PEDS Advance Access published online on April 28, 2004
Protein Engineering Design and Selection, doi:10.1093/protein/gzh037
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1 Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, Technical University of Denmark DK-2800 Lyngby, Denmark
* To whom correspondence should be addressed. E-mail: email: brunak{at}cbs.dtu.dk.
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 nonclassical secretion. Predictions can be made at http://www.cbs.dtu.dk/services/SecretomeP.
Keywords:
Extracellular, growth factor, hormone, neural network, secretome
Revised April 4, 2004
Accepted April 6, 2004
Article
Feature based prediction of non-classical
and leaderless protein secretion
2 Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, Technical University of Denmark DK-2800 Lyngby, Denmark; Current affiliations: Computational Biology Unit,
EMBL-Heidelberg, D-69117 Heidelberg, Germany, and Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Strasse 10, D-13092 Berlin, Germany
3 Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, Technical University of Denmark DK-2800 Lyngby, Denmark
4 Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
Abstract 
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  R. Shah, Y. Lu, C. C. Hinkle, F. C. McGillicuddy, R. Kim, S. Hannenhalli, T. P. Cappola, S. Heffron, X. Wang, N. N. Mehta, et al. Gene Profiling of Human Adipose Tissue During Evoked Inflammation In Vivo Diabetes, October 1, 2009; 58(10): 2211 - 2219. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Lamounier-Zepter, C. Look, J. Alvarez, T. Christ, U. Ravens, W.-H. Schunck, M. Ehrhart-Bornstein, S. R. Bornstein, and I. Morano Adipocyte Fatty Acid-Binding Protein Suppresses Cardiomyocyte Contraction: A New Link Between Obesity and Heart Disease Circ. Res., August 14, 2009; 105(4): 326 - 334. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Bernay, M.-C. Gaillard, V. Guryca, A. Emadali, L. Kuhn, A. Bertrand, I. Detraz, C. Carcenac, M. Savasta, E. Brouillet, et al. Discovering New Bioactive Neuropeptides in the Striatum Secretome Using in Vivo Microdialysis and Versatile Proteomics Mol. Cell. Proteomics, May 1, 2009; 8(5): 946 - 958. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Roelofsen, M. Dijkstra, D. Weening, M. P. de Vries, A. Hoek, and R. J. Vonk Comparison of Isotope-labeled Amino Acid Incorporation Rates (CILAIR) Provides a Quantitative Method to Study Tissue Secretomes Mol. Cell. Proteomics, February 1, 2009; 8(2): 316 - 324. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Laohavisit, J. C. Mortimer, V. Demidchik, K. M. Coxon, M. A. Stancombe, N. Macpherson, C. Brownlee, A. Hofmann, A. A.R. Webb, H. Miedema, et al. Zea mays Annexins Modulate Cytosolic Free Ca2+ and Generate a Ca2+-Permeable Conductance PLANT CELL, February 1, 2009; 21(2): 479 - 493. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Revert, I. Ventura, P. Martinez-Martinez, F. Granero-Molto, F. Revert-Ros, J. Macias, and J. Saus Goodpasture Antigen-binding Protein Is a Soluble Exportable Protein That Interacts with Type IV Collagen: IDENTIFICATION OF NOVEL MEMBRANE-BOUND ISOFORMS J. Biol. Chem., October 31, 2008; 283(44): 30246 - 30255. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. L. Chaffin Candida albicans Cell Wall Proteins Microbiol. Mol. Biol. Rev., September 1, 2008; 72(3): 495 - 544. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. M. Hauck, C. J. Gloeckner, M. E. Harley, S. Schoeffmann, K. Boldt, P. A. R. Ekstrom, and M. Ueffing Identification of Paracrine Neuroprotective Candidate Proteins by a Functional Assay-driven Proteomics Approach Mol. Cell. Proteomics, July 1, 2008; 7(7): 1349 - 1361. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Ma, L. Visser, H. Roelofsen, M. de Vries, A. Diepstra, G. van Imhoff, T. van der Wal, M. Luinge, G. Alvarez-Llamas, H. Vos, et al. Proteomics analysis of Hodgkin lymphoma: identification of new players involved in the cross-talk between HRS cells and infiltrating lymphocytes Blood, February 15, 2008; 111(4): 2339 - 2346. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Zhu, S. Alvarez, E. L. Marsh, M. E. LeNoble, I.-J. Cho, M. Sivaguru, S. Chen, H. T. Nguyen, Y. Wu, D. P. Schachtman, et al. Cell Wall Proteome in the Maize Primary Root Elongation Zone. II. Region-Specific Changes in Water Soluble and Lightly Ionically Bound Proteins under Water Deficit Plant Physiology, December 1, 2007; 145(4): 1533 - 1548. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Alvarez-Llamas, E. Szalowska, M. P. de Vries, D. Weening, K. Landman, A. Hoek, B. H. R. Wolffenbuttel, H. Roelofsen, and R. J. Vonk Characterization of the Human Visceral Adipose Tissue Secretome Mol. Cell. Proteomics, April 1, 2007; 6(4): 589 - 600. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. A. Lease and J. C. Walker The Arabidopsis Unannotated Secreted Peptide Database, a Resource for Plant Peptidomics Plant Physiology, November 1, 2006; 142(3): 831 - 838. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X.-L. Yuan, C. Goosen, H. Kools, M. J. E. C. van der Maarel, C. A. M. J. J van den Hondel, L. Dijkhuizen, and A. F. J. Ram Database mining and transcriptional analysis of genes encoding inulin-modifying enzymes of Aspergillus niger. Microbiology, October 1, 2006; 152(Pt 10): 3061 - 3073. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Cattaneo, M. E. Pasini, J. Intra, M. Matsumoto, F. Briani, M. Hoshi, and M. E. Perotti Identification and expression analysis of Drosophila melanogaster genes encoding {beta}-hexosaminidases of the sperm plasma membrane Glycobiology, September 1, 2006; 16(9): 786 - 800. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Saha and G. P. S. Raghava AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W202 - W209. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Yu, S. L. Harris, and A. J. Levine The Regulation of Exosome Secretion: a Novel Function of the p53 Protein. Cancer Res., May 1, 2006; 66(9): 4795 - 4801. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Juarez-Diaz, B. McClure, S. Vazquez-Santana, A. Guevara-Garcia, P. Leon-Mejia, J. Marquez-Guzman, and F. Cruz-Garcia A Novel Thioredoxin h Is Secreted in Nicotiana alata and Reduces S-RNase in Vitro J. Biol. Chem., February 10, 2006; 281(6): 3418 - 3424. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Zhu, S. Chen, S. Alvarez, V. S. Asirvatham, D. P. Schachtman, Y. Wu, and R. E. Sharp Cell Wall Proteome in the Maize Primary Root Elongation Zone. I. Extraction and Identification of Water-Soluble and Lightly Ionically Bound Proteins Plant Physiology, January 1, 2006; 140(1): 311 - 325. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Xie, A. Li, M. Wang, Z. Fan, and H. Feng LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST Nucleic Acids Res., July 1, 2005; 33(suppl_2): W105 - W110. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. I. Olason Integrating protein annotation resources through the Distributed Annotation System Nucleic Acids Res., July 1, 2005; 33(suppl_2): W468 - W470. [Abstract] [Full Text] [PDF]
|
|