About the C.elegans 4 Database

Usage note: Filters and cookies
cisRED manages your 'Filter' settings via a browser 'cookie'. You must allow your web browser to accept cookies from cisred.org for your filter settings to take effect.

The C. elegans v4 database contains conserved motifs in the upstream regions of 3847 C. elegans transcripts from the WS170 release. Motifs are based on sequence similarity with the upstream regions of orthologous transcripts in C. briggsae, C. remanei, C. brenneri, C. japonica, Pristionchus pacificus, Brugia malayi, and Trichinella spiralis. All orthologue predictions were made using WABA. Only transcripts with at least 3 orthologues were used in this analysis. The C. elegans genome was repeatmasked. The upstream region of each gene was defined as: 1500 bases upstream of the ATG, not counting repeats, or until the end of the next-most upstream gene, whichever is shorter.

Motif discovery on these sequence sets was performed using only MotifSampler. For any motif, click on its ID in the Atomic Motif ID column to see more information about that motif, including what the motif sequence was in the orthologous sequence. Plus, click on any motif logo to see a larger version of the logo.

To search for a transcript, enter its WormPep transcript ID in the search field. Alternatively, you can browse the transcripts in alphabetical order, search by motif sequence, or search by genomic region.

Preliminary annotation: 17740 motifs have been annotated with TRANSFAC models at a p-value threshold 1e-05; 23331 motifs have been annotated with JASPAR models at a p-value threshold of 1e-04; 7449 motifs have been annotated with models based on experimentally proven C. elegans TFBS from the ORegAnno database at a p-value threshold of 1.5e-04.

To cite this work, please cite both the NAR Database Issue paper and 'M. Sleumer personal communication'.

Direct SQL queries can be run against the database cisred_Cele_4 at db.cisred.org, with the username 'anonymous', and no password.