Human skeletal muscle fiber heterogeneity beyond myosin heavy chains by Roger Moreno-Justicia, Thibaux Van der Stede, Ben Stocks, Jenni Laitila, Robert A. Seaborne, Alexia Van de Loock, Eline Lievens, Diana Samodova, Leyre Marín-Arraiza, Oksana Dmytriyeva, Robin Browaeys, Kim Van Vossel, Lukas Moesgaard, Nurten Yigit, Jasper Anckaert, Anneleen Weyns, Ruud Van Thienen, Ronni E. Sahl, Edmar Zanoteli, Michael W. Lawlor, Michael Wierer, Pieter Mestdagh, Jo Vandesompele, Julien Ochala, Morten Hostrup, Wim Derave, Atul S. Deshmukh

“…Proteomics was conducted in males, while transcriptomics included ten males and two females. …”
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Metabolic mapping of the human solute carrier superfamily by Tabea Wiedmer, Shao Thing Teoh, Eirini Christodoulaki, Gernot Wolf, Chengzhe Tian, Vitaly Sedlyarov, Abigail Jarret, Philipp Leippe, Fabian Frommelt, Alvaro Ingles-Prieto, Sabrina Lindinger, Barbara M G Barbosa, Svenja Onstein, Christoph Klimek, Julio Garcia, Iciar Serrano, Daniela Reil, Diana Santacruz, Mary Piotrowski, Stephen Noell, Christoph Bueschl, Huanyu Li, Gamma Chi, Stefan Mereiter, Tiago Oliveira, Josef M Penninger, David B Sauer, Claire M Steppan, Coralie Viollet, Kristaps Klavins, J Thomas Hannich, Ulrich Goldmann, Giulio Superti-Furga

“…Targeted metabolomics provided a fingerprint of 189 intracellular metabolites, while transcriptomics offered insights into cellular programs modulated by SLC expression. …”
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Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data by Joshua Chuah, Carmalena V. Cordi, Juergen Hahn, Jennifer M. Hurley

“…Abstract Background The circadian clock is a central driver of many biological and behavioral processes, regulating the levels of many genes and proteins, termed clock controlled genes and proteins (CCGs/CCPs), to impart biological timing at the molecular level. While transcriptomic and proteomic data has been analyzed to find potential CCGs and CCPs, multi-omic modeling of circadian data, which has the potential to enhance the understanding of circadian control of biological timing, remains relatively rare due to several methodological hurdles. …”
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IFN-β and ARTS deficiency promote the generation of hyper-efferocytic Ly6C+ macrophages in resolving inflammation in male mice by Orly Zeituni-Timor, Soaad Soboh, Ahmad Zaid, Hiba Yaseen, Senthil Kumaran Satyanarayanan, Maha Abu Zeid, Esther Silberberg, Priya Goswami, Sagie Schif-Zuck, Sarit Larisch, Amiram Ariel

“…Notably, IFN-β also promotes the emergence of Ly6C+ macrophages during the resolution of liver fibrosis, while transcriptomic analysis further links this rejuvenated phenotype to macrophage subsets found in human inflammatory liver disease. …”
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Dynamic Coordination of Alternative Splicing and Subgenome Expression Bias Underlies Rusty Root Symptom Response in <i>Panax ginseng</i> by Jing Zhao, Juzuo Li, Xiujuan Lei, Peng Di, Hongwei Xun, Zhibin Zhang, Jian Zhang, Xiangru Meng, Yingping Wang

“…Ginseng rusty root symptoms (GRSs) compromise the yield and quality of <i>Panax ginseng</i>. While transcriptomic analyses have demonstrated extensive remodeling of stress signaling networks, the post-transcriptional defense circuitry remains obscure. …”
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Patient-specific data fusion defines prognostic cancer subtypes. by Yinyin Yuan, Richard S Savage, Florian Markowetz

“…In cancer studies, for example, data on copy number alterations indicate losses and amplifications of genomic regions in tumours, while transcriptomic data point to the impact of genomic and environmental events on the internal wiring of the cell. …”
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Genome-wide identification and functional analysis of R2R3-MYB genes in Acer pseudosieboldianum: insights into low temperature stress response and anthocyanin biosynthesis by Shikai Zhang, Dong Zeng, Heng Zhang, Luwei Ding, Dongyuan Guo, Peilin Sun, Zhiming Han, Guanzheng Qu, Tuya Siqin, Xiangling You

“…Cis-regulatory element analysis identified 34 genes enriched in low-temperature response motifs, while transcriptomic and qPCR validation highlighted 22 cold-responsive and 14 leaf color-associated ApseMYB genes, including ApseMYB31 (28-fold induction at 4 °C) and ApseMYB16 (52-fold upregulation during leaf reddening). …”
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Transcriptional landscape of pleural mesothelioma patients in relation to NF2 gene mutational status by Carlos Orozco-Castaño, Alejandro Mejía-Garcia, Hsuan Megan Tsao, Diego A. Bonilla, Carlos Carvajal-Fierro, Ricardo Bruges-Maya, Alba Combita, Rafael Parra-Medina

“…Logistic regression was used to evaluate associations with clinical variables, while transcriptomic differences were examined through differential expression and functional enrichment analyses. …”
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Integrative metabolomics and transcriptomics analysis of hippocampus reveals taurine metabolism and sphingolipid metabolism dysregulation associated with sleep deprivation-induced... by Ting Chen, Junke Jia, Chenyi Gao, Qi Zhong, Lijuan Tang, Xiaokai Sui, Shuang Li, Chang Chen, Zongze Zhang

