RNA-Seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats. by B Alex Merrick, Dhiral P Phadke, Scott S Auerbach, Deepak Mav, Suzy M Stiegelmeyer, Ruchir R Shah, Raymond R Tice

“…Several potentially novel exons were found and exon refinements were made including AFB1 exon-specific induction of homologous family members, Ugt1a6 and Ugt1a7c. We find the rat transcriptome contains many previously unidentified, AFB1-responsive exons and transcripts supporting RNA-Seq's capabilities to provide new insights into AFB1-mediated gene expression leading to hepatocellular carcinoma.…”
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Identification of metabolism-associated molecular classification for effect and prognosis in lung adenocarcinoma based on multidatabases including the cancer genome atlas and gene... by Lilin Que, Zhibing Liu, Yinghui Wu, Lan Luo, Leifeng Liang

“…Using unsupervised transcriptome analysis, we identified three distinct subtypes (C1, C2, and C3). …”
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Distinct transcriptional profiles of Leptospira borgpetersenii serovar Hardjo strains JB197 and HB203 cultured at different temperatures. by Ellie J Putz, Sathesh K Sivasankaran, Luis G V Fernandes, Brian Brunelle, John D Lippolis, David P Alt, Darrell O Bayles, Richard L Hornsby, Jarlath E Nally

“…<h4>Conclusions/significance</h4>Investigation of the L. borgpetersenii JB197 and HB203 transcriptome provides unique insight into the mechanistic differences between acute and chronic disease. …”
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Characteristics and Functions of Different Intestinal Segments in Juvenile Greater Amberjack (<i>Seriola dumerili</i>) by Kunfeng Zhu, Mouyan Jiang, Mengyao Yan, Yang Huang, Tonglin Yang, Chunhua Zhu

“…In this study, we divided the intestine of <i>S. dumerili</i> into foregut, midgut, and hindgut, and conducted a multi-omics analysis integrating histological staining (H&E/AB-PAS), digestive enzyme assays, transcriptome sequencing, and 16S rRNA microbiota profiling to characterize structural, functional, molecular, and microbial differences across intestinal segments. …”
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The 7-Methylguanosine (m7G) methylation METTL1 acts as a potential biomarker of clear cell renal cell carcinoma progression by Yi Liu, Yanji Zhan, Jiao Liu, Zhengze Shen, Yudong Hu, Ling Zhong, Yuan Yu, Bin Tang, Jing Guo

“…These results provide a new perspective on the role of M7G-related RNAs in ccRCC pathogenesis.…”
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Molecular mechanism of nano-vitamin A-mediated regulation of intramuscular fat deposition involving noncoding RNAs in pigs by Meng Li, Wenrun Cai, Ruotong Li, Wenye Zhao, Jiaxin Zhang, Xiaoyin Rong, Ting Zhang, Yang Yang, Bugao Li, Xiaohong Guo

“…Results To elucidate the mechanisms by which Nano VA affects pork quality via noncoding RNAs, whole transcriptome sequencing was performed on the longissimus dorsi muscle from control and Nano VA treated groups. …”
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Identification and Validation of circDOCK1/miR-138-5p/GRB7 Axis for Promoting Breast Cancer Progression by Zhang Y, Yang M, Wang Y, Zhao J, Lee PY, Ma Y, Qu S

“…Patients with high circDOCK1 level had poor outcomes.Conclusion: A novel circDOCK1/miR-138-5p/GRB7 axis promotes HER2 positive breast cancer metastasis and progression, providing a potential therapeutic target in the treatment of breast cancer.Keywords: circular DOCK1, ceRNA, breast cancer, progression, patient survival…”
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Common bean pan-genome reveals abundant variation patterns and relationships of stress response genes and pathways by Xu Wang, Ming Yan, Shanshan Cui, Fang Li, Qingqing Zhao, Qingnan Wang, Bin Jiang, Yixin Huang, Yang Sun, Xiangdong Kong

“…In conclusion, our study provides a comprehensive genome resource, which will be useful for further common bean breeding and study.…”
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T cell-mediated immune surveillance conferred by latent Epstein-Barr virus genes suppresses a broad spectrum of tumor formation through NKG2D-NKG2DL interactions by Yuqi Jin, Yun Guo, Yohei Kawano, Megumi Sasatani, Shun Ohki, Keita Yamane, Yusei Ota, Yumi Tamura, Yusuke Sotomaru, Yoshihiro Baba, Tomoharu Yasuda

“…These results suggest that LMP1/2A-expression associated with EBV infection contributes to pan-tumor surveillance, implicating a beneficial aspect of EBV infection in humans and providing important insights into cancer prevention.…”
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From bench to bedside: elucidating VEGF(R) inhibitor-related heart failure in cancer treatment by Shengkun Peng, MinHong Cai, Hongyu Kuang, Anqi Lin, Qinghua Ma, Xiaoqin Dai, Peng Luo, Yijun Liu, Guo Zhang, Yifeng Bai

