Simultaneous expression profiling and transcription start site (TSS) detection

In Digital Gene Expression (DGE) techniques such as SAGE (Serial analysis of gene expression), tags generated from the end of cDNAs are identified and quantified by sequencing, resulting in quantitative mRNA expression profiles representative to the starting samples. In contrast to conventional SAGE, CAGE is capable of quantitative expression profiling and promoter identification at the same time. CAGE has been successfully employed in large-scale projects such as the RIKEN FANTOM and NIH ENCODE Projects.

What CAGE can do for you:

• Link of expression values to promoter
• Shift the focus on transcript analysis from 3'-end related information to the true 5'-ends of mRNA for the Identification of Transcriptional Start Sites (TSS)
• Evidence of rare transcripts
• Tagging of novel genes or gene variants, any transcript (known or unknown) can be quantified
• No false positives due to cross-hybridization, identification via highly specific tag
• Experimental validation of TSS where bioinformatics cannot predict transcriptional start-points
• Digital Expression Profiling: absolute expression values

Example for the output of CAGE experiments:

1. Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Affymetrix ENCODE Transcriptome Project & Cold Spring Harbor Laboratory ENCODE Transcriptome Project. Nature 2009 Feb 19;457(7232):1028-32 more in PDF
2. Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer. Maeda et al. Biotechniques. 2008 Jul;45(1):95-7.
3. Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference. de Hoon M, Hayashizaki Y. Biotechniques. 2008 Apr;44(5):627-8, 630, 632.
4. A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Faulkner et al. Genomics. 2008 Mar;91(3):281-8
5. Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Barrera et al. Genome Res. 2008 Jan;18(1):46-59.
6. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. ENCODE Project Consortium. Nature. 2007 Jun 14;447(7146):799-816.
7. Large-scale clustering of CAGE tag expression data. Shimokawa et al. BMC Bioinformatics. 2007 May 21;8:161.
8. CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts. Katayama et al. Genome Biol. 2007 Mar 26;8(3):R42.
9. Tagging mammalian transcription complexity. Carninci P. Trends Genet. 2006 Sep;22(9):501-10.
10. The complexity of the mammalian transcriptome. Gustincich et al. J Physiol. 2006 Sep 1;575(Pt 2):321-32.
11. CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Kawaji et al. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D632-6.
12. CAGE: cap analysis of gene expression. Kodzius et al. Nat Methods. 2006 Mar;3(3):211-22
13. A method for similarity search of genomic positional expression using CAGE. Seno et al. PLoS Genet. 2006 Apr;2(4):e44.
14. Genome-wide analysis of mammalian promoter architecture and evolution. Carninci et al. Nat Genet. 2006 Jun;38(6):626-35. Comment in: Nat Genet. 2006 Jun;38(6):608-9.
15. The transcriptional landscape of the mammalian genome. Carninci P et al. Science. 2005 Sep 2;309(5740):1559-63. Erratum in: Science. 2006 Mar 24;311(5768):1713. Comment in: Science. 2006 Mar 24;311(5768):1709-11; author reply 1709-11.
16. Mice and men: their promoter properties. Bajic et al. PLoS Genet. 2006 Apr;2(4):e54.
17. Tag-based approaches for transcriptome research and genome annotation. Harbers M, Carninci P. Nat Methods. 2005 Jul;2(7):495-502.
18. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Shiraki et al. Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15776-81.