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RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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MISSION esiRNA for RNAi Screening in Mammalian Cells
15:31

MISSION esiRNA for RNAi Screening in Mammalian Cells

Published on: May 12, 2010

ScreenSifter: analysis and visualization of RNAi screening data.

Pankaj Kumar1, Germaine Goh, Sarawut Wongphayak

  • 1Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos 138673, Singapore. fbard@imcb.a-star.edu.sg.

BMC Bioinformatics
|October 4, 2013
PubMed
Summary

ScreenSifter is a new open-source application for RNAi screening data analysis. It offers intuitive visualization and data mining, accelerating biological discovery from RNA interference screens.

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MISSION esiRNA for RNAi Screening in Mammalian Cells
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Published on: May 12, 2010

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Area of Science:

  • Genetics
  • Molecular Biology
  • Bioinformatics

Background:

  • RNA interference (RNAi) screening is vital for studying intracellular genetics in metazoans.
  • RNAi screening draws inspiration from compound screening techniques, including data analysis.
  • Unlike compounds, RNAi agents link to extensive gene-centric public data, but analysis tools lack interactive gene information visualization.

Purpose of the Study:

  • To develop an open-source desktop application for RNAi screening data analysis.
  • To enhance biological data mining through interactive visualization.
  • To facilitate storage, statistical analysis, and discovery from RNAi screening datasets.

Main Methods:

  • Developed ScreenSifter, an open-source desktop application.
  • Implemented features for meta-data acquisition and secure data storage.
  • Integrated a graphical user interface for hit list definition and biological module visualization.
  • Incorporated Gene Ontology and protein-protein interaction analyses.
  • Enabled screen-to-screen comparison visualization.

Main Results:

  • ScreenSifter facilitates storing and statistical analysis of RNAi screening datasets.
  • The application provides rapid and intuitive biological data mining.
  • Interactive visualization of biological modules and gene information is supported.
  • Screen-to-screen comparisons can be visualized.

Conclusions:

  • ScreenSifter accelerates and simplifies RNAi screen data analysis.
  • The software enables biological discovery through unique data visualization capabilities.
  • It provides a user-friendly platform for researchers analyzing RNAi screening data.