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- Text/Documents:
- GoMiner: a resource for biological interpretation of genomic and proteomic data (2003) (online version)
Zeeberg et al., NIH, Bethesda, MD
We have developed GoMiner, a program package that organizes lists of 'interesting' genes (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. GoMiner provides quantitative and statistical output files and two useful visualizations. The first is a tree-like structure analogous to that in the AmiGO browser and the second is a compact, dynamically interactive 'directed acyclic graph'. Genes displayed in GoMiner are linked to major public bioinformatics resources.
- Software Downloads:
- Slide Presentations:
- Proteomics
Maggie Werner-Washburne, (Date Unkn.)
Definition/How to organize information?/Transposon tagging to identify ORFS/High throughput tests of function/Yeast deletion strains/Microscopic localization/Process for protein isolation/2D gel electrophoresis/Antibody arrays/Array-based protein interaction detection/Protein microarrays...
- Video Lectures:
- Sample Scripts:
- Useful Tandem Scripts: DAT2Tandem
- This script coverts a directory of Mascot output "DAT" files into MGF "Mascot generic" formatted peak lists and then automatically searches these with Tandem using a Method and database you input into the configuration file.
- this script requires Mascot Parser so you must either purchase it from Matrix Science or run this script on your Mascot 2.0 server which has the parser on it.
- Sample Data:
- General Web Resources:
- ProDom - a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases.
- "Structural Classification of Proteins" (SCOP) - structural and evolutionary relationships between known proteins
- RCSB PDB Structural Genomics Information Portal - dedicated to the initiative of quickly determining a large number of protein structures using X-ray crystallographic and NMR technologies
- KEGG LIGAND Database- database of chemical substances and reactions that are relevant to life
- BRENDA - “The Comprehensive Enzyme Information System” - lots of enzyme data, including real-life functional parameters
- Applied Biosystems: online store - products for a variety of applications
- Michigan Proteome Consortium - Cutting-edge proteomics services for industry and academic research institutions. Proteome data workshop is available, among other links.
- Harvard Microchemistry & Proteomics Analysis Facility - provides strategic consulting and technologies in proteomics analysis for the Harvard community and researchers worldwide. This website is also well designed and maintained.
- Spectroscopynow.com - Proteomics - A guide to the application of spectroscopy in proteomics. For the latest news features e-zine and much more. Website is well-designed.
- MSU Proteomics Facility - part of the Michigan Proteome Consortium. Fee for service and collaboration on a wide variety of proteomic based projects to investigators is provided.
- Midwest Bio Services, LLC - "Most sensitive nanoLC/MS/MS technique for Protein Identification. Accurate results in 4 business days."
New company dedicated to providing reliable and affordable services in the areas of protein expression, protein purification and analytical characterization of proteins and peptides.
- JPT Peptide Technologies - From ultra-fast custom peptide synthesis to the assembly of highly sophisticated peptide arrays and ready-to-use kits for biomedical research. Peptide synthesis, peptide arrays, immuno tools, kinase profiling tools, phosphatase profiling tools, protease profiling tools.
- Cell Signaling Technology - Many cell-signaling diagrams are made available.
- Enzyme Structures Database - Database contains the known enzyme structures that have been deposited in the Protein Data Bank (PDB). Special features: Not only can proteins be displayed as ribbon models, but ligand's interactions with proteins can also be visualized in a 2D molecular model. Provided by the EBI.
- Proteomics tools from the University of Louisville - Web-based tools for sequence manipulation, protein identification, structure/topology prediction, and structure analysis.
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