TromER Database

Transcriptome Analysis Database

Description: The transcriptome analyser (TromER) project aims at providing powerful tools to determine and document all the transcribed elements of a genome. The transcribed parts are defined by analysing experimental evidence, like expressed sequence tags (EST) and other mRNA sequences. The transcriptome data include transcribed regions, splice variants, SAGE mappings, MPSS mappings, Affymetrix chips mappings, etc., for several organisms. The Tromer Web Service provides a user-friendly web interface to gene predictions, or transcriptome units of several genomes (such us human, mouse, rat, drosophila and worm).

Access to the TromER Database

   Genome                                              Assembly


   in TROMER DB by TROMER ID, SwissProt ID
   NCBI-GENE ID or GENE name


An atlas of human gene expression from massively parallel signature sequencing (MPSS).
Jongeneel CV, Delorenzi M, Iseli C, et al.
Genome Res. 2005 15: 1007-1014.
trome, trEST and trGEN: databases of predicted protein sequences.
Sperisen P, Iseli C, Pagni M, Stevenson BJ, Bucher P, and Jongeneel CV.
NAR 2004 32: D509-D511..
Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing.
Jongeneel CV, Iseli C, Stevenson BJ, et al.
PNAS 2003 100: 4702-4705.
Long-range heterogeneity at the 3' ends of human mRNAs.
Iseli C, Stevenson BJ, De Souza SJ, et al.
Genome Res. 2002 12: 1068-1074.

Other Databases and Tool at SIB External Genome Browsers
  • CleanEx A database which provides access to public gene expression data
  • EPD Eukarytic Promoter database
  • HTPSELEX A database of in vitro selected TFBS sequences obtained with high-throughput SELEX
  • myHITS A database and web tools devoted to protein domains
  • EMBnet Swiss Node Of The EMBnet Group
  • ENSEMBL ENSEMBL Genome Browser   
  • UCSC UCSC Genome Browser
  • NCBI Entrez NCBI Entrez cross-database search page

Last update 13 May 2010