LnCeVar 2.0: an updated resource and web tools for genomic variations disrupting ceRNA networks from...

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Competing endogenous RNA (ceRNA) networks play crucial roles in gene regulation.
• Genomic variations, particularly single nucleotide variants (SNVs), can disrupt these networks.
• Understanding these disruptions is vital for deciphering complex disease mechanisms.

Purpose of the Study:

• To update and expand the LnCeVar database with novel genomic variation data impacting ceRNA networks.
• To provide tools for analyzing SNV-ceRNA interactions at single-cell and spatial resolution.
• To facilitate high-resolution investigation of regulatory mechanisms in disease ecosystems.

Main Methods:

• Integration of 16,937 cancer biomarkers and 5,785 validated ceRNA interactions.
• Inclusion of 812 single-cell RNA sequencing/spatial transcriptomics datasets covering 102 diseases.
• Analysis of over 5.2 million SNV-ceRNA events across millions of cells/spots.
• Development of 17 tools for multilevel crosstalk analysis and 3D visualization.

Main Results:

• LnCeVar 2.0 contains extensive data on SNV-ceRNA events linked to cancer pathogenesis.
• The database includes millions of cell- and spatial-specific SNV-ceRNA events.
• Novel inference of SNV effects on cell types, states, and functions is provided.
• User-friendly interfaces (CeVarState, CeVarSC3D, CeVarST3D) enable detailed analysis and visualization.

Conclusions:

• LnCeVar 2.0 offers a comprehensive resource for studying genomic variations in ceRNA networks.
• The database facilitates high-resolution investigation of SNV-ceRNA interactions.
• This resource advances the understanding of regulatory mechanisms in complex disease ecosystems.