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Ferroptosis-related genes participate in the microglia-induced neuroinflammation of spinal cord injury via NF-κB signaling: evidence from integrated single-cell and spatial transcriptomic analysis.
J Transl Med
January 2025
Division of Spine, Department of Orthopedics, Tongji Hospital affiliated to Tongji University, Tongji University School of Medicine, Shanghai, 200065, China.
Background: Ferroptosis and immune responses are critical pathological events in spinal cord injury (SCI), whereas relative molecular and cellular mechanisms remain unclear.
Methods: Micro-array datasets (GSE45006, GSE69334), RNA sequencing (RNA-seq) dataset (GSE151371), spatial transcriptome datasets (GSE214349, GSE184369), and single cell RNA sequencing (scRNA-seq) datasets (GSE162610, GSE226286) were available from the Gene Expression Omnibus (GEO) database. Through weighted gene co-expression network analysis and differential expression analysis in GSE45006, we identified differentially expressed time- and immune-related genes (DETIRGs) associated with chronic SCI and differentially expressed ferroptosis- and immune-related genes (DEFIRGs), which were validated in GSE151371.
Homo Sapiens Chromosomal Location Ontology: A Framework for Genomic Data in Biomedical Knowledge Graphs.
Sci Data
January 2025
The Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
The Homo sapiens Chromosomal Location Ontology (HSCLO) is designed to facilitate the integration of human genomic features into biomedical knowledge graphs from releases GRCh37 and GRCh38 at multiple resolutions. HSCLO comprises two distinct versions, HSCLO37 and HSCLO38, each tailored to its respective human genome release. This ontology supports the efficient integration and analysis of human genomic data across scales ranging from entire chromosomes to individual base pairs, thereby enhancing data retrieval and interoperability within large-scale biomedical datasets.
View Article and Find Full Text PDFHoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.
Database (Oxford)
January 2025
European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues.
View Article and Find Full Text PDFProgressive Bounded Error Piecewise Linear Approximation with Resolution Reduction for Time Series Data Compression.
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December 2024
Department of Information Management, Tunghai University, Taichung 407224, Taiwan.
Today, huge amounts of time series data are sensed continuously by AIoT devices, transmitted to edge nodes, and to data centers. It costs a lot of energy to transmit these data, store them, and process them. Data compression technologies are commonly used to reduce the data size and thus save energy.
View Article and Find Full Text PDFIntegrated Analysis of Single-Cell and Bulk RNA Data Reveals Complexity and Significance of the Melanoma Interactome.
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January 2025
Department of Dermatology, University of Florida College of Medicine, Gainesville, FL 32606, USA.
Despite significant strides in anti-melanoma therapies, resistance and recurrence remain major challenges. A deeper understanding of the underlying biology of these challenges is necessary for developing more effective treatment paradigms. Melanoma single-cell data were retrieved from the Broad Single Cell Portal (SCP11).
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