Feature based prediction of non-classical and leaderless protein secretion.
J. Dyrløv Bendtsen1, L. Juhl Jensen1,
N. Blom1, G. von Heijne2
and S. Brunak1.
Protein Eng. Des. Sel., 17(4):349-356, 2004
Center for Biological Sequence Analysis, The Technical University of Denmark,
DK-2800 Lyngby, Denmark
Stockholm Bioinformatics Center, Department of Biochemistry,
Stockholm University, S-106 91 Stockholm, Sweden
We present a sequence based
method - SecretomeP
- for prediction of mammalian secretory
proteins targeted to the non-classical secretory pathway, i.e.
proteins without an N-terminal signal peptide. So far only a
limited number of proteins have been shown experimentally to
enter the non-classical secretory pathway. These are mainly
fibroblast growth factors, interleukins and galectins found in
the extracellular matrix. We have discovered that certain
pathway independent features are shared among secreted proteins.
The method presented here is also capable of predicting (signal
peptide containing) secretory proteins where only the mature
part of the protein has been annotated, or cases where the
signal peptide remains uncleaved. By scanning the entire human
proteome we identify new proteins potentially undergoing
Jannick Dyrløv Bendtsen,