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Title: BioTrac 25 Proteomics: Principles and Methods


1
Tutorial Bioinformatics Resources

(http//pir.georgetown.edu/pirwww/workshop/bioinfo
_resource.html)
  • Bio-Trac 25 (Proteomics Principles and Methods)
  • October 6, 2006
  • Zhang-Zhi Hu, M.D.
  • Research Associate Professor
  • Protein Information Resource, Department of
  • Biochemistry and Molecular Cellular Biology
  • Georgetown University Medical Center

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.oxfordjournals.org/cgi/content/full/34
/suppl_1/D3/DC1)
4
Database Collection in Nucleic Acids Res.
5
2006
Online Access to Database Collection
http//pir.georgetown.edu/pirwww/workshop/2005_dat
abase_update.html
http//www.oxfordjournals.org/nar/database/cap/
6
Overview
Database Contents, Search and Retrieval
  • Text search / Information retrieval
  • Sequence genomics databases
  • Protein family databases
  • Database of protein functions
  • Databases of protein structures
  • Proteomics databases

7
Entrez Text Searches
(http//www.ncbi.nlm.nih.gov/Entrez/)
8
PubMed Literature Database
(http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD
SearchDBPubMed)
9
UniProt Text Search
(http//www.pir.uniprot.org/cgi-bin/textSearch)
Google type search vs. Boolean searches AND, OR,
NOT
10
PIR Text Search (I)
(http//pir.georgetown.edu/pirwww/search/textsearc
h.html)
Search alpha crystallin A chain and protein
family?
Search for synonyms
11
PIR Text Search (II)
Search what crystallins are enzymes ?
Can you find which crystallin that has 3D
structure determined?
12
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
    resource, a central repository of protein
    sequence and function.
  • Entrez Gene Gene-centered information at NCBI.
  • 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
  • International HapMap Project Genes associated
    with human disease

13
UniProt Consortium Databases
Universal Protein Resource
(http//www.uniprot.org)
UniProtKB UniRef UniParc
14
UniProt Sequence Report (I)
UniProtKB
Whats the difference between CRYAA_RABIT
CYRBAA?
(http//www.pir.uniprot.org/cgi-bin/unipEntry?idC
RYAA_RABIT)
15
UniProt Sequence Report (II)
(http//www.pir.uniprot.org/cgi-bin/unipEntry?idU
niRef100_P02489)
UniRef100 90
(http//www.pir.uniprot.org/cgi-bin/unipEntry?idU
niRef90_P02489)
16
Entrez Gene Gene centric information
http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?dbg
enecmdRetrievedoptGraphicslist_uids12954ubo
r0_RefSeq
17
OMIM Online Mendelian inheritance in man
(http//www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?i
d123580)
18
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

19
Protein Clustering
Initial version
COGs (http//www.ncbi.nlm.nih.gov/COG/)
New version Includes Eukaryotic Clusters
20
Domain Classification
(http//www.sanger.ac.uk/cgi-bin/Pfam/swisspfamget
.pl?nameCRYAA_RABIT)
(http//pir.georgetown.edu/cgi-bin/ipcEntry?idCRY
AA_RABIT)
21
Pfam Domain
(http//www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF005
25)
22
Integrated Family Classification
  • InterPro
  • An integrated resource unifying PROSITE, PRINTS,
    ProDom, Pfam, SMART, and TIGRFAMs, PIRSF.
    (http//www.ebi.ac.uk/interpro/search.html)

Mapping of families
23
PIRSF Full Length Classification iProClass
Family Report
(http//pir.georgetown.edu/cgi-bin/ipcSF?idSF0022
80)
24
Protein Motifs PROSITE A database of protein
families and domains. It consists of biologically
significant sites, patterns and profiles.
(http//us.expasy.org/prosite/)
25
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)
  • BRENDA Enzyme Database
  • UM-BBD Microbial Biocatalytic Reactions and
    Biodegradation Pathways
  • Inter-Molecular interactions and Regulatory
    Pathways
  • IntAct Protein interaction data from literature
    and user submission
  • BIND Descriptions of interactions, molecular
    complexes and pathways
  • DIP Catalogs experimentally determined
    interactions between proteins
  • Reactome - A curated knowledgebase of biological
    pathways
  • BioCarta Biological pathways of human and mouse
  • GO Gene Ontology Consortium Database

26
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)
27
BioCyc EcoCyc/MetaCyc Metabolic Pathways
  • The BioCyc Knowledge Library is a collection of
    Pathway/Genome Databases (http//biocyc.org/)

28
BioCarta Cellular Pathways
(http//www.biocarta.com/index.asp)
29
Reactome http//www.reactome.org/
30
BIND Protein-Protein Interaction
(http//www.bind.ca/)
31
Gene Ontology(http//www.geneontology.org/)
Three GOs Molecular Function Biological
Process Cellular Component
32
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

33
PDB Experimental 3D Structure Repository
Rat gamma-crystallin, chain A, B.
Can you do a text search at PIR to find this?
(http//www.rcsb.org/pdb/)
34
PDBsum
Summary and Analysis (http//www.ebi.ac.uk/thornto
n-srv/databases/pdbsum/)
Search
3-D structure summary
2-D structure
35
Protein Structural Classification (1)
CATH Hierarchical domain classification of
protein structures (http//www.biochem.
ucl.ac.uk/bsm/cath_new/)
36
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)
37
SWISS-MODEL Repository
A database of annotated three-dimensional
comparative protein structure models
(http//swissmodel.expasy.org/repository/smr.php?s
ptr_acCRGE_RATjob2)
38
VI. Proteomic Resources
  • GELBANK (http//gelbank.anl.gov) 2D-gel patterns
    of species with completed genomes.
  • SWISS-2DPAGE (http//www.expasy.org/ch2d/) index
    of 2D-gels
  • PEP (http//cubic.bioc.columbia.edu/ pep/)
    Predictions for Entire Proteomes summarized
    analyses of protein sequences
  • Integr8 (http//www.ebi.ac.uk/integr8/) A
    browser for information relating to completed
    genomes and proteomes, based on data contained in
    Genome Reviews and the UniProt proteome sets
  • PRIDE (http//www.ebi.ac.uk/pride/) PRoteomics
    IDEntifications database Expression Profiling
    databases
  • GPMdb (http//gpmdb.thegpm.org/) Mass Spec
    Proteomics Databases

39
2D-Gel Image Databases (1)
(http//us.expasy.org/ch2d/2d-index.html)
Part of WORLD-2DPAGE Index to 2-D PAGE
databases and services
(http//us.expasy.org/cgi-bin/nice2dpage.pl?P02489
)
40
2D-Gel Image Databases (2)
(http//gelbank.anl.gov/2dgels/index.asp)
41
GPMdb MS Data Search
http//gpmdb.thegpm.org/
Craig, et al., J Proteome Res. 2004, 31234-42.
42
iProLINK Protein Literature Mining Resource
Text mining of protein phosphorylation
Gene/protein name thesaurus synonyms, ambiguous
names
http//pir.georgetown.edu/iprolink/
43
Lab
  • Rabbit alpha crystallin A (UniProt
    CRYAA_RABIT/P02493)
  • Delta crystallin II (Argininosuccinate lyase)
    (UniProt ARLY2_ANAPL/P24058)
  • Choose additional protein IDs to browse the
    variety of molecular biology databases each
    sequence report links to.
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