Locating Gene/Protein Information January 11, 2011 Ansuman Chattopadhyay, PhD Head, Molecular...
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Locating Gene/Protein Information
January 11, 2011
Ansuman Chattopadhyay, PhDHead, Molecular Biology Information ServicesHealth Sciences Library SystemUniversity of [email protected]
http://www.hsls.pitt.edu/molbio
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Objectives
Generate a gene list
Mine gene/protein information
http://www.hsls.pitt.edu/molbio
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Topics
Literature Informatics
Gene / Protein Information Gateways
Search Engine for MolBio / Bioinformatics Databases and Software
http://www.hsls.pitt.edu/molbio
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Topics
Literature Informatics Comprehensive search:
MESH term based PubMed Search PubMed Special topics query
Next-generation literature search tools: Gopubmed GLAD4U HugeNavigator
http://www.hsls.pitt.edu/guides/genetics
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Literature InformaticsWhich genes/proteins are reported to be associated with the disease - Schizophrenia?
http://www.hsls.pitt.edu/guides/genetics
Citations: 19 millionJournals: 5200
Schizophrenia: 86,384.. 96234Schizophrenia gene: 5851…7295
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Challenges in Literature Search Am I getting everything? Too much Information.. How to digest?
http://www.hsls.pitt.edu/guides/genetics
A list with citations
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Medical Subject Heading (MESH)
http://www.hsls.pitt.edu/guides/genetics
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Medical Subject Headings (MeSH)
http://www.hsls.pitt.edu/guides/genetics
The U.S. National Library of Medicine's controlled vocabulary (thesaurus)
Arranged in a hierarchical manner called the MeSH Tree Structures
Updated annually
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MeSH Vocabulary Headings
over 24,000 representing concepts found in the biomedical literature (Body Weight, Kidney, Radioactive Waste)
Subheadings attached to headings to describe a specific aspect of a concept
(adverse effects , metabolism, diagnosis, therapy)
Supplementary Concept Records over 172,000 terms in a separate chemical thesaurus -updated
weekly (cordycepin , valspodar , tacrolimus binding protein 4)
Publication Types(Letter, Review, Randomized Controlled Trial)
http://www.hsls.pitt.edu/guides/genetics
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MeSH Tree Structure A. Anatomy
B. OrganismsC. DiseasesD. Chemical and DrugsE. Analytical, Diagnostic and
Therapeutic Techniques and EquipmentF. Psychiatry and PsychologyG. Biological SciencesH. Physical SciencesI. Anthropology, Education,
Sociology and Social PhenomenaJ. Technology and Food and BeveragesK. Humanities L. Information Science M. Persons N. Health CareV. Publication Characteristics Z. Geographic Locations
http://www.hsls.pitt.edu/guides/genetics
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MeSH Indexing
http://www.hsls.pitt.edu/guides/genetics
Source: NLM
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MeSH Indexing
http://www.hsls.pitt.edu/guides/genetics
Genes/Chemicals
MeSH Terms
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PubMed Query Using MeSH http://www.ncbi.nlm.nih.gov/mesh
http://www.hsls.pitt.edu/guides/genetics
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http://www.hsls.pitt.edu/molbio
Find articles on “Dengue outbreaks in India” by searching PubMed
using Mesh terms
Link to the video tutorial:http://media.hsls.pitt.edu/media/molbiovideos/pubmedsearch1.swf
Resources
• Mesh Browser : http://www.ncbi.nlm.nih.gov/mesh• PubMed: http://www.ncbi.nlm.nih.gov/pubmed
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Building PubMed QueriesTerm Boolean Term Boolean Term # papers
Dengue AND Outbreaks 823
Dengue * AND Outbreaks 746
Dengue AND Outbreaks AND India 131
Dengue* AND Outbreaks AND India 116
Dengue AND Outbreaks/statistics and numerical data
AND India 7
Dengue* AND Outbreaks/statistics and numerical data
AND India 7
http://www.hsls.pitt.edu/guides/genetics
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Useful links for MESH
MESH Browser: http://www.ncbi.nlm.nih.gov/mesh Link to Wikipedia, Youtube videos, blogs etc on “medical
subject heading”: http://www.kosmix.com/topic/Medical_Subject_Headings?
