Article
Cell Biology
Luling He, Andrea Palos-Jasso, Yao Yi, Manman Qin, Liang Qiu, Xiaofeng Yang, Yifeng Zhang, Jun Yu
Summary: This study used bioinformatic analysis to identify metabolic pathways and immune-related pathways involved in the progression of atherosclerosis. Key genes and modules associated with immune and muscle system function were also identified. This research improves our understanding of the molecular mechanisms underlying atherosclerosis and provides potential biomarkers and drug targets for its management.
Article
Genetics & Heredity
Jaeyeon Jang, Inseung Hwang, Inuk Jung
Summary: This article introduces an online service called TimesVector-web for analyzing time course gene expression data. The service helps researchers analyze gene expression patterns under multiple conditions and provides downstream biological interpretation, including transcription factor, miRNA target, gene ontology, and pathway analysis.
Article
Cell Biology
Yang Liu, Lanlan Chen, Xiangbo Meng, Shujun Ye, Lianjun Ma
Summary: This study identified hub genes associated with colorectal adenocarcinoma and constructed a 3-gene signature to predict the prognosis of patients. The findings provide valuable insights into the molecular mechanisms and potential prognosis factors of colorectal adenocarcinoma.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Yang Xu, Rachel Patton McCord
Summary: The study introduces a new method called CoSTA, which uses convolutional neural network clustering to learn spatial relationships between gene expression matrices, emphasizing broader spatial patterns. CoSTA provides a quantitative measure of expression pattern similarity between each pair of genes, identifying narrower but biologically relevant sets of significantly related genes compared to other approaches.
BMC BIOINFORMATICS
(2021)
Article
Automation & Control Systems
Mohsen Rahmanian, Eghbal G. Mansoori
Summary: Gene expression data analysis is challenging due to complex and high-dimensional samples and genes. This paper proposes an unsupervised gene selection scheme based on information theoretic measures to reduce the risk of overfitting and improve the predictability and readability of genetic data. Experimental results demonstrate the effectiveness of this approach in both unsupervised and supervised scenarios.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2022)
Article
Plant Sciences
Pajaree Sonsungsan, Pheerawat Chantanakool, Apichat Suratanee, Teerapong Buaboocha, Luca Comai, Supachitra Chadchawan, Kitiporn Plaimas
Summary: This study identified key genes for salt-stress responses in rice by analyzing the transcriptomes of a local Thai rice variety with high salt tolerance. The research focused on understanding which genes play crucial roles in salt-stress tolerance, potentially offering new insights for improving salt tolerance cultivars.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Microbiology
Ji-Su Jun, Hyang-Eun Jeong, Su-Yeong Moon, Se-Hee Shin, Kwang-Won Hong
Summary: Transcriptome analysis was performed to study the changes in gene expression of B. subtilis DB104 during growth on a complete medium. Results showed that ABC transporter was down-regulated during exponential growth, metabolic changes occurred at the transition point of sporulation initiation, and stress response genes were turned on. The genes involved in lipid catabolic process were briefly up-regulated at 15 h due to programmed cell death postponing sporulation. This study provides insights into gene expression and regulatory mechanisms in B. subtilis species.
Article
Medicine, Research & Experimental
Ye Seon Lim, Do-Young Lee, Hye-Yoon Kim, Yejin Ok, Seonyeong Hwang, Yuseok Moon, Sik Yoon
Summary: EGFL8 plays a negative regulatory role in mouse cTECs, affecting various cellular processes and gene expressions, ultimately leading to inhibition of cTEC proliferation. The altered expression of genes associated with EGFL8 in cTECs highlights its involvement in important physiological processes and provides insight into its biological functions.
INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE
(2021)
Article
Multidisciplinary Sciences
Soudeh Ghafouri-Fard, Arash Safarzadeh, Mohammad Taheri, Elena Jamali
Summary: A co-expression network of differentially expressed genes (DEGs) related to colorectal cancer (CRC) and their target genes was constructed using the weighted gene co-expression network analysis (WGCNA) algorithm. GO and KEGG pathway analysis revealed that these genes were mainly involved in the regulation of hormone levels, extracellular matrix organization, and extracellular structure organization. The study also identified DKC1, PA2G4, LYAR and NOLC1 as the key hub genes of CRC.
SCIENTIFIC REPORTS
(2023)
Article
Parasitology
Kennedy W. Mwangi, Rosaline W. Macharia, Joel L. Bargul
Summary: The study constructed a gene co-expression network of insect-stage trypanosomes using RNA-Seq data and identified enriched modules for genes that play key roles in the parasite's development in the tsetse fly. Additionally, potential 3' UTR regulatory elements for genes in the same module were predicted using the FIRE tool. This network provides a valuable resource for identifying candidate genes for functional studies and understanding the molecular mechanisms underlying important biological processes during the parasite's development in the tsetse fly, which could lead to the identification of potential molecular targets for disease control.
