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Related Concept Videos

Ribosome Profiling02:24

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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Related Experiment Video

Updated: Jun 15, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

SplicerAV: a tool for mining microarray expression data for changes in RNA processing.

Timothy J Robinson1, Michaela A Dinan, Mark Dewhirst

  • 1Molecular Cancer Biology Program, Duke University Medical Center, Durham, USA.

BMC Bioinformatics
|February 27, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces SplicerAV, a tool to analyze mRNA processing from existing microarray data. It identified hundreds of oncogene-induced changes and linked isoform alterations to breast cancer aggressiveness.

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Using the E1A Minigene Tool to Study mRNA Splicing Changes
10:25

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Published on: April 22, 2021

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Extensive microarray data exists from Affymetrix HG-U133 and HG-U95 platforms.
  • Previous analyses focused on gene expression, not mRNA processing.
  • Archival datasets offer potential for studying alternative mRNA processing.

Purpose of the Study:

  • To explore the use of HG-U133 microarray data for identifying alternative mRNA processing changes.
  • To develop and apply a program, SplicerAV, for analyzing transcript isoform abundance from microarray data.

Main Methods:

  • Utilized SplicerAV to analyze in vivo and in vitro breast cancer microarray datasets.
  • Performed gene and isoform-specific expression profiling on Affymetrix U133 plus 2.0 data.
  • Reanalyzed data from oncogene over-expression experiments and clinical breast tumor samples.

Main Results:

  • Identified hundreds of oncogene-induced mRNA isoform changes, including a novel EGFR activation mechanism.
  • Predicted 241 isoform changes between low and high-grade breast tumors.
  • Found 15 isoform changes associated with aggressive cancer across three datasets.

Conclusions:

  • SplicerAV enables the detection of RNA isoform changes in archival microarray data.
  • Revealed novel insights into oncogene-induced alternative mRNA processing and EGFR activation.
  • Conducted the largest clinical dataset analysis for mRNA processing changes linked to cancer survival.