Presentation on theme: "1 Eukaryotic Secretome Prediction and Knowledge-Base Development Xiang-Jia “Jack” Min Ph.D., Assistant Professor 2 nd International Conferences on Proteomics."— Presentation transcript:
1 Eukaryotic Secretome Prediction and Knowledge-Base Development Xiang-Jia “Jack” Min Ph.D., Assistant Professor 2 nd International Conferences on Proteomics & Bioinformatics. Las Vegas, July 2 - 4, 2012
3 Genome Transcriptome Proteome Secretome mRNA (protein-coding DNA sequences) Protein sequences Proteins with secretory signal peptide Transcription Translation Secretion
9 How to identify secreted proteins? Genome Transcriptome Proteome Secretome Transcription Translation Secretion (1) Direct identification using proteomics methods (Tsang et al. 2009) (2) Computational prediction from predicted proteome (3) EST data mining
10 Secreted Proteins Classical secreted proteins have a signal peptide at N-terminus; Not all proteins have a signal peptide are secreted: Signal peptide = secreted protein
11 SignalP: a program to predict if a protein contains a signal peptide. Phobius: signal peptide and transmembrane domain predicton. WolfPsort: a multiple subcellular location predictor TargetP: detect proteins targeted to mitochondria. TMHMM: transmembrane domain prediction. PS-Scan: detection ER- retention signals
21 Summary Different prediction tools have different accuracies for prediction of secretomes in different kingdoms of species; Combining these tools often increases the prediction accuracy. However, differential combination are needed for species in different kingdoms. Optimal methods are proposed.
25 Views gi accession UniProt ID Keywords Species User Inputs Manual Curation Subcellular Location FunSecKB fragAnchor PS-SCAN TMHMM TargetP WolfPsort Phobius SignalP Database RefSeq UniProt Prediction Tools External Links Lum G & Min XJ (2011) Database.
26 Summary of FunSecKB Currently the database contains a total of 478,073 fungal protein sequences 23,878 predicted and / or curated secreted proteins A total of 118 fungal species including 52 fungal species having a complete proteome