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Related Concept Videos

Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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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Related Experiment Video

Updated: May 31, 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

Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants.

Ping Chen1, Tatiana Lepikhova, Yizhou Hu

  • 1Research Programs Unit, Genome-Scale Biology and Institute of Biomedicine, Biochemistry and Developmental Biology, 00014 University of Helsinki, Finland.

Nucleic Acids Research
|July 13, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces Multiple Exon Array Preprocessing (MEAP), a new method for analyzing exon array data. MEAP provides reliable quantification of alternative splicing events, aiding cancer research.

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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

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Last Updated: May 31, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
09:58

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Alternative splicing of pre-mRNA generates protein diversity, crucial for cellular function.
  • Splicing machinery dysfunction and aberrant transcript expression are implicated in cancer progression and drug resistance.
  • Exon microarray technology offers genome-wide quantification of exon expression and alternative splicing events.

Purpose of the Study:

  • To introduce a novel, computationally efficient methodology, Multiple Exon Array Preprocessing (MEAP), for exon array data pre-processing, analysis, and visualization.
  • To address the challenges in analyzing exon array data for reliable quantification of exons and alternatively spliced variants.
  • To validate the accuracy of MEAP by comparing its expression estimates with quantitative PCR (qPCR).

Main Methods:

  • Developed and implemented the Multiple Exon Array Preprocessing (MEAP) methodology.
  • Compared MEAP with existing pre-processing methods for exon array data.
  • Validated MEAP's expression estimates for six exons and two alternatively spliced variants using qPCR.
  • Analyzed exon array data from head and neck squamous cell carcinoma (HNSCC) cell lines.

Main Results:

  • MEAP demonstrated reliable expression quantification at exon, alternatively spliced variant, and gene levels.
  • Validation using qPCR corroborated MEAP's expression estimates.
  • Analysis of HNSCC data identified several transcripts associated with 11q13 amplification.
  • These transcripts are linked to decreased survival and metastasis in HNSCC patients.

Conclusions:

  • MEAP is a reliable and computationally efficient tool for exon array data analysis.
  • MEAP facilitates the discovery of novel, experimentally testable predictions regarding alternative splicing in cancer.
  • The findings highlight the role of specific transcripts in HNSCC progression associated with 11q13 amplification.