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Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.

Jüri Reimand1, Meelis Kull, Hedi Peterson

  • 1Institute of Computer Science, University of Tartu, Liivi 2, 50409 Tartu, Estonia.

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Summary

g:Profiler is a web tool for analyzing gene lists from high-throughput data. It offers Gene Ontology, pathway enrichment, and ortholog analysis for 31 species.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • High-throughput genomic data analysis generates large gene lists requiring interpretation.
  • Gene list enrichment analysis is crucial for understanding biological processes and pathways.
  • Existing tools may lack comprehensive features for gene list manipulation and analysis.

Purpose of the Study:

  • To present g:Profiler, a public web server for characterizing and manipulating gene lists.
  • To provide powerful visualization for Gene Ontology (GO), pathway, and transcription factor binding site enrichments.
  • To offer integrated modules for identifier conversion, ortholog searching, and co-expression analysis.

Main Methods:

  • Development of a user-friendly web interface for gene list analysis.
  • Implementation of efficient algorithms for enrichment analysis and ranked gene list interpretation.
  • Integration of modules: g:Convert (identifier conversion), g:Orth (ortholog identification), and g:Sorter (co-expression analysis).
  • Inclusion of an improved method for estimating multiple testing effects in complex structures like GO.

Main Results:

  • g:Profiler supports enrichment analysis for Gene Ontology, pathways, and transcription factor binding sites.
  • The tool facilitates interpretation of ranked gene lists derived from genomic data.
  • Integrated modules provide essential bioinformatics functionalities, supporting 31 species with regularly updated data.

Conclusions:

  • g:Profiler offers a comprehensive and integrated solution for gene list analysis in bioinformatics.
  • The web server enhances the interpretation of high-throughput genomic data through powerful visualization and analysis tools.
  • g:Profiler supports the broader bioinformatics community with accessible and up-to-date functionalities.