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Title: Bio-Trac 25 (Proteomics: Principles and Methods)


1
Tutorial Bioinformatics Resources(http//pir.ge
orgetown.edu/huz/class/bioinfo_resource.html)
  • Bio-Trac 25 (Proteomics Principles and Methods)
  • March 26, 2004
  • Zhang-Zhi Hu, M.D.
  • Senior Bioinformatics Scientist
  • Protein Information Resource
  • National Biomedical Research Foundation, GUMC

2
What is Bioinformatics?
computer mouse bioinformatics
(information) (biology)
  • NIH Biomedical Information Science and Technology
    Initiative (BISTI) Working Definition (2000) -
    Research, development, or application of
    computational tools and approaches for expanding
    the use of biological, medical, behavioral or
    health data, including those to acquire, store,
    organize, archive, analyze, or visualize such
    data.

3
Molecular Biology Database Collection
(http//nar.oupjournals.org/cgi/content/full/32/su
ppl_1/D3)
-- 548 key databases of 11 categories
4
(http//pir.georgetown.edu/huz/class/2004_databas
e_update.html)
5
Overview
Database Contents, Search and Retrieval
  1. Text search / Information retrieval
  2. Sequence genomics databases
  3. Protein family databases
  4. Database of protein functions
  5. Databases of protein structures
  6. 2D-gel databases
  7. Proteomics databases

6
Entrez Text Searches
(http//www.ncbi.nlm.nih.gov/Entrez/)
7
PubMed Literature Database(http//www.ncbi.nlm.ni
h.gov/entrez/query.fcgi?CMDSearchDBPubMed)
8
UniProt Text Search
(http//www.pir.uniprot.org/cgi-bin/textSearch)
9
PIR Text Search (I)
(http//pir.georgetown.edu/pirwww/search/textsearc
h.html)
Whats different between CRAA_RABIT CYRBAA?
How about Search Crystallin and SuperFamily?
10
PIR Text Search (II)
Can you find which crystallin that has 3D
structure determined using PIR text search?
11
I. Sequence Genomics Databases
  • GenBank An annotated collection of all publicly
    available nucleotide and protein sequences.
  • RefSeq NCBI non-redundant set of reference
    sequences, including genomic DNA, transcript
    (RNA), and protein products
  • UniProt Consortium Database Universal protein
    knowledgebase, a central resource of protein
    sequence and function from Swiss-Prot, TrEMBL and
    PIR.
  • LocusLink Curated sequences and descriptions of
    genetic loci.
  • UniGene Unified clusters of ESTs and full-length
    mRNA sequences .
  • OMIM Online Mendelian inheritance in man a
    catalog of human genetic and genomic disorders.
  • Model Organism Genome Databases MGD, RGD, SGD,
    Flybase
  • GeneCards Integrated database of human genes,
    maps, proteins and diseases.
  • SNP Consortium Database

12
UniProt Consortium Database
UniProt (knowledgebase) UniRef (100,90,50) UniParc
(archive)
(http//www.uniprot.org)
13
UniProt Sequence Report (I)
(http//www.pir.uniprot.org/cgi-bin/unipEntry?idC
RAA_RABIT)
14
UniProt Sequence Report (II)
(http//www.pir.uniprot.org/cgi-bin/unipEntry?idU
niRef90_P02489)
15
NCBI LocusLink
(http//www.ncbi.nlm.nih.gov/LocusLink)
16
OMIM Online Mendelian inheritance in man
(http//www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?i
d123580)
17
II. Protein Family Databases
  • Whole Proteins
  • PIRSF A Network Classification System of Protein
    Families
  • COG (Clusters of Orthologous Groups) of Complete
    Genomes
  • ProtoNet Automated Hierarchical Classification
    of Proteins
  • Protein Domains
  • Pfam Alignments and HMM Models of Protein
    Domains
  • SMART Protein Domain Families
  • CDD Conserved Domain Database
  • Protein Motifs
  • PROSITE Protein Patterns and Profiles
  • BLOCKS Protein Sequence Motifs and Alignments
  • PRINTS Protein Sequence Motifs and Signatures
  • Integrated Family Databases
  • iProClass Superfamilies/Families, Domains,
    Motifs, Rich Links
  • InterPro Integrate Pfam, PRINTS, PROSITES,
    ProDom, SMART, PIRSF, SuperFamily

18
Domain Classification
(http//www.sanger.ac.uk/cgi-bin/Pfam/swisspfamget
.pl?nameCRAA_RABIT)
(http//pir.georgetown.edu/cgi-bin/ipcEntry?idCRA
A_RABIT)
19
Pfam Domain
(http//www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF005
25)
20
Integrated Family Classification
  • InterPro
  • An integrated resource unifying PROSITE, PRINTS,
    ProDom, Pfam, SMART, and TIGRFAMs, PIRSF.
    (http//www.ebi.ac.uk/interpro/search.html)