“…Conclusions Our findings present the first comprehensive characterization of VirHF clinical features and elucidate its underlying molecular mechanisms, thereby providing a theoretical framework for optimizing the clinical safety of VEGF(R)i therapy.…”
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Fe-doped MOF nanoparticles: the LIFR and BMP4 dual-signaling pathways activated regulator for in vitro expansion of mouse embryonic stem cells by Youyuan Li, Hong Wang, Zhilei Li, Huichao Wang, Yi Gao, Chaoran Wu, Bangguo Wei, Zhanyun Guo, Xijin Wang, Guoxin Jing, Shilong Wang

“…This study demonstrates that Fe MOF could not only replace the LIF factor, but also has a stronger ability to promote the self-renewal of mESCs owe to its multi-signal pathway regulation function, providing application prospects in the in vitro cultivation of mESCs.…”
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The underlying molecular mechanisms and biomarkers of Hip fracture combined with deep vein thrombosis based on self sequencing bioinformatics analysis by Guanghua Shi, Xiaocui Shi, Meng Zhang, Rui Cheng, Mengqing Hu, Yu Zhao, Shimei Li, Xiuxiu Li, Haiyun Ma, Pengcui Li

“…Conclusions In conclusion, five feature genes (RGS1, HSF2, ARL4A, AAED1, and WDR81) were identified, and functional enrichment analyses were conducted, providing a foundation for predicting the diagnosis of fractures associated with thrombosis.…”
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Major facility superfamily sugar transporter protein SsMFSST1 regulates Sporisorium scitamineum mating, pathogenicity, and sugar transport/absorption by Yi Zhang, Yongding He, Meixin Yan, Shilong Zhang, Sisi Zhou, Wankuan Shen

“…This study was based on the transcriptome sequencing data of two isolates with different pathogenicities (Ss16 and Ss47) of the S. scitamineum and screened out a gene encoding the Major Facility Superfamily (MFS) sugar transporter protein and named it SsMFSST1. …”
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Cross-Tissue Regulatory Network Analyses Reveal Novel Susceptibility Genes and Potential Mechanisms for Endometriosis by Mingrui Zou, Mingmei Lin, Kai-Lun Hu, Rong Li

“…This study aims to integrate transcriptome-wide association study (TWAS), Mendelian randomization (MR), and bioinformatics analyses to reveal novel putatively causal genes and potential mechanisms. …”
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Screening of ferroptosis genes related to the prognosis of cervical cancer and construction of a prognostic model by Yue CHEN, Wenxin CHEN, Yi JIANG, Dong ZHANG, Boqun XU

“…Model 2 (C-index = 0.727) had better predictive ability than Model 1 (C-index = 0.502).Conclusion The prognostic model composed of 15 prognostic-related genes selected based on bioinformatics has better predictive performance for the survival outcomes of cervical cancer patients, providing important reference value for the prognostic assessment of cervical cancer patients.…”
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Bioinformatics and experimental approach identify DNMT3A as a diagnostic marker associated with regulated cell death patterns in psoriasis by Linyu Zhu, Zhiyu Ye, Ling Wang, Shaomin Chen, Menger Guo, Lvya Zhang, Yuansheng Wu

“…Regulated cell death (RCD) is crucial for the advancement of psoriasis, and providing opportunities as diagnostic indicators and drug sensitivity markers for psoriasis. …”
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From Cell to Gene: Deciphering the Mechanism of Heart Failure With Single‐Cell Sequencing by Dan Zhang, Qiang Wen, Rui Zhang, Kun Kou, Miao Lin, Shiyu Zhang, Jun Yang, Hangchuan Shi, Yan Yang, Xiaoqiu Tan, Shigang Yin, Xianhong Ou

“…Traditional high‐throughput sequencing methods provide an average measure of gene expression, failing to capture the “heterogeneity” between cells and impacting the accuracy of gene function knowledge. …”
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Histone deacetylase 9 promotes osteogenic trans-differentiation of vascular smooth muscle cells via ferroptosis in chronic kidney disease vascular calcification by Lin Xiong, Qiong Xiao, Rong Chen, Liming Huang, Jun Gao, Li Wang, Guisen Li, Yi Li

“…In summary, our findings suggest that HDAC9 promotes VSMCs osteogenic trans-differentiation involving ferroptosis, providing new insights for the therapy of CKD vascular calcification.…”
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Machine learning and multi-omics analysis reveal key regulators of proneural–mesenchymal transition in glioblastoma by Can Xu, Jin Yang, Huan Xiong, Xiaoteng Cui, Yuhao Zhang, Mingjun Gao, Lei He, Qiuyue Fang, Changxi Han, Wei Liu, Yangyang Wang, Jin Zhang, Ying Yuan, Zhaomu Zeng, Ruxiang Xu

“…Differentially expressed genes (DEGs) were identified using GBM transcriptome datasets, and prognostic analysis was performed to screen for PMT-related genes (PMTRGs). …”
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Identification and characterization of the tumor necrosis factor receptor superfamily in the Chinese tree shrew (Tupaia belangeri chinensis) by Zongjian Huang, Nan Shi, Zhenqiu Luo, Fangfang Chen, Xunwei Feng, Yongjing Lai, Jian Li, Xiang Yi, Wei Xia, Anzhou Tang

“…As expected, the multi-species collinearity analysis revealed that tTNFRSF genome bears a greater resemblance to humans than to mice. Transcriptome data from 28 samples across ten organ types showed high TNFRSF expression predominantly in immune organs. …”
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