“…The analysis revealed that sleep deprivation caused abnormalities in several metabolic pathways, with particularly pronounced effects observed in glycerophospholipid metabolism, linoieic acid metabolism, alanine, aspartate, glutamate metabolism, taurine and hypotaurine metabolism, and purine metabolism. While transcriptomic analysis releaved 97 differentially expressed genes (DEGs) (51 were down-regulated and 46 were up-regulated DEGs). …”
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Transcriptomic and metabolomic analyses for the mechanism underlying anthocyanin synthesis during the growth and development of purple eggplant (Solanum melongena L) by Ting Yang, Wanping Lv, Runjie Zhuang, Shiyu Wang, Shuqi Fan, Yongxian Wen, Yongxian Wen

“…Metabolomic profiling identified anthocyanin types, while transcriptomic data highlighted differentially expressed genes. …”
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Therapeutic Potential of Emricasan, a Pan-Caspase Inhibitor, in Reducing Cell Death and Extracellular Matrix Accumulation in Fuchs Endothelial Corneal Dystrophy by Sohya Fujimoto, Mako Endo, Shigehito Tonomura, Fuuga Tsuji, Hirotaka Haraguchi, Kanna Hasegawa, Taisuke Numao, Ayaka Izumi, Theofilos Tourtas, Ursula Schlötzer-Schrehardt, Friedrich Kruse, Yuki Oyama, Masahito Ikawa, Albert S. Jun, Noriko Koizumi, Naoki Okumura

“…Endothelial cell density, hexagonality, cell size variation, and guttae area were evaluated by contact specular microscopy, while transcriptomic changes were analyzed via RNA sequencing. …”
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TMEM132A: a novel susceptibility gene for lung adenocarcinoma combined with venous thromboembolism identified through comprehensive bioinformatic analysis by Pei Xie, Yingli Liu, Pingping Bai, Yue Ming, Qi Zheng, Li Zhu, Yong Qi

“…This study utilized public databases to identify crosstalk genes (CGs) between LUAD and VTE, applied machine learning methods to discover shared diagnostic biomarkers, and explored their underlying mechanisms.MethodsDisease-specific genes for VTE were extracted from comprehensive genomic databases (CTD, DisGeNET, GeneCards, OMIM), while transcriptomic profiles of LUAD and VTE cohorts were retrieved from GEO via GEOquery implementation. …”
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Conserved cross-domain protein-to-mRNA ratios enable proteome prediction in microbes by Mengshi Zhang, Changyi Zhang, Anayancy Ramos, Rachel J. Whitaker, Marvin Whiteley

“…This cross-domain framework enables more accurate functional inference in microbiomes without requiring organism-specific proteomic data, offering a powerful new tool for microbial ecology, systems biology, and functional genomics.IMPORTANCEDeciphering the biology of natural microbial communities is limited by the lack of functional data. While transcriptomics enables gene expression profiling, mRNA levels often fail to predict protein abundance, the primary indicator of microbial function. …”
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Transcriptome Analysis of the Hippocampus in Domestic Laying Hens with Different Fear Responses to the Tonic Immobility Test by Jingyi Zhang, Min Li, Liying Pan, Ye Wang, Hui Yuan, Zhiwei Zhang, Chaochao Luo, Runxiang Zhang

“…The neuronal alterations observed in high fear individuals suggest neural damage, while transcriptomic variations point to potential disruptions in neurogenesis, synaptic signaling, and stress-related pathways. …”
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Transcriptomic Profiling of Buds Unveils Insights into Floral Initiation in Tea-Oil Tree (<i>Camellia oleifera</i> ‘changlin53’) by Hongyan Guo, Zongshun Zhou, Jian Zhou, Chao Yan, Wenbin Zhong, Chang Li, Ying Jiang, Yaqi Yuan, Linqing Cao, Wenting Pan, Jinfeng Wang, Jia Wang, Tieding He, Yikai Hua, Yisi Liu, Lixian Cao, Chuansong Chen

“…UPLC-MS/MS was used to analyze endogenous gibberellin (GA) concentrations, while transcriptomic analysis was performed to reveal the underlying transcriptional regulatory network. …”
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Single-cell transcriptome and multi-omics integration reveal ferroptosis-driven immune microenvironment remodeling in knee osteoarthritis by Yushun Wu, Jing Liu, Wenying Yu, Xiaoding Wang, Jian Li, Weiquan Zeng

“…BackgroundKnee osteoarthritis (KOA) is a chronic inflammatory joint disorder marked by cartilage degradation and immune microenvironment dysregulation. While transcriptomic studies have identified key pathways in KOA, the interplay between ferroptosis (an iron-dependent cell death mechanism) and immune dysfunction at single-cell resolution remains unexplored. …”
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Calcium overload via PVT1 reprograms neutrophil fate and constrains gastric cancer progression by Dong Wang, Yunlong Li, Xiaoyu Peng, Lulu Zhang, Ying Zhang, Xue Guan, Xiao Liang, Songbin Fu, Jingcui Yu

“…Functional validation through in vitro and in vivo models demonstrated PVT1’s oncogenic role, while transcriptomic profiling further decoded neutrophil activation mechanisms regulated by PVT1. …”
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