PARASITES & VECTORS
(2021)
Article
Neurosciences
Siqiao Wang, Weijin Qian, Shaofeng Chen, Shuyuan Xian, Minghao Jin, Yifan Liu, Hao Zhang, Hengwei Qin, Xinkun Zhang, Jiwen Zhu, Xi Yue, Chaofeng Shi, Penghui Yan, Runzhi Huang, Zongqiang Huang
Summary: This bibliometric study analyzed SCI-related studies from 2000 to 2022 and found that China was the most productive country, while the United States had the highest influence. Research hotspots mainly focused on molecular and pathological mechanisms of SCI, as well as novel therapies. Future studies should continue to explore more viable therapeutic methods for SCI.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Article
Computer Science, Hardware & Architecture
Zhifei Song, Yue Wu, Ji Hao, Guoqiang Cui, Qingxia Guan
Summary: The arrival of big data has brought about changes and impacts in people's lives. To achieve better development, universities need to prioritize the application of big data in talent development. An improved k-nearest neighbors density peak clustering algorithm (iKDPC) combined with principal components is proposed to enhance the hierarchical classification's impact on talent development in universities. The experimental results demonstrate the effectiveness of iKDPC in classifying talents in universities and providing scientific and quantitative references for exploring talent classification issues.
COMPUTERS & ELECTRICAL ENGINEERING
(2023)
Article
Biology
Zuhier Awan, Nuha Alrayes, Zeenath Khan, Majid Almansouri, Abdul Ibrahim Hussain Bima, Haifa Almukadi, Hussam Ibrahim Kutbi, Preetha Jayasheela Shetty, Noor Ahmad Shaik, Babajan Banaganapalli
Summary: This study identified potential genetic biomarkers for familial hypercholesterolemia (FH) by studying the global gene expression profile of blood cells. Dysregulated expression of genes related to lipid homeostasis, immune responses, and cell adhesion molecules was found in FH patients. The involvement of dysregulated thyroid hormone and ErbB signaling pathways, as well as the enrichment of specific genes, were observed. The key hub genes JAK3, PLCG2, and ZEB2 were identified to contribute to inflammation and immune response related phenotypes. These findings provide insights into the immune dysregulation underlying atherosclerosis among FH patients and may contribute to the development of genomic medicine for cardiovascular diseases.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Biochemical Research Methods
Jakob P. Pettersen, Eivind Almaas
Summary: This research developed an R package, csdR, for differential co-expression network analysis. Benchmarking on a real dataset showed that csdR has good performance and ease of use, and is able to generate robust results in a relatively short period of time.
BMC BIOINFORMATICS
(2022)
Article
Plant Sciences
Harshraj Shinde, Ambika Dudhate, Atul Sathe, Neha Paserkar, Sopan Ganpatrao Wagh, Ulhas Sopanrao Kadam
Summary: This study identified genes involved in regulating chlorophyll content (CC) and relative water content (RWC) in pearl millet under abiotic stress through weighted gene coexpression network analysis (WGCNA). The dark green module was positively correlated with CC and highlighted ribosome synthesis and plant hormone signaling as significant pathways. The black module showed a negative correlation with CC and RWC. The findings provide novel insights into the molecular mechanisms controlling CC and RWC in pearl millet.
Article
Medical Laboratory Technology
Jee-Young Yeon, Yun Jung Bae, Eun-Young Kim, Eun-Ju Lee
CLINICA CHIMICA ACTA
(2015)
Article
Genetics & Heredity
Yun Jung Bae, Sung-Eun Kim, Seong Yeon Hong, Taesun Park, Sang Gyu Lee, Myung-Sook Choi, Mi-Kyung Sung
GENES AND NUTRITION
(2016)
Article
Nutrition & Dietetics
Mi-Kyeong Choi, Yun-Jung Bae
NUTRITION RESEARCH AND PRACTICE
(2016)
Article
Multidisciplinary Sciences
Samuel Sunghwan Cho, Yongkang Kim, Joon Yoon, Minseok Seo, Su-kyung Shin, Eun-Young Kwon, Sung-Eun Kim, Yun-Jung Bae, Seungyeoun Lee, Mi-Kyung Sung, Myung-Sook Choi, Taesung Park
Article
Biochemistry & Molecular Biology
Mi-Kyeong Choi, Yun-Jung Bae
BIOLOGICAL TRACE ELEMENT RESEARCH
(2013)
Article
Biochemistry & Molecular Biology
Yun-Jung Bae, Mi-Hyun Kim, Je-Hyuk Lee, Mi-Kyeong Choi
BIOLOGICAL TRACE ELEMENT RESEARCH
(2015)
Article
Multidisciplinary Sciences
Mi-Kyeong Choi, Yun Jung Bae
Article
Multidisciplinary Sciences
Sung-Eun Kim, Jinsil Choo, Joon Yoon, Jae Ryang Chu, Yun Jung Bae, Seungyeoun Lee, Taesung Park, Mi-Kyung Sung
Article
Nutrition & Dietetics
Mi-Kyeong Choi, Yeon-Kyung Lee, Young-Ran Heo, Taisun Hyun, Eun-Soon Lyu, Haeryun Park, Hee-Kyong Ro, Yun Jung Bae
ECOLOGY OF FOOD AND NUTRITION
(2019)