AIMC Topic: Signal Transduction

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Screening of key immunerelated gene in Parkinsons disease based on WGCNA and machine learning.

Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences
OBJECTIVES: Abnormal immune system activation and inflammation are crucial in causing Parkinson's disease. However, we still don't fully understand how certain immune-related genes contribute to the disease's development and progression. This study a...

Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis.

Nucleic acids research
Plant Reactome (https://plantreactome.gramene.org) is a freely accessible, comprehensive plant pathway knowledgebase. It provides curated reference pathways from rice (Oryza sativa) and gene-orthology-based pathway projections to 129 additional speci...

The Reactome Pathway Knowledgebase 2024.

Nucleic acids research
The Reactome Knowledgebase (https://reactome.org), an Elixir and GCBR core biological data resource, provides manually curated molecular details of a broad range of normal and disease-related biological processes. Processes are annotated as an ordere...

PPICT: an integrated deep neural network for predicting inter-protein PTM cross-talk.

Briefings in bioinformatics
Post-translational modifications (PTMs) fine-tune various signaling pathways not only by the modification of a single residue, but also by the interplay of different modifications on residue pairs within or between proteins, defined as PTM cross-talk...

Defining the characteristics of interferon-alpha-stimulated human genes: insight from expression data and machine learning.

GigaScience
BACKGROUND: A virus-infected cell triggers a signalling cascade, resulting in the secretion of interferons (IFNs), which in turn induces the upregulation of the IFN-stimulated genes (ISGs) that play a role in antipathogen host defence. Here, we condu...

PRECOGx: exploring GPCR signaling mechanisms with deep protein representations.

Nucleic acids research
In this study we show that protein language models can encode structural and functional information of GPCR sequences that can be used to predict their signaling and functional repertoire. We used the ESM1b protein embeddings as features and the bind...

Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase.

Database : the journal of biological databases and curation
ABSTRACT: Reactome is a database of human biological pathways manually curated from the primary literature and peer-reviewed by experts. To evaluate the utility of Reactome pathways for predicting functional consequences of genetic perturbations, we ...

The reactome pathway knowledgebase 2022.

Nucleic acids research
The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary and acquired dise...

Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins.

Proceedings of the National Academy of Sciences of the United States of America
RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-at...