21
PIRSF Full Length Classification iProClass
Family Report
(http//pir.georgetown.edu/cgi-bin/ipcSF?idSF0022
80)
22
III. Databases of Protein Functions
  • Metabolic Pathways, Enzymes, and Compounds
  • Enzyme Classification Classification and
    Nomenclature of Enzyme-Catalysed Reactions
    (EC-IUBMB)
  • KEGG (Kyoto Encyclopedia of Genes and Genomes)
    Metabolic Pathways
  • LIGAND (at KEGG) Chemical Compounds, Reactions
    and Enzymes
  • EcoCyc Encyclopedia of E. coli Genes and
    Metabolism
  • MetaCyc Metabolic Encyclopedia (Metabolic
    Pathways)
  • WIT Functional Curation and Metabolic Models
  • BRENDA Enzyme Database
  • UM-BBD Microbial Biocatalytic Reactions and
    Biodegradation Pathways
  • Cellular Regulation and Gene Networks
  • EpoDB Genes Expressed during Human
    Erythropoiesis
  • BIND Descriptions of interactions, molecular
    complexes and pathways
  • DIP Catalogs experimentally determined
    interactions between proteins
  • BioCarta Biological pathways of human and mouse
  • GO Gene Ontology Consortium Database

23
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)
24
BioCyc (EcoCyc/MetaCyc Metabolic Pathways)
  • The BioCyc Knowledge Library is a collection of
    Pathway/Genome Databases (http//biocyc.org/)

25
BioCarta Cellular Pathways
(http//www.biocarta.com/index.asp)
26
Protein-Protein Interaction BIND
(http//www.bind.ca/)
27
Gene Ontology(http//www.geneontology.org/)
Three GOs Molecular Function Biological
Process Cellular Component
28
IV. Databases of Protein Structures
  • Protein Structure
  • PDB Structure Determined by X-ray
    Crystallography and NMR
  • PDBsum Summaries and analyses of PDB structures
  • MMDB NCBIs database of 3D structures, part of
    NCBI Entrez
  • SWISS-MODEL Repository Database of annotated
    protein 3D models
  • ModBase Annotated comparative protein structure
    models
  • Structure Classification
  • CATH Hierarchical Classification of Protein
    Domain Structures
  • SCOP Familial and Structural Protein
    Relationships
  • FSSP Protein Fold Classification Based on
    Structure--Structure Alignment

29
PDB 3D Structure
Rat gamma-crystallin, chain A, B. Can you do a
text search at PIR to find this?
(http//www.rcsb.org/pdb/)
30
PDBsum
Summary and Analysis (http//www.biochem.ucl.ac.uk
/bsm/pdbsum)
31
Protein Structural Classification (1)
CATH Hierarchical domain classification of
protein structures (http//www.biochem.
ucl.ac.uk/bsm/cath_new/)
32
Protein Structural Classification (2)
SCOP comprehensive description of structural
and evolutionary relationships between all
proteins whose structure is known.
(http//scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.ht
ml)
33
SWISS-MODEL Repository
A database of annotated three-dimensional
comparative protein structure models
(http//swissmodel.expasy.org/repository/smr.php?s
ptr_acCRGE_RATjob2)
34
VI. Proteomic Resources
  • GELBANK (http//gelbank.anl.gov) 2D-gel patterns
    from completed genomes SWISS-2DPAGE
    (http//www.expasy.org/ch2d/)
  • PEP Predictions for Entire Proteomes
    (http//cubic.bioc.columbia.edu/ pep/)
    Summarized analyses of protein sequences
  • Proteome BioKnowledge Library (http//www.proteom
    e.com) Detailed information on human, mouse and
    rat proteomes
  • Proteome Analysis Database (http//www.ebi.ac.uk/p
    roteome/) Online application of InterPro and
    CluSTr for the functional classification of
    proteins in whole genomes
  • Expression Profiling databases GNF
    (http//expression.gnf.org/cgi-bin/index.cgi,
    human and mouse transcriptome), SMD
    (http//genome-www5.stanford.edu/MicroArray/SMD/,
    Stanford microarray data analysis), EBI
    Microarray Informatics (http//www.ebi.ac.uk/micro
    array/ index.html , managing, storing and
    analyzing microarray data)

35
2D-Gel Image Databases (1)
(http//us.expasy.org/ch2d/2d-index.html)
(http//us.expasy.org/cgi-bin/nice2dpage.pl?P02489
)
36
2D-Gel Image Databases (2)
(http//gelbank.anl.gov/2dgels/index.asp)
37
Expression Profiling
  • Human and Mouse Transcriptome

(http//genome-www.stanford.edu/serum/)
(http//expression.gnf.org/cgi-bin/index.cgi)
(http//expression.gnf.org/cgi-bin/index.cgi/)
38
Lab
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