Many genes are involved in mammalian cell apoptosis pathway. These apoptosis genes often contain characteristic functional domains, and can be classified into at least 15 functional groups, according to previous reports. Using an integrated bioinformatics platform for motif or domain search from three public mammalian proteomes (International Protein Index database for human, mouse, and rat), we systematically cataloged all of the proteins involved in mammalian apoptosis pathway. By localizing those proteins onto the genomes, we obtained a gene locus centric apoptosis gene catalog for human, mouse and rat. Further phylogenetic analysis showed that most of the apoptosis related gene loci are conserved among these three mammals. Interestingly, about one-third of apoptosis gene loci form gene clusters on mammal chromosomes, and exist in the three species, which indicated that mammalian apoptosis gene orders are also conserved. In addition, some tandem duplicated gene loci were revealed by comparing gene loci clusters in the three species. All data produced in this work were stored in a relational database and may be viewed at http://pcas.cbi.pku.edu.cn/database/apd.php.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1111/j.1745-7270.2005.00043.x | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Spatially explicit estimation of recent migration rates in plants using genotypic data.
Genetics
January 2025
Institute of Forest Sciences (ICIFOR-INIA), CSIC, Ctra. De la Coruña km 7.5, 28040 Madrid, Spain.
We present a new hierarchical Bayesian method using multilocus genotypes to estimate recent seed and pollen migration rates in a spatially explicit framework that incorporates distance effects separately for each type of dispersal. The method additionally estimates population allelic frequencies, population divergence values, individual inbreeding coefficients, individual maternal and paternal ancestries, and allelic dropout rates. We conduct a numerical simulation analysis that indicates that the method can provide reliable estimates of seed and pollen migration rates and allow accurate inference of spatial effects on migration, at affordable sample sizes (25-50 individuals/population) when population genetic divergence is not low (FST≥0.
View Article and Find Full Text PDFExploring potential therapeutic targets for small cell lung cancer based on transcriptomics combined with Mendelian randomization analysis.
Front Immunol
January 2025
Department of Medical Oncology, Wenzhou TCM Hospital of Zhejiang Chinese Medical University, Wenzhou, China.
Objective: The main objective of this study was to explore and identify new genetic targets in small-cell lung cancer (SCLC) through transcriptomics analysis and Mendelian randomization (MR) analysis, which will help in the subsequent development of new therapeutic interventions.
Methods: In this study, we extracted the SCLC dataset from the Gene Expression Omnibus (GEO) database, processed the data, and screened out differentially expressed genes (DEGs) using R software. Based on expression quantitative trait loci data and the genome-wide association study data of SCLC, MR analysis was used to screen the genes closely related to SCLC disease, which intersect with DEGs to obtain co-expressed genes (CEGs), and the biological functions and pathways of CEGs were further explored by enrichment analysis.
Genetic dissection of a reduced seed-shattering trait acquired in rice domestication.
Breed Sci
September 2024
Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo 657-8501, Japan.
Asian rice ( L.) was domesticated from wild rice ( Griff.).
View Article and Find Full Text PDFThe 3D genome and its impacts on human health and disease.
Life Med
April 2023
MOE Key Laboratory of Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.
Eukaryotic genomes are highly compacted in the cell nucleus. Two loci separated by a long linear distance can be brought into proximity in space through DNA-binding proteins and RNAs, which contributes profoundly to the regulation of gene expression. Recent technology advances have enabled the development and application of the chromosome conformation capture (3C) technique and a host of 3C-based methods that enable genome-scale investigations into changes in chromatin high-order structures during diverse physiological processes and diseases.
View Article and Find Full Text PDFIdentifying Key Biomarkers Related to Immune Response in the Progression of Diabetic Kidney Disease: Mendelian Randomization Combined With Comprehensive Transcriptomics and Single-Cell Sequencing Analysis.
J Inflamm Res
January 2025
Department of Nephrology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China.
Background: Renal failure related death caused by diabetic kidney disease (DKD) is an inevitable outcome for most patients. This study aimed to identify the critical genes involved in the onset and progression of DKD and to explore potential therapeutic targets of DKD.
Methods: We conducted a batch of protein quantitative trait loci (pQTL) Mendelian randomization analysis to obtain a group of proteins with causal relationships with DKD and then identified key proteins through colocalization analysis to determine correlations between variant proteins and disease outcomes.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!