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Multidisciplinary Sciences
Lulu Chen, Yingzhou Lu, Chiung-Ting Wu, Robert Clarke, Guoqiang Yu, Jennifer E. Van Eyk, David M. Herrington, Yue Wang
Summary: The study introduces a new method for detecting SDEGs, which was applied to gene expression datasets and demonstrated superior performance in improving deconvolution accuracy.
SCIENTIFIC REPORTS
(2021)
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Oncology
Weiqian Guo, Xiaomin Zheng, Lei Hua, Xianbin Zheng, Yangyang Zhang, Bin Sun, Zhenchao Tao, Jin Gao
Summary: Differentiated expressed genes for nasopharyngeal carcinoma were identified and potential biomarkers were explored through bioinformatical analysis. The core genes screened may serve as prognostic and diagnostic biomarkers for NPC.
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Biology
Bokang Ko, Jeremy M. Van Raamsdonk
Summary: Gene expression studies provide valuable insights into biological processes, such as aging. This study shows that pooling individual RNA samples before sequencing can yield similar results as sequencing them individually, reducing the cost of experiments. Analysis of gene expression changes across the genome is a powerful and unbiased tool for understanding molecular mechanisms.
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Multidisciplinary Sciences
Changsheng Guo, Yuanqing Hua, Zuanhao Qian
Summary: This study identified differentially expressed lncRNAs and genes in Kawasaki disease (KD), as well as constructed ceRNA networks involving miRNAs and mRNAs. The study found specific lncRNAs (PSORS1C3, LINC00999, SNHG5) and genes (GATA3, SOD2, MAPK14, PPARG) that may play a key role in the pathogenesis and development of KD. Validation in a separate dataset showed that intravenous immunoglobulin treatment alleviated the deregulated RNA profiles in KD patients.
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Biochemical Research Methods
Zimo Huang, Jun Wang, Zhongmin Yan, Maozu Guo
Summary: This paper proposes a Multiple Self-Attention (Epi-MSA) model for predicting differentially expressed genes (DEGs) from epigenetic data. The model uses convolutional neural networks for information embedding and multiple self-attention encoders to learn important gene locations. Experimental results show that Epi-MSA outperforms existing methods in performance and stability, and has good interpretability.
BRIEFINGS IN BIOINFORMATICS
(2022)
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Genetics & Heredity
Weitao Hu, Taiyong Fang, Xiaoqing Chen
Summary: This study identified DEGs associated with ulcerative colitis (UC) using bioinformatics analysis, providing potential diagnostic and therapeutic targets. The DEGs, hub genes and miRNAs identified may serve as biomarkers for UC, but further research is needed to understand their biological roles in the disease.
FRONTIERS IN GENETICS
(2022)
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Oncology
Reem Altaf, Umair Ilyas, Anmei Ma, Meiqi Shi
Summary: In this study, bioinformatics analysis was used to evaluate four datasets for differentially expressed genes (DEGs) associated with non-small cell lung cancer (NSCLC). Ten significant DEGs were identified and their expression was validated. Gene-gene and drug-gene network analysis revealed important interactions and potential drug targets. This study highlights the importance of systemic genetics in identifying potential targeted therapies for NSCLC.
FRONTIERS IN ONCOLOGY
(2023)
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Biochemistry & Molecular Biology
Seung-Hoon Lee, Na Rae Park, Jung-Eun Kim
Summary: In this study, gene expression changes during megakaryocyte maturation were analyzed using the GeneChip microarray technology, and functional classification and protein interaction analysis of the differentially expressed genes were performed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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Engineering, Chemical
Yuan-Shuo Hsueh, Hui Hua Chang, Shun-Yao Ko, Yi-Pai Lin, Wei-Yu Lin
Summary: Chronic partial bladder outlet obstruction (PBOO) can lead to bladder fibrosis, and gene expression alterations may play a significant role in its pathogenesis.
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Plant Sciences
Jing-xuan Wang, Bo Wang, Lu-bin Cui, Hao Xie, Run-zhi Li, Cheng Wang, Zhang-jie Nan, Yu-shu Liu, Jing-yu Ma, Yun-jin Sun, Wei-yu Li
Summary: This study identified key genes involved in aluminum resistance in soybeans, which are crucial for functions such as cell junction and phenylpropanoid biosynthesis, providing important information for breeding aluminum-resistant varieties.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2021)
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Education, Scientific Disciplines
Zhongxiang Du, Xiajun Zhang, Weiya Gao, Jie Yang
Summary: This study analyzed differentially expressed genes in gastric cancer patients and identified three genes (PCCA, ECHS1, and HADH) with prognostic value. ECHS1 and HADH were significantly associated with disease-free survival, while PCCA was significantly correlated with overall survival rate. These genes may serve as new biomarkers for predicting the prognosis of gastric cancer.
