AIMC Topic: Gene Ontology

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Identifying the missing proteins in human proteome by biological language model.

BMC systems biology
BACKGROUND: With the rapid development of high-throughput sequencing technology, the proteomics research becomes a trendy field in the post genomics era. It is necessary to identify all the native-encoding protein sequences for further function and p...

Grouping miRNAs of similar functions via weighted information content of gene ontology.

BMC bioinformatics
BACKGROUND: Regulation mechanisms between miRNAs and genes are complicated. To accomplish a biological function, a miRNA may regulate multiple target genes, and similarly a target gene may be regulated by multiple miRNAs. Wet-lab knowledge of co-regu...

Gogadget: An R Package for Interpretation and Visualization of GO Enrichment Results.

Molecular informatics
Gene expression profiling followed by gene ontology (GO) term enrichment analysis can generate long lists of significant GO terms. To interpret these results and get biological insight in the data, filtering and rearranging these long lists of GO ter...

Expansion of the Gene Ontology knowledgebase and resources.

Nucleic acids research
The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our conti...

Prediction of Protein-Protein Interactions by Evidence Combining Methods.

International journal of molecular sciences
Most cellular functions involve proteins' features based on their physical interactions with other partner proteins. Sketching a map of protein-protein interactions (PPIs) is therefore an important inception step towards understanding the basics of c...

Analysis of Important Gene Ontology Terms and Biological Pathways Related to Pancreatic Cancer.

BioMed research international
Pancreatic cancer is a serious disease that results in more than thirty thousand deaths around the world per year. To design effective treatments, many investigators have devoted themselves to the study of biological processes and mechanisms underlyi...

SGFSC: speeding the gene functional similarity calculation based on hash tables.

BMC bioinformatics
BACKGROUND: In recent years, many measures of gene functional similarity have been proposed and widely used in all kinds of essential research. These methods are mainly divided into two categories: pairwise approaches and group-wise approaches. Howev...

Comprehensive analysis of epigenetically regulated genes in anergic T cells.

Cellular immunology
T cell anergy is one of the important mechanisms for immune tolerance. The results of many studies investigating the mechanism for T cell anergy induction have revealed that the expression of several genes was up-regulated in anergic T cells. It has ...

Combining sequence and Gene Ontology for protein module detection in the Weighted Network.

Journal of theoretical biology
Studies of protein modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approaches have played an important role in locating ...

Integrating network, sequence and functional features using machine learning approaches towards identification of novel Alzheimer genes.

BMC genomics
BACKGROUND: Alzheimer's disease (AD) is a complex progressive neurodegenerative disorder commonly characterized by short term memory loss. Presently no effective therapeutic treatments exist that can completely cure this disease. The cause of Alzheim...