2004 Pubmed) was then used to obtain know mouse orthologs for each human protein and a linking table producedĪ web interface was then created to allow searches for human proteins containing TMDs of a given topology containing or notĬontaining either known motifs or user defined motifs. The Ensembl Perl API (Stabenau et al, Genome Res. These data for both mouse and human were entered into a relational MySQL database as separate data sets. These entries were in turn parsed to find data pertaining to the position of the TMD, its topology,Īny external identifiers, subcellular locations from gene ontology (GO) identifiers and known motifs. These XML files were then parsed using an in house written Perl script to obtain entries for proteins containing only a single Initially, data files for both Human and Mouse were obtained from the LOCATE (PMID: 17986452) downloads website. Signals retrograde transport from Golgi to ER Signals endocytosis, TGN-endosome-lysosome sorting, melanosome biogenesis Signals endocytosis, TGN-endosome-lysosome sorting, melanosome biogenesis, basolateral sorting MGP (that exact motif, but anywhere in the sequence)Īn M followed by at least two G’s followed by a PĪn M followed by two, three or four G’s followed by a P MG\wPĪn M followed by a G, followed by any two, three or four amino acids followed by a P If this orthologue exists in our mouse database there is a clickable tick mark which links to this entry to compare common motifs between the orthologues. Also for each human protein, where possible, a mouse orthologue is displayed in the last column. The results table consists of proteins that fit your search criteria.įor each protein, links are provided to external sites and relevant information displayed. You will be able to get by if you use the table below (adapted from )). This can get very complicated but essentially These should be in the form of a pattern or more specifically a Perl regular expression. Second, choose any motifs you want the proteins to contain or not to contain.įinally, enter any other motifs that you want to search for. First, choose if you want to limit the results to Type I transmembrane proteins, Type II transmembrane proteins, or both.
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