FEBS Letters 2003Last updated: 2003/10/28

Absolute Expression Values for Mouse Transcripts: Re-Annotation of the READ Expression Database by the Use of CAGE and EST Sequence Tags.

R Kodzius, Y Matsumura, T Kasukawa, K Shimokawa, S Fukuda, T Shiraki, M Nakamura, T Arakawa, D Sasaki, J Kawai, M Harbers, P Carninci, Y Hayashizaki


This internet site http://genome.gsc.riken.jp/absolute contains following tables with tab delimited text.
These files can be easily open using Microsoft Excel as well.

Web_Table 1 - file absolute_count_20k_50tissues.txt
Contains READ absolute values for FANTOM1 clones in 50 tissues.

TU - transcriptional unit
READ_ID - READ Identification number
Tissues - tissues used for READ
Annotation - Functional Annotation for TU

Web_Table 2 - file absolute_count_60k_21tissues.txt
Contains READ absolute values for FANTOM2 clones in 20 tissues.

TU - transcriptional unit
READ_ID - READ Identification number
Tissues - tissues used for READ
Annotation - Functional Annotation for TU

Web_Table 3 - file validation_CAGE_SAGE_EST.txt
Contains TU counts in libraries used for READ absolute values validation.

TU - transcriptional unit
READ_ID - READ Identification number
Library - Library used for READ validation
Annotation - Functional Annotation for TU
GO IDs - Gene Ontology ID

Web_Table 4 - file tpm_count_libr_READ.txt
Contains tpm expression information for libraries used in bioinformatic analysis.

TU - transcriptional unit
EST - tags originating from EST library
CAGE - tags originating from CAGE library
SAGE - tags originating from SAGE library
READ - absolute values in READ for TUs in particular tissue
READ_ID - READ Identification number
Annotation - Functional Annotation for TU

Internet sites for READ database containing relative values
For FANTOM1 - http://read.gsc.riken.jp/
For FANTOM2 - http://read.gsc.riken.jp/fantom2/


Comments or suggestions should be sent to:
carninci@riken.jp - corresponding author
ah3q@gsc.riken.jp - database manager