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Locating Gene/Protein Information September 26, 2013 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of Pittsburgh ansuman@pitt.edu 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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Literature Informatics Which genes/proteins are reported to be associated with the disease - Schizophrenia? http://www.hsls.pitt.edu/guides/genetics Citations: 19 million Journals: 5200 Schizophrenia: 86,384.. 96234 Schizophrenia 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. Organisms C. Diseases D. Chemical and Drugs E. Analytical, Diagnostic and Therapeutic Techniques and Equipment F. Psychiatry and Psychology G. Biological Sciences H. Physical Sciences I. Anthropology, Education, Sociology and Social Phenomena J. Technology and Food and Beverages K. Humanities L. Information Science M. Persons N. Health Care V. 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 http://www.ncbi.nlm.nih.gov/mesh PubMed: http://www.ncbi.nlm.nih.gov/pubmed http://www.ncbi.nlm.nih.gov/pubmed
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Building PubMed Queries TermBooleanTermBooleanTerm# papers DengueANDOutbreaks823 Dengue *ANDOutbreaks746 DengueANDOutbreaksANDIndia131 Dengue*ANDOutbreaksANDIndia116 DengueANDOutbreaks/ statistics and numerical data ANDIndia7 Dengue*ANDOutbreaks/ statistics and numerical data ANDIndia7 http://www.hsls.pitt.edu/guides/genetics
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Useful links for MESH MESH Browser: http://www.ncbi.nlm.nih.gov/meshhttp://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? 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- pubmed-searches/ http://bitesizebio.com/2008/03/05/18-ways-to-improve-your- pubmed-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.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 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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Search Filters 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 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://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 IssueAnnual databases Issue NAR: Annual Web Server IssueAnnual Web Server Issue Oxford Journal : BioinformaticsBioinformatics BioMedCentral: BMC 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 Genetics CDC HuGENavigator : http://hugenavigator.net/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 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 Genetics CDC HuGENavigator : http://hugenavigator.net/http://hugenavigator.net/ http://www.hsls.pitt.edu/guides/genetics
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Search Engine Just for Human Genetics http://hugenavigator.net/HuGENavigator/huGEPedia.do http://www.hsls.pitt.edu/guides/genetics
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Search Engine Just for Human Genetics CDC HuGENavigator : http://hugenavigator.net/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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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 Vadlo http://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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Citation Trackers http://www.hsls.pitt.edu/guides/genetics
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Searh PubMed Articles on Databases and Software : “phosphorylation” http://www.hsls.pitt.edu/guides/genetics
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Articles on Databases and Software http://www.hsls.pitt.edu/guides/genetics
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Articles on Prediction of Phosphorylation Sites http://www.hsls.pitt.edu/guides/genetics
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Prediction of Phosphorylation Sites http://www.hsls.pitt.edu/guides/genetics
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MetaPredPS http://www.hsls.pitt.edu/guides/genetics
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Clustering Remix 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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Entrez Gene 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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Protocols: http://www.hsls.pitt.edu/guides/genetics
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Seminar Talks Video http://www.hsls.pitt.edu/guides/genetics
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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. http://www.hsls.pitt.edu/guides/genetics
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Faculty of 1000 http://www.hsls.pitt.edu/guides/genetics
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Recommended Articles http://www.hsls.pitt.edu/guides/genetics
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Recommended Articles 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 Home page Site map Site map Resource Guide Resource Guide European Bioinformatics Institute (EBI) Home page Home page Databases Databases Software 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 Partners 3D 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 ViewerRefSeq 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 infoMore 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 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 nucleotidecore 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: U49845U49845 Sample GenBank record Sample GenBank record Sequence Revision History tool 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 Function What is its function? Entrez Gene Page: Summary (TOC) Gene Ontology GeneRIFs Pathways (TOC) Biosystems (Links) http://www.hsls.pitt.edu/guides/genetics
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Gene Ontology (GO)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 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: Display Change 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 Diseases What diseases are associated with it? Entrez Gene Page:TOC General Information_Phe notype Links OMIM HuGE Navigator http://www.hsls.pitt.edu/guides/genetics Video Tutorials
