Services Offered

CAGE: Cap Analysis of Gene Expression
Developed by RIKEN, this is a high-throughput gene expression analysis which uses next-generation sequencing technology.


Cap Analysis of Gene Expression (CAGE) is a unique technique developed by RIKEN which thoroughly elucidates transcription start sites by identifying the base sequence of the 5’ ends of capped RNA molecules. In combination with next-generation sequencers, CAGE offers an excellent solution for expression profiling and genome annotation.

Through CAGE, the following analyses are possible:

  • Analysis of mRNA transcription start sites
  • Prediction of promoter regions
  • Selective analysis of promoter regions in different organs, cells or stages
  • Quantitative mRNA expression profiling
  • Directional expression analysis of sense and antisense strands

Schematic Diagram of CAGE

Histogram depicting CAGE tags mapped to a reference genome

CAGE provides a wider dynamic range and a more quantitative gene expression profile than conventional microarray analysis. Because the technique does not rely on the use of probes to detect transcription start sites, a comprehensive and quantitative analysis, including analysis of previously unknown transcription start sites, is possible. For example, in the figure above, it is possible to differentiate between transcription start sites expressed only in a normal cell and those expressed in a cancerous cell.

Sample Requirement

  • Starting material :total RNA
  • Amount : > 5 μg/sample
  • Concentration : >1 μg/μl in RNase-free solution

Analysis Steps of CAGE

  • Preparing CAGE library
  • Sequencing the library using HiSeq2500 (e.g. 50-base single read sequencing)
  • Filtering reads (optional)
  • Mapping and clustering (optional)
  • Differential gene expression analysis and motif search (optional)

Delivered Data

  • Sequencing data (Base sequence information in text format following base-calling and quality assessment data)
  • CAGE tag sequence data (CAGE tags determined through sequencing)
  • Genome mapping data (All CAGE tags mapped to a reference genome)
  • CAGE tag clustering data (Clustering information about mapped CAGE tags)
  • CAGE tag annotation data (Genome information related to clusters of CAGE tags)
  • Genome Browser (A Genome Browser which displays mapped CAGE tags)
  • Quality Report (Results of quality check of CAGE library and sequencing data)
  • Analysis Report (Summary of analysis results)
  • Please contact us to discuss other result formats.

*According to the nature of the CAGE analysis, limitations may arise due to the species of the sample
(e.g. accuracy of the reference genome).                                                                               


Quantitativity, Sensitivity and Resolution of the CAGE Technique

The figure to the left compares results from CAGE and microarray analysis of two different samples which were mixed in varying proportions.
CAGE analysis provides excellent resolution and distinguishes variations as little as 5% in the expression profile. It is difficult to distinguish such a variation with the microarray analysis. Additionally, CAGE analysis offers excellent reproducibility of experimental results, equal or superior to that offered by microarray analysis.