Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

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...
siRNA - Small Interfering RNAs02:30

siRNA - Small Interfering RNAs

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the ATP-dependent...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Roles of microRNAs in cancers and development.

Methods in molecular biology (Clifton, N.J.)·2014
Same author

Using decision tree learning to predict the responsiveness of hepatitis C patients to drug treatment.

FEBS open bio·2013
Same author

Japanese Alzheimer's disease and other complex disorders diagnosis based on mitochondrial SNP haplogroups.

International journal of Alzheimer's disease·2012
Same author

Efficient prediction methods for selecting effective siRNA sequences.

Computers in biology and medicine·2009
Same author

Mitochondrial haplogroups associated with Japanese Alzheimer's patients.

Journal of bioenergetics and biomembranes·2009
Same author

Selecting effective siRNA target sequences by using Bayes' theorem.

Computational biology and chemistry·2009

Related Experiment Video

Updated: May 18, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Methods for selecting effective siRNA target sequences using a variety of statistical and analytical techniques.

Shigeru Takasaki1

  • 1Toyo University, Ora-gun, Gunma, Japan. s_takasaki@toyo.jp

Methods in Molecular Biology (Clifton, N.J.)
|October 3, 2012
PubMed
Summary

Selecting effective short interfering RNA (siRNA) for gene silencing is challenging. New methods using machine learning and probability predict siRNA efficacy, improving gene function studies in mammalian cells.

More Related Videos

MISSION esiRNA for RNAi Screening in Mammalian Cells
15:31

MISSION esiRNA for RNAi Screening in Mammalian Cells

Published on: May 12, 2010

Genome-wide RNAi Screening to Identify Host Factors That Modulate Oncolytic Virus Therapy
08:51

Genome-wide RNAi Screening to Identify Host Factors That Modulate Oncolytic Virus Therapy

Published on: April 3, 2018

Related Experiment Videos

Last Updated: May 18, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

MISSION esiRNA for RNAi Screening in Mammalian Cells
15:31

MISSION esiRNA for RNAi Screening in Mammalian Cells

Published on: May 12, 2010

Genome-wide RNAi Screening to Identify Host Factors That Modulate Oncolytic Virus Therapy
08:51

Genome-wide RNAi Screening to Identify Host Factors That Modulate Oncolytic Virus Therapy

Published on: April 3, 2018

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genetics

Background:

  • Short interfering RNA (siRNA) is crucial for gene function studies in mammalian cells.
  • However, siRNA efficacy varies significantly, and existing design guidelines lack consistency.
  • This variability complicates the selection of effective siRNA sequences.

Purpose of the Study:

  • To review existing siRNA design guidelines.
  • To propose novel computational methods for selecting effective siRNA sequences.
  • To enhance the predictability of siRNA gene silencing efficacy.

Main Methods:

  • Decision tree learning
  • Bayes' theorem
  • Average silencing probability calculations
  • Hidden Markov models
  • Analysis of dinucleotide frequencies

Main Results:

  • Developed probabilistic methods to predict siRNA effectiveness.
  • These methods offer an alternative to score-based design techniques.
  • Evaluated methods using known effective and ineffective siRNA sequences.
  • Demonstrated general utility for selecting effective siRNA for mammalian genes.

Conclusions:

  • The proposed methods improve the selection of effective siRNA sequences.
  • These approaches enhance the reliability of gene silencing studies.
  • Offers a valuable tool for researchers in mammalian genetics and molecular biology.