis between brain biomarkers and neurotransmitter receptor/transporter distribution were also performed to uncover genetic and molecular mechanisms contributing to the observed sex differences in mental rotation. …”
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Integrated Transcriptomic and Metabolomic Analysis Reveals Nitrogen-Mediated Delay of Premature Leaf Senescence in Red Raspberry Leaves by Qiang Huo, Feiyang Chang, Peng Jia, Ziqian Fu, Jiaqi Zhao, Yiwen Gao, Haoan Luan, Ying Wang, Qinglong Dong, Guohui Qi, Xuemei Zhang

“…Superoxide sismutase (SOD) and peroxidase (POD) activities in the middle and lower functional leaves of T150 were higher than in CK, while catalase (CAT) activity was lower. Transcriptomic analysis identified 4350 significantly differentially expressed genes, including 2062 upregulated and 2288 downregulated genes. …”
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Integrating multiple “omics” analysis for plant metabolites and their functions by ZHOU Guoyan, HU Wangxiong, XU Jianhong, XUE Qingzhong

“…A comprehensive analysis of a series of metabolites that produced by the organisms in the life processes will help to reveal the biological links between genotype and phenotype. …”
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Physiological and Transcriptomic Mechanisms Underlying Vitamin C-Mediated Cold Stress Tolerance in Grafted Cucumber by Panpan Yu, Junkai Wang, Xuyang Zhang, Zhenglong Weng, Kaisen Huo, Qiuxia Yi, Chenxi Wu, Sunjeet Kumar, Hao Gao, Lin Fu, Yanli Chen, Guopeng Zhu

“…However, 200 mg L⁻¹ treatment elevated malondialdehyde (MDA) content, indicating potential oxidative stress. For transcriptomic analysis, leaves from the 150 mg L⁻¹ Vc and CK treatments were sampled at 0, 1, 2, and 3 days of cold stress. …”
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Exploring the landscape of Parkinson’s disease transcriptomics: a quantitative review of research progress and future directions by Yiran Wang, Yiran Wang, Yiran Wang, Tong Li, Xiaoqing Zhang, Xiaoqing Zhang, Haoran Tai, Haoran Tai, Weihong Li, Weihong Li, Bingyin Su, Bingyin Su

“…Citation burst analysis identified key references related to genetics, transcriptomics, and data analysis tools that have significantly influenced the field.ConclusionThis study offers the first comprehensive bibliometric analysis of Parkinson’s disease (PD) transcriptomics research from 2011 to 2025. …”
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