18 ways to improve your Pubmed searches by Carrie Iwema http://bitesizebio.com/2008/03/05/18-ways-to-improve-your-pubm
ed-searches/ Searching by using the MeSH Database. NCBI
Handbook : http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed
&part=pubmedhelp#pubmedhelp.Searching_by_using_t
http://www.hsls.pitt.edu/guides/genetics
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http://www.hsls.pitt.edu/molbio
Find genes that are reported to be associated with the disease SCHIZOPHRENIA by searching PubMed
Link to the video tutorial:http://media.hsls.pitt.edu/media/molbiovideos/pubmedsearch2.swf
Resources
• PubMed Clinical Queries: http://www.ncbi.nlm.nih.gov/pubmed/clinical
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Topic-Specific PubMed Queries http://www.nlm.nih.gov/bsd/special_queries.html
http://www.hsls.pitt.edu/guides/genetics
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Research on Optimal Search Strategies
http://www.hsls.pitt.edu/guides/genetics
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PubMed Special Topic Queries
http://www.hsls.pitt.edu/guides/genetics
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PubMed Search Filter: Medical Genetics ("schizophrenia"[MeSH Terms] OR
"schizophrenia"[All Fields]) AND (("genetics, medical"[MeSH Terms] OR ("genetics"[All Fields] AND "medical"[All Fields]) OR "medical genetics"[All Fields] OR ("medical"[All Fields] AND "genetics"[All Fields])) OR ("genotype"[MeSH Terms] OR "genotype"[All Fields]) OR "genetics"[Subheading] AND ("genetics"[Subheading] OR "genetics"[All Fields] OR "genetics"[MeSH Terms]))
http://www.hsls.pitt.edu/guides/genetics
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PubMed Search Result Display
http://www.hsls.pitt.edu/guides/genetics
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Latest Innovations in Literature Searching
GoPubMed Display search results sorted into meaningful topics and subtopics
http://www.hsls.pitt.edu/guides/genetics
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GoPubMed
http://www.hsls.pitt.edu/guides/genetics
www.gopubmed.com
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http://www.hsls.pitt.edu/molbio
Find genes that are reported to be associated with the disease
SCHIZOPHRENIA by using GoPubMed
Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/gopubmed.swf
Resources
• GoPubMed: http://www.gopubmed.org/web/gopubmed/2?WEB10O00h00100090000
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GoPubMed Search Result
http://www.hsls.pitt.edu/guides/genetics
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GoPubMed Search Result Analysis
http://www.hsls.pitt.edu/guides/genetics
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GoPubMed Search Result Analysis
http://www.hsls.pitt.edu/guides/genetics
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Latest Innovations in Literature Searching
http://www.hsls.pitt.edu/guides/genetics
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PubMed driven Web Tools
http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/
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Literature to Gene List
GLAD4U http://bioinfo.vanderbilt.edu/glad4u/
http://www.hsls.pitt.edu/guides/genetics
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Gene list to common functions
http://www.hsls.pitt.edu/guides/genetics
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Literature to Gene list
http://www.hsls.pitt.edu/guides/genetics
http://www.quertle.info/
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NIH Grant Applications to Gene List
http://www.hsls.pitt.edu/guides/genetics
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Curated Molecular Databases
http://www.hsls.pitt.edu/guides/genetics
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Molecular Databases
Nucleic Acids Research : Annual databases Issue NAR: Annual Web Server Issue Oxford Journal : Bioinformatics BioMedCentral: BMC Bioinformatics
http://www.hsls.pitt.edu/guides/genetics
Growth of bioinformatics tools
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Growth of Molecular Databases
Source: Nodal Point Blog
2008: 1078
http://www.hsls.pitt.edu/guides/genetics
2011: 1330
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GWA Studies Catalog
http://www.hsls.pitt.edu/guides/genetics
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GWA Studies Catalog
http://www.hsls.pitt.edu/guides/genetics
http://www.genome.gov/gwastudies/
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Search Engine Just for Human GeneticsCDC HuGENavigator : http://hugenavigator.net/
http://www.hsls.pitt.edu/guides/genetics
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http://www.hsls.pitt.edu/molbio
Find human genes that are reported to be associated with the Asthma
Find human SNPs that are reported to be associated with the Asthma
Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/asthma.swf
Resources
• HugeNavigator:
http://hugenavigator.net/HuGENavigator/home.do
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Search Engine Just for Human Genetics
http://www.hsls.pitt.edu/guides/genetics
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Search Engine Just for Human GeneticsCDC HuGENavigator : http://hugenavigator.net/
http://www.hsls.pitt.edu/guides/genetics
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Search Engine Just for Human Geneticshttp://hugenavigator.net/HuGENavigator/huGEPedia.do
http://www.hsls.pitt.edu/guides/genetics
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Search Engine Just for Human GeneticsCDC HuGENavigator : http://hugenavigator.net/
http://www.hsls.pitt.edu/guides/genetics
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Find Disease Causing SNPs
What SNPs are associated with “Schizophrenia”?
http://hugenavigator.net/HuGENavigator/gWAHitStartPage.do
http://www.hsls.pitt.edu/guides/genetics
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Hands-On exercise on lit search
Which proteins are related to Alzheimer’s disease?
Where/who are the leading centers and scientists for liver transplantation?
Which hormones are Autistic Disorder associated with?
http://www.hsls.pitt.edu/guides/genetics
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Gene/Protein Information Mining
http://www.hsls.pitt.edu/guides/genetics
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Bioinformatics Databases & Software Providers
National Center for Biotechnology Information (NCBI) Home page Site map Resource Guide
European Bioinformatics Institute (EBI) Home page Databases Software
http://www.hsls.pitt.edu/guides/genetics
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Gene Information Gateways
o Open access resources:
National Center for Biotechnology Information (NCBI) Genbank Refseq
Entrez Gene Gene Expression Omnibus (GEO) OMIM
http://www.hsls.pitt.edu/guides/genetics
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Protein Information Hubs
o Open access resources: European Bioinformatics Institute (EBI)
Uniprot Interpro Prosite STRING
UCSC Genome Bioinformatics BLAT Search Gene Detail Page
http://www.hsls.pitt.edu/guides/genetics
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Protein Information Hubs
o Open access resources:
National Center for Biotechnology Information (NCBI) Refseq Entrez Gene Conserved Domain Database (CDD) Molecular Modeling Database (MMDB) 3D structure viewer: Cn3D
http://www.hsls.pitt.edu/guides/genetics
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Gene/Protein Information
Chromosomal location, mRNA,
genomic seq, orthologs, paralogs,
regulatory elements,
Amino acid seq, domain architecture,
protein structure, post translational modifications
Gene expression, biological pathways,
protein interaction map, disease association, biomarkers
http://www.hsls.pitt.edu/guides/genetics
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Gene Questions ?
What is its function?
What are its neighboring genes?
What is its genomic seq?How many splice varients are there?
What are its intron-exon architechure?
What diseases are associated with it?
Which tissues it expressed ?
How can I get its cDNA clone?
http://www.hsls.pitt.edu/guides/genetics
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SNP
Genomic Sequence
Expression Profile
Interacting Partners3D Structure
mRNA Sequence
Chromosomal Localization
Disease
Amino acid Sequence
Homologous Sequences
http://www.hsls.pitt.edu/guides/genetics
NCBI : Entrez Gene
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Entrez Gene
Find: gene symbols and aliases sequences: genomic, mRNA, protein intron-exon architecture genomic context: neighboring and antisense
genes Interacting partners associated gene ontology terms: function,
cellular component and biological process
http://www.hsls.pitt.edu/guides/genetics
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Entrez Gene
a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer
Statistics Gene: 7974 organisms Genbank: 160,000 organisms
each record represents a single gene from a given organism
http://www.hsls.pitt.edu/guides/genetics
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NCBI Sequence Databases
GenBank archival database of nucleotide sequences
from >160,000 organisms More info GenPept
conceptual translation of GenBank CDS Refseq
based on GenBank record, non-redundant expert verified databases of reference sequences
http://www.hsls.pitt.edu/guides/genetics
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International Nucleotide Sequence Database Collaboration
http://www.hsls.pitt.edu/guides/genetics
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Primary Vs Derivative databases
http://www.hsls.pitt.edu/guides/genetics
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RefSeq Scope & Accessions
Genomic DNA NC_123456 - complete genome, complete
chromosome, complete plasmid NG_123456 - genomic region NT_123456 - genomic contig
mRNA - NM_123456 Protein - NP_123456
more about RefSeq scope and accessions...
http://www.hsls.pitt.edu/guides/genetics
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RefSeq Status Codes
Provisional Reviewed Predicted Genome Annotation
more about RefSeq status codes
http://www.hsls.pitt.edu/guides/genetics
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Hands on
Find mRNA sequence for your gene of interest (p53, BRCA1, EGFR, PLCg1)
Start page: Entrez core nucleotide Use Limits, History and Preview Index
http://www.hsls.pitt.edu/guides/genetics
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Sequence Format
GenBank Header Features Sequence
FASTA Sequence
Example: U49845 Sample GenBank record Sequence Revision History tool
http://www.hsls.pitt.edu/guides/genetics
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Video Tutorials
http://www.hsls.pitt.edu/molbio/videos?c=3
http://www.hsls.pitt.edu/guides/genetics
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Find mRNA Sequence for Reelin Gene.
http://www.hsls.pitt.edu/guides/genetics
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Gene FunctionWhat is its function?
Entrez Gene Page:
Summary (TOC)Gene Ontology
GeneRIFsPathways (TOC)
Biosystems (Links)
http://www.hsls.pitt.edu/guides/genetics
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Gene Ontology (GO)
Controlled vocabulary tagging
• Function• Biological Processes• Cellular Component
http://www.hsls.pitt.edu/guides/genetics
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Gene Ontology (GO) and KEGG GO
information page GO evidence codes
KEGG Information page
http://www.hsls.pitt.edu/guides/genetics
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Function How many splice variants are there?What is/are its sequence?
Entrez Gene Page:
Genomic regions…(TOC)
UCSC (Links)
http://www.hsls.pitt.edu/guides/genetics
Video Tutorials
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Alternative Splicing
http://www.hsls.pitt.edu/guides/genetics
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Intron-Exon Coordinates
What are its intron-exon architechure?
Entrez Gene Page:
DisplayChange it from
Full report to Gene Table
http://www.hsls.pitt.edu/guides/genetics
Video Tutorials
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Neighboring Genes
What are its neighboring genes?
Entrez Gene Page:
Genomic context(TOC)
http://www.hsls.pitt.edu/guides/genetics
Video Tutorials
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Chromosomal location
http://www.hsls.pitt.edu/guides/genetics
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Associated DiseasesWhat diseases are associated with it? Entrez Gene
Page:TOC• General
Information_Phenotype
LinksOMIM
HuGE Navigator
http://www.hsls.pitt.edu/guides/genetics
Video Tutorials
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HomologeneWhat are its homologous genes?
Entrez Gene Page:
LinkHomologenechange Display
settings
http://www.hsls.pitt.edu/guides/genetics
Video Tutorials
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ReagentsHow can I get its cDNA clone?
..antibodies? .. siRNA ?
Entrez Gene Page:
TOC:Additional Links
Research MateriasExact Antigen
http://www.hsls.pitt.edu/guides/genetics
Video Tutorials
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Protein Information Gateways
http://www.hsls.pitt.edu/guides/genetics
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UniprotKB : Universal Protein Resource : a comprehensive, centralized protein
information resource Developed by a consortium:
European Bioinformatics Institute (EBI) the Swiss Institute of Bioinformatics (SIB) the Protein Information Resource (PIR) Comprised of:
--Swiss-Prot: biologist-curated annotation data
--TrEMBL: computationally annotation data
--PIR-International Protein Sequence Database (PIR-PSD): the most comprehensive and expertly-curated protein sequence database in the public domain for over 20 years.
Funded by: NIH, NSF, the European Union and the Swiss Federal government
Link to Wiki, YouTube, Blogs and Tweets: http://www.kosmix.com/topic/uniprot?
Tutorial Video: http://www.youtube.com/watch?v=TCF3qWn7siI&feature=youtube_gdata
http://www.hsls.pitt.edu/guides/genetics
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Protein Questions ?
http://www.hsls.pitt.edu/guides/genetics
What is its Function?Amino acid sequence?
… molecular wt? isoelectric point (PI)? …post translational modifications? … presence of domain/pattern/profile? … hydrophobicity? … homologous orthologs? Etc.
Structure? … secondary and tertiary?
Interaction Partner?
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Uniprot Video Tutorial
http://www.hsls.pitt.edu/molbio/videos/play?v=19
http://www.hsls.pitt.edu/guides/genetics
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Protein Function from UniprotKB Uniprot Search:
http://www.hsls.pitt.edu/guides/genetics
Look under: general annotation_Function, ontologies_keywords, geneontology
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Protein Sequence
Uniprot
•Sequence annotations•sequences
Gene•Genomic regions, transcripts, and
products•ccds (consensus cds report)
UCSC
•Sequence and links
http://www.hsls.pitt.edu/guides/genetics
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Protein Sequence Analysis
http://www.hsls.pitt.edu/guides/genetics
PTM
•Uniprot•Seq annt
•IPA•Modificatio-ns and Regulation
PI/MW
•Uniprot
•Seq_Tool•Compute PI
Hydroph-obicity
•Uniprot
•Seq_Tool•ProtScale
Peptide Digest
•Uniprot•Seq_Tools•PeptideMass•PeptideCutter
Homologous Seq
•Entrez Gene•Homologene
Domain/pattern•Uniprot•Sequence annotation•InterPro•Entrez gene•Conserved Domain
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Protein Domain Resources
Protein Domain Databases:
InterPro
http://www.hsls.pitt.edu/guides/genetics
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Protein Domains Wikipedia:
A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural domains. One domain may appear in a variety of evolutionarily related proteins. Domains vary in length from between about 25 amino acids up to 500 amino acids in length. The shortest domains such as zinc fingers are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin.
http://www.hsls.pitt.edu/guides/genetics
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Protein Domain: SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands
with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway
components and mediate multiprotein complex assemblies.
http://www.hsls.pitt.edu/guides/genetics
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Protein Structure
Primary
Secondary
Tertiary
Quarternary
http://www.hsls.pitt.edu/guides/genetics
Useful links: http://www.kosmix.com/topic/protein_structure?
Taken from wikipedia
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Protein Structure
http://www.hsls.pitt.edu/guides/genetics
NCBI
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Finding Protein Structure
PDB
Entrez Structure
NCBI BLINK via Entrez Gene/Protein
http://www.hsls.pitt.edu/guides/genetics
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Structure Databases and Viewer Databases:
RCSB Protein Data Bank (PDB) State University of New Jersey (Rutgers), the San Diego Supercomputer Center at the University of California San
Diego, the University of Wisconsin-Madison Link http://www.kosmix.com/topic/protein_data_bank?
MMDB NCBI's structure database is called MMDB (Molecular Modeling DataBase), and it is a
subset of three-dimensional structures obtained from the Protein Data Bank (PDB), excluding theoretical models..
Viewer: Cn3D :
a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.
Rasmol: EBI First glance in j mol : A simple tool for macromolecular visualization. (More..)
http://www.hsls.pitt.edu/guides/genetics
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Protein Structure
Search for the 3D structure of P53 Entrez structure
View the crystal structure of mouse p53 core domain (MMDB: 42987) or Crystal Structure Of A P53 Core Dimer Bound To Dna ( PDB:2GEQ)
http://www.hsls.pitt.edu/guides/genetics
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Manipulating the Structure Viewer Window
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Find Similar Structure: NCBI VAST
http://www.hsls.pitt.edu/guides/genetics
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NCBI BLink
BLink ("BLAST Link") displays the results of BLAST searches that have been done for every protein sequence in the Entrez Proteins data domain.
To access it, follow the BLink link displayed beside any hit in the results of an Entrez Proteins search.
http://www.hsls.pitt.edu/guides/genetics
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Hands-on Protein Structure
View the crystal structure of Chronophin (PDB entry: 2P69).
A variant of this protein with mutations in its amino acid sequence has been isolated. Can you predict any effect of its mutations into its function?
Hint: Find the amino acid residues which are in close contact (3.5 A) with PYRIDOXAL-5'-PHOSPHATE (PLP).
Label the amino acids and save the picture in PNG format. Learn more on Chronophin structure at:http://kb-dev.psi-structuralgenomics.org/KB/archives.jsp?pageshow=3
http://www.hsls.pitt.edu/guides/genetics
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Hands-on Protein Structure of Chronophin
http://kb-dev.psi-structuralgenomics.org/KB/archives.jsp?pageshow=3
http://www.hsls.pitt.edu/guides/genetics
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Sequence Alignment in Cn3D
NCBI
http://www.hsls.pitt.edu/guides/genetics
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Hands-On Can you identify the human protein which contains a
short peptide sequence: GPDGMPVIYHGHTLTTKIKFSDVLHTIKE ?
What is its function? What is its calculated PI and molecular wt? Which region of this protein is most hydrophobic? Locate five experimentally verified S/T/Y phosphorylation sites present in this
protein. Find the homologous mouse and fruit fly orthologs of this human protein and
report the % protein identity it shares with these orthologs. How many protein domains are reported to be present in this human protein? Find the location of its largest domain.
http://www.hsls.pitt.edu/guides/genetics
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Licensed Tools for Gene/Protein Information
http://www.hsls.pitt.edu/guides/genetics
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HSLS Licensed Tools
BioBase Metacore Ingenuity IPA
http://www.hsls.pitt.edu/guides/genetics
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Gene/Protein facts from Biobase
http://www.hsls.pitt.edu/guides/genetics
http://goo.gl/9wpwG
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BioBase BioKnowledge Library
http://www.hsls.pitt.edu/guides/genetics
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Protein Function from IPA
http://www.hsls.pitt.edu/guides/genetics
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Search Engine for Bioinformatics Tools
http://www.hsls.pitt.edu/guides/genetics
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Biomedical and Life Sciences Search Engines
OBRC : University of Pittsburgh
http://www.hsls.pitt.edu/guides/genetics/obrc
Vadlohttp://vadlo.com/
OReFil : University of Tokyo
http://orefil.dbcls.jp/
http://www.hsls.pitt.edu/guides/genetics
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Search.HSLS.MolBio
http://www.hsls.pitt.edu/guides/genetics
http://www.hsls.pitt.edu/molbio
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Search.HSLS.MolBio Integrated search system
Databases & Software Articles on Databases & Software Genes/Proteins Pathways Protocols Seminar/Talks Videos Recommended Articles
Tabbed browsing Clustered search results
http://www.hsls.pitt.edu/guides/genetics
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Search term: “phosphorylation”
http://www.hsls.pitt.edu/guides/genetics
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Molecular Databases and Software:search term: “Phosphorylation”
http://www.hsls.pitt.edu/guides/genetics
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Search Result Page
http://www.hsls.pitt.edu/guides/genetics
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Searh PubMed Articles on Databases and Software : “phosphorylation”
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Articles on Databases and Software
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Articles on Prediction of Phosphorylation Sites
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Prediction of Phosphorylation Sites
http://www.hsls.pitt.edu/guides/genetics
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Genes/Proteins Info
http://www.hsls.pitt.edu/guides/genetics
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BioBase Knowledge Library
http://www.hsls.pitt.edu/guides/genetics
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Seminar Talks Video
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Seminar Talks Video
http://www.hsls.pitt.edu/guides/genetics
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Recommended Articles
Faculty of 1000 Biology: a literature awareness tool that highlights and reviews the most interesting papers published
in the biological sciences, based on the recommendations of a faculty of well over 2300 selected leading researchers.
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Recommended Articles
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Recommended Articles
http://www.hsls.pitt.edu/guides/genetics
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Thank you!Any questions?
Carrie Iwema Ansuman [email protected] [email protected] 412-383-6887 412-648-1297
http://www.hsls.pitt.edu/molbio