Ramp Atlas

Ramp Atlas provides tissue- and cell-type-resolved analysis of ramp sequences to characterize 5' translational efficiency patterns that modulate ribosomal collisions and influence gene expression.

Key Features:

• Ramp sequence definition: Ramp sequences are characterized by lower average translational efficiency at the 5' end of highly expressed genes, which reduces ribosomal collisions downstream and can enhance overall translation.
• Precomputed dataset: Precomputed ramp sequence data are available across 18,388 genes in 62 tissues and 66 cell types.
• FASTA-based computation: Computes tissue-specific ramp sequences from input FASTA files.
• Tissue- and cell-type variation: Identified 3,108 genes with tissue- and cell-type-specific ramp sequence variations.
• Expression correlation: Associates ramp sequence variations with increased gene expression in specific tissues and cell types.
• Viral and host analysis: Detected tissue-specific ramp sequences in seven SARS-CoV-2 viral genes and seven human entry factor genes.

Scientific Applications:

• Tissue- and cell-type gene regulation: Characterizing how ramp sequences fine-tune translation and gene expression across tissues and cell types.
• Expression association studies: Linking ramp sequence variation to increased gene expression in specific tissues and cells.
• Viral pathogenesis investigations: Investigating tissue-specific ramp sequences in SARS-CoV-2 viral genes and human entry factor genes to generate hypotheses about tissue-specific viral proliferation.

Methodology:

Uses precomputed ramp sequence datasets across 18,388 genes in 62 tissues and 66 cell types, computes tissue-specific ramp sequences from input FASTA files, and identifies genes with tissue- and cell-type-specific ramp variations and correlations with gene expression, including detection of tissue-specific ramp sequences in SARS-CoV-2 and human entry factor genes.