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Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish
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shinySISPA: A web tool for defining sample groups using gene sets from multiple-omics data.

Bhakti Dwivedi1, Jeanne Kowalski1,2

  • 1Winship Cancer Institute , Emory University, Atlanta, GA, 30322, USA.

F1000Research
|November 16, 2018
PubMed
Summary
This summary is machine-generated.

Gene panels enable simultaneous testing of many samples for specific genes, aiding cancer treatment identification. shinySISPA is a web tool that analyzes gene panel data to find clinical associations.

Keywords:
Gene set profileGenomicsIntegrated analysisSample profile

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • Gene panels offer targeted genetic analysis for numerous samples, contrasting with genome-wide approaches.
  • Cancer gene panels, often testing ~50 genes, can identify mutations and guide treatment strategies.
  • Technological advancements have led to gene panels analyzing diverse data types like gene expression and mutations.

Purpose of the Study:

  • To develop a web-based tool for analyzing gene panel data.
  • To identify molecular profiles within samples based on user-defined criteria.
  • To facilitate the examination of clinical associations using gene panel data.

Main Methods:

  • Development of shinySISPA, a web-based shiny tool for Sample Integrated Set Profile Analysis.
  • Utilizing user-specified molecular profiles and gene panel data matrices (gene expression, variants).
  • Defining two sample groups: those with and without molecular profile support.

Main Results:

  • shinySISPA enables the classification of samples based on predefined molecular profiles.
  • The tool allows for the identification of samples supporting specific gene expression and mutation patterns.
  • Facilitates the examination of clinical associations between molecular profiles and sample groups.

Conclusions:

  • shinySISPA provides a user-friendly platform for analyzing complex gene panel data.
  • The tool supports the discovery of clinical associations by comparing sample groups with and without specific molecular profiles.
  • shinySISPA is accessible online for researchers studying gene panels in various contexts, including cancer.