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Biochemical Research Methods
Shaoheng Liang, Qingnan Liang, Rui Chen, Ken Chen
Summary: The Van Elteren test, combined with modified effect size, has shown to effectively control false positives and false negatives in differential expression analysis of single-cell sequencing data. This method achieves higher sensitivity and specificity compared to other state-of-the-art methods when assessing differences between cell types.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
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Biochemical Research Methods
Igor Deyneko, Orkhan N. Mustafaev, Alexander A. Tyurin, Ksenya Zhukova, Alexander Varzari, Irina Goldenkova-Pavlova
Summary: This study developed a method to clean RNA-seq data, improving the detection of differentially expressed genes, particularly those with low expression levels, by removing technical noise.
BMC BIOINFORMATICS
(2022)
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Pharmacology & Pharmacy
Shun Ying Quah, Charng Choon Wong, Hui Chyn Wong, Kok Lian Ho, Nizar Abdul Manan, Pran Kishore Deb, Sreenivasa Rao Sagineedu, Johnson Stanslas
Summary: The study revealed that acquired chemoresistance to SRJ09 and SRJ23 in colon and prostate cancer cells may be attributed to alterations in the expression of genes related to the PI3K and autophagy pathways.
TOXICOLOGY AND APPLIED PHARMACOLOGY
(2021)
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Biotechnology & Applied Microbiology
Yan Zhou, Bin Yang, Junhui Wang, Jiadi Zhu, Guoliang Tian
Summary: The study treats differentially expressed genes as outliers and proposes a scaling-free method for detecting them. The SFMEB method outperforms existing methods in various settings, especially for heterogeneous data or biological replicates.
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Biochemical Research Methods
Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
BMC BIOINFORMATICS
(2015)
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Biochemistry & Molecular Biology
Ayumi Kudo, Shuji Shigenobu, Koji Kadota, Masafumi Nozawa, Tomoko F. Shibata, Yukio Ishikawa, Takashi Matsuo
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
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Biochemical Research Methods
Shitao Zhao, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
BIOLOGICAL PROCEDURES ONLINE
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Biochemical Research Methods
Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu
ALGORITHMS FOR MOLECULAR BIOLOGY
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Biochemical Research Methods
Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, Koji Kadota
BMC BIOINFORMATICS
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Biotechnology & Applied Microbiology
Susumu Katsuma, WonKyung Kang, Tadasu Shin-i, Kazuko Ohishi, Koji Kadota, Yuji Kohara, Toru Shimadar
JOURNAL OF GENERAL VIROLOGY
(2011)
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Clinical Neurology
Reiko Nakao, Saori Yamamoto, Yuki Yasumoto, Koji Kadota, Katsutaka Oishi
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Multidisciplinary Sciences
Koyomi Miyazaki, Nanako Itoh, Sumika Ohyama, Koji Kadota, Katsutaka Oishi
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Biochemistry & Molecular Biology
Shinpei Kawaoka, Koji Kadota, Yuji Arai, Yutaka Suzuki, Tsuguru Fujii, Hiroaki Abe, Yuji Yasukochi, Kazuei Mita, Sumio Sugano, Kentaro Shimizu, Yukihide Tomari, Toru Shimada, Susumu Katsuma
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Biochemistry & Molecular Biology
Shinpei Kawaoka, Yuji Arai, Koji Kadota, Yutaka Suzuki, Kahori Hara, Sumio Sugano, Kentaro Shimizu, Yukihide Tomari, Toru Shimada, Susumu Katsuma
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Genetics & Heredity
Takahiro Ohde, Shinichi Morita, Shuji Shigenobu, Junko Morita, Takeshi Mizutani, Hiroki Gotoh, Robert A. Zinna, Moe Nakata, Yuta Ito, Kenshi Wada, Yasuhiro Kitano, Karen Yuzaki, Kouhei Toga, Mutsuki Mase, Koji Kadota, Jema Rushe, Laura Corley Lavine, Douglas J. Emlen, Teruyuki Niimi
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Plant Sciences
Yoshiaki Ueda, Namie Ohtsuki, Koji Kadota, Ayumi Tezuka, Atsushi J. Nagano, Taro Kadowaki, Yonghyun Kim, Mitsue Miyao, Shuichi Yanagisawa
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Biochemical Research Methods
Takayuki Osabe, Kentaro Shimizu, Koji Kadota
BIOINFORMATICS AND BIOLOGY INSIGHTS
(2019)
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Biology
Wei Su, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
BMC RESEARCH NOTES
(2019)