locating gene/protein information january 11, 2011 ansuman chattopadhyay, phd head, molecular...

Locating Gene/Protein Information

January 11, 2011

Ansuman Chattopadhyay, PhDHead, Molecular Biology Information ServicesHealth Sciences Library SystemUniversity of Pittsburghansuman@pitt.edu

http://www.hsls.pitt.edu/molbio

Objectives

Generate a gene list

Mine gene/protein information

Topics

Literature Informatics

Gene / Protein Information Gateways

Search Engine for MolBio / Bioinformatics Databases and Software

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

Literature InformaticsWhich genes/proteins are reported to be associated with the disease - Schizophrenia?

Citations: 19 millionJournals: 5200

Schizophrenia: 86,384.. 96234Schizophrenia gene: 5851…7295

Challenges in Literature Search Am I getting everything? Too much Information.. How to digest?

A list with citations

Medical Subject Heading (MESH)

Medical Subject Headings (MeSH)

The U.S. National Library of Medicine's controlled vocabulary (thesaurus)

Arranged in a hierarchical manner called the MeSH Tree Structures

Updated annually

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)

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

MeSH Indexing

Source: NLM

MeSH Indexing

Genes/Chemicals

MeSH Terms

PubMed Query Using MeSH http://www.ncbi.nlm.nih.gov/mesh

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

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

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

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

Topic-Specific PubMed Queries http://www.nlm.nih.gov/bsd/special_queries.html

Research on Optimal Search Strategies

PubMed Special Topic Queries

Search Filters

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]))

PubMed Search Result Display

Latest Innovations in Literature Searching

GoPubMed Display search results sorted into meaningful topics and subtopics

GoPubMed

www.gopubmed.com

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

GoPubMed Search Result

GoPubMed Search Result Analysis

Latest Innovations in Literature Searching

PubMed driven Web Tools

http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/

Literature to Gene List

GLAD4U http://bioinfo.vanderbilt.edu/glad4u/

Gene list to common functions

Literature to Gene list

http://www.quertle.info/

NIH Grant Applications to Gene List

Curated Molecular Databases

Molecular Databases

Nucleic Acids Research : Annual databases Issue NAR: Annual Web Server Issue Oxford Journal : Bioinformatics BioMedCentral: BMC Bioinformatics

Growth of bioinformatics tools

Growth of Molecular Databases

Source: Nodal Point Blog

2008: 1078

2011: 1330

GWA Studies Catalog

http://www.genome.gov/gwastudies/

Search Engine Just for Human GeneticsCDC HuGENavigator : http://hugenavigator.net/

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

Search Engine Just for Human Genetics

Search Engine Just for Human Geneticshttp://hugenavigator.net/HuGENavigator/huGEPedia.do

Find Disease Causing SNPs

What SNPs are associated with “Schizophrenia”?

http://hugenavigator.net/HuGENavigator/gWAHitStartPage.do

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?

Gene/Protein Information Mining

Bioinformatics Databases & Software Providers

National Center for Biotechnology Information (NCBI) Home page Site map Resource Guide

European Bioinformatics Institute (EBI) Home page Databases Software

Gene Information Gateways

o Open access resources:

National Center for Biotechnology Information (NCBI) Genbank Refseq

Entrez Gene Gene Expression Omnibus (GEO) OMIM

Protein Information Hubs

o Open access resources: European Bioinformatics Institute (EBI)

Uniprot Interpro Prosite STRING

UCSC Genome Bioinformatics BLAT Search Gene Detail Page

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

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

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?

Genomic Sequence

Expression Profile

Interacting Partners3D Structure

mRNA Sequence

Chromosomal Localization

Disease

Amino acid Sequence

Homologous Sequences

NCBI : Entrez Gene

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

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

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

International Nucleotide Sequence Database Collaboration

Primary Vs Derivative databases

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...

RefSeq Status Codes

Provisional Reviewed Predicted Genome Annotation

more about RefSeq status codes

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

Sequence Format

GenBank Header Features Sequence

FASTA Sequence

Example: U49845 Sample GenBank record Sequence Revision History tool

Video Tutorials

http://www.hsls.pitt.edu/molbio/videos?c=3

Find mRNA Sequence for Reelin Gene.

Gene FunctionWhat is its function?

Entrez Gene Page:

Summary (TOC)Gene Ontology

GeneRIFsPathways (TOC)

Biosystems (Links)

Gene Ontology (GO)

Controlled vocabulary tagging

• Function• Biological Processes• Cellular Component

Gene Ontology (GO) and KEGG GO

information page GO evidence codes

KEGG Information page

Function How many splice variants are there?What is/are its sequence?

Entrez Gene Page:

Genomic regions…(TOC)

UCSC (Links)

Video Tutorials

Alternative Splicing

Intron-Exon Coordinates

What are its intron-exon architechure?

Entrez Gene Page:

DisplayChange it from

Full report to Gene Table

Video Tutorials

Neighboring Genes

What are its neighboring genes?

Entrez Gene Page:

Genomic context(TOC)

Video Tutorials

Chromosomal location

Associated DiseasesWhat diseases are associated with it? Entrez Gene

Page:TOC• General

Information_Phenotype

LinksOMIM

HuGE Navigator

Video Tutorials

HomologeneWhat are its homologous genes?

Entrez Gene Page:

LinkHomologenechange Display

settings

Video Tutorials

ReagentsHow can I get its cDNA clone?

..antibodies? .. siRNA ?

Entrez Gene Page:

TOC:Additional Links

Research MateriasExact Antigen

Video Tutorials

Protein Information Gateways

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

Protein Questions ?

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?

Uniprot Video Tutorial

http://www.hsls.pitt.edu/molbio/videos/play?v=19

Protein Function from UniprotKB Uniprot Search:

Look under: general annotation_Function, ontologies_keywords, geneontology

Protein Sequence

Uniprot

•Sequence annotations•sequences

Gene•Genomic regions, transcripts, and

products•ccds (consensus cds report)

•Sequence and links

Protein Sequence Analysis

•Uniprot•Seq annt

•IPA•Modificatio-ns and Regulation

•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

Protein Domain Resources

Protein Domain Databases:

InterPro

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.

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.

Protein Structure

Primary

Secondary

Tertiary

Quarternary

Useful links: http://www.kosmix.com/topic/protein_structure?

Taken from wikipedia

Protein Structure

Finding Protein Structure

Entrez Structure

NCBI BLINK via Entrez Gene/Protein

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..)

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)

Manipulating the Structure Viewer Window

Find Similar Structure: NCBI VAST

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.

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

Hands-on Protein Structure of Chronophin

http://kb-dev.psi-structuralgenomics.org/KB/archives.jsp?pageshow=3

Sequence Alignment in Cn3D

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.

Licensed Tools for Gene/Protein Information

HSLS Licensed Tools

BioBase Metacore Ingenuity IPA

Gene/Protein facts from Biobase

http://goo.gl/9wpwG

BioBase BioKnowledge Library

Protein Function from IPA

Search Engine for Bioinformatics Tools

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/

Search.HSLS.MolBio

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

Search term: “phosphorylation”

Molecular Databases and Software:search term: “Phosphorylation”

Search Result Page

Citation Trackers

Searh PubMed Articles on Databases and Software : “phosphorylation”

Articles on Databases and Software

Articles on Prediction of Phosphorylation Sites

Prediction of Phosphorylation Sites

MetaPredPS

Clustering Remix

Genes/Proteins Info

Entrez Gene

BioBase Knowledge Library

Protocols:

Seminar Talks Video

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