Bio-Trac 25 (Proteomics: Principles and Methods)

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Tutorial Bioinformatics Resources

(http//pir.georgetown.edu/pirwww/workshop/bioinfo
_resource.html)

• Bio-Trac 25 (Proteomics Principles and Methods)
• October 3, 2008
• Zhang-Zhi Hu, M.D.
• Research Associate Professor
• Protein Information Resource, Department of
• Biochemistry and Molecular Cellular Biology
• Georgetown University Medical Center

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Lab

• Protein Examples
• Rabbit alpha crystallin A (UniProtKB
  CRYAA_RABIT/P02493)
• Delta crystallin II (Argininosuccinate lyase)
  (ARLY2_ANAPL/P24058)
• Any additional proteins of your interest for
  search and retrieval

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Lab Overview
Database Contents, Search and Retrieval

• Text search / Information retrieval
• Literature search and text mining
• Finding synonyms (BioThesaurus)
• Information extraction (e.g., protein
  phosphorylation sites)
• Find the sequence for the rabbit alpha crystallin
  A chain
• Find all alpha crystallin A chain classified in
  protein families
• Search crystallins that have active enzyme
  activities
• Find crystallins that have determined 3D
  structures
• Database contents (reports)
• Sequence genomics databases (UniProt)
• Protein family databases (PIRSF)
• Database of protein functions (KEGG)
• Databases of protein structures (PDB)
• Proteomics databases (Swiss-2D)

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Entrez Text Searches
(http//www.ncbi.nlm.nih.gov/Entrez/)
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PubMed Literature Database
(http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD
SearchDBPubMed)
PMID14640721
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iProLINK Protein Literature Mining Resource
RLIMS-P
Text mining for protein phosphorylation
BioThesaurus
Gene/protein name thesaurus synonyms, ambiguous
names
http//pir.georgetown.edu/iprolink/
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BioThesaurus Gene/protein name searches -
synonyms, ambiguous names
Synonyms CRYAA crystallin, alpha A CRYA1 HSPB4
http//pir.georgetown.edu/iprolink/biothesaurus
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RLIMS-P Text mining for protein phosphorylation
http//pir.georgetown.edu/iprolink/rlimsp/
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PIR Text Search (I)
(http//pir.georgetown.edu/pirwww/search/textsearc
h.html)
Google type search vs.
Boolean searches AND, OR, NOT
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PIR Text Search (II)
Search alpha crystallin A chain that are in
protein families?
null absent not null present
Search for synonyms
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PIR Text Search (III)
Search what crystallins are enzymes and what
families they belong to?
Can you find which crystallins have 3D structure
determined?
Argininosuccinate lyase (EC 4.3.2.1)
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UniProt Text Search
http//www.uniprot.org/
Find proteins related to diabetes and with
3D-structure determined?
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Search continues
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UniProt Report (I)
Sections of the record
Entry View Sequence Annotation
http//www.uniprot.org/uniprot/P02493
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UniProt Report (II) sequence and features
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PIRSF Full Length Classification iProClass
Family Report
(http//pir.georgetown.edu/cgi-bin/ipcSF?idSF0022
80)
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KEGG Metabolic Regulatory Pathways

• KEGG is a suite of databases and associated
  software, integrating our current knowledge
• on molecular interaction networks, the
  information of genes and proteins, and of
  chemical
• compounds and reactions. (http//www.genome.ad.
  jp/kegg/kegg2.html)

(http//www.genome.ad.jp/dbget-bin/show_pathway?hs
a002204.3.2.1)
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PDB Experimental 3D Structure Repository
Rat gamma-crystallin (chain A, B.)
Can you do a text search at PIR to find this
(CRGE_RAT)?
(http//www.rcsb.org/pdb/)
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2D-Gel Image Databases
(http//us.expasy.org/swiss-2dpage/)
Part of WORLD-2DPAGE index to 2-D PAGE databases
and services
(http//us.expasy.org/swiss-2dpage/acP02489)
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