K.K. DNAFORM


CAGE™ Library Preparation & Analysis : Technology Overview

Technical Information

CAGE is an unique approach for identifying promoters and gene expression profiling.

 

Based on our full-length cDNA library technology, where an adaptor is ligated to the 5’ end Cap site of each full-length cDNA, CAGE proves comprehensive collection of 5' end tags. By high-throughput CAGE sequencing reads . and mapping them onto genomic sequences, transcriptional start sites can be identified. Thus, CAGE can be a powerful tool for discovery of novel genes, genome-wide gene-expression profiling, and promoter analysis.

 

CAGE Analysis Overview

 

Comparison with other gene expression analysis techniques

There are numerous techniques for analyzing gene expression, and each method has its advantages. CAGE differs from other major gene expression analysis techniques in its capability to accurately identify transcriptional start sites in a genome-wide fashion.

Since CAGE enables detailed analyses of the promoter regions of a gene, it is possible to further analyze the expression of a specific gene regulated by each promoter. Therefore, CAGE can serve as a “new-perspective” approach for genome annotation, by elucidating transcriptional signaling cascades, and performing other functions.

 

 

Comparison among major gene expression analysis techniques
  CAGE RNA-seq SAGE Microarray
de novo Gene Finding good good good N/A
Gene Expression Quantification

superior

※ free of PCR bias unaffected by gene size

good good average
Determining Promoter Site superior average N/A N/A
Motif Finding for Transcription Factor Binding Site superior average

average

※ depending on known 5' end sequence information

average

※ depending on known 5' end sequence information

Identification of Bidirectional Enhancer RNA superior N/A N/A N/A
Determining Transcription Start/1st Exon Site superior average N/A N/A
Determining Gene Structure (intron/exon, alternative splicing variants) N/A

average

※ depending on sequence depth

N/A N/A
Duration of Work Process average average average good
Library Preparation Complicatedness ※Long Time (8 days) average average easy
Data Analysis Tools average good average good

("N/A" means not applicable)

References

FANTOM Main Paper

Others