Locating Gene/Protein Information January 11, 2011 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System

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

mailto:[email protected]


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


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


http://media.hsls.pitt.edu/media/molbiovideos/pubmedsearch1.swf


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



http://www.kosmix.com/topic/Medical_Subject_Headings?

http://bitesizebio.com/2008/03/05/18-ways-to-improve-your-pubmed-searches/

http://bitesizebio.com/2008/03/05/18-ways-to-improve-your-pubmed-searches/

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed&part=pubmedhelp

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed&part=pubmedhelp



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


http://media.hsls.pitt.edu/media/molbiovideos/pubmedsearch2.swf

http://www.ncbi.nlm.nih.gov/pubmed/clinical

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


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


http://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


http://media.hsls.pitt.edu/media/clres2705/gopubmed.swf

http://www.gopubmed.org/web/gopubmed/2?WEB10O00h00100090000

GoPubMed Search Result



GoPubMed Search Result Analysis



GoPubMed Search Result Analysis



Latest Innovations in Literature Searching



PubMed driven Web Tools

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

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

Literature to Gene List

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


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


Gene list to common functions



Literature to Gene list


http://www.quertle.info/


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

http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl

http://nar.oxfordjournals.org/content/vol35/suppl_2/index.dtl

http://bioinformatics.oxfordjournals.org/

http://www.biomedcentral.com/bmcbioinformatics/

http://www.biomedcentral.com/bmcbioinformatics/


Growth of Molecular Databases

Source: Nodal Point Blog

2008: 1078


2011: 1330


GWA Studies Catalog



GWA Studies Catalog


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


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

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


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


http://media.hsls.pitt.edu/media/clres2705/asthma.swf

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

Search Engine Just for Human Genetics







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


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






Find Disease Causing SNPs

What SNPs are associated with “Schizophrenia”?

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


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


http://www.ncbi.nlm.nih.gov/

http://www.ncbi.nlm.nih.gov/Sitemap/AlphaList.html

http://www.ncbi.nlm.nih.gov/Sitemap/ResourceGuide.html

http://www.ebi.ac.uk/

http://www.ebi.ac.uk/Databases/

http://www.ebi.ac.uk/Tools/

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?


SNP

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


http://www.ncbi.nlm.nih.gov/RefSeq/

http://www.ncbi.nlm.nih.gov/projects/Gene/gentrez_stats.cgi


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.ncbi.nlm.nih.gov/Sitemap/ResourceGuide.html


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...


http://www.ncbi.nlm.nih.gov/RefSeq/key.html



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


http://www.ncbi.nlm.nih.gov/sites/entrez


Sequence Format

GenBank Header Features Sequence

FASTA Sequence

Example: U49845 Sample GenBank record Sequence Revision History tool


http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=nuccore&term=U49845%5Bpacc%5D&doptcmdl=GenBank

http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html



http://www.ncbi.nlm.nih.gov/Sitemap/sequencerevisionhistory.html

http://www.ncbi.nlm.nih.gov/Sitemap/sequencerevisionhistory.html


Video Tutorials

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


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


http://www.geneontology.org/


Gene Ontology (GO) and KEGG GO

information page GO evidence codes

KEGG Information page


http://www.kosmix.com/topic/gene_ontology?

http://www.geneontology.org/GO.evidence.shtml

http://www.kosmix.com/topic/Kyoto_Encyclopedia_of_Genes_and_Genomes?


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


http://www.kosmix.com/topic/uniprot?

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


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)

UCSC

•Sequence and links



Protein Sequence Analysis


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


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.


http://en.wikipedia.org/wiki/Structural_domain

http://en.wikipedia.org/wiki/Tertiary_structure

http://en.wikipedia.org/wiki/Biological_evolution

http://en.wikipedia.org/wiki/Protein_folding

http://en.wikipedia.org/wiki/EF-hand

http://en.wikipedia.org/wiki/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


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

Protein Structure


NCBI


Finding Protein Structure

PDB

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..)


http://www.kosmix.com/topic/protein_data_bank?

http://www.rcsb.org/

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure

http://molvis.sdsc.edu/fgij/whatis.htm


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.


http://www.ncbi.nlm.nih.gov/sutils/static/blinkhelp.html

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein


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


Hands-on Protein Structure of Chronophin





Sequence Alignment in Cn3D

NCBI


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


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/


http://www.hsls.pitt.edu/guides/genetics/obrc

http://vadlo.com/

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



Seminar Talks Video



rtsp://nihvideo.nih.gov/special/ncbc040809.rm

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Thank you!Any questions?

Carrie Iwema Ansuman [email protected] [email protected] 412-383-6887 412-648-1297





Documents

Locating Gene/Protein Information January 11, 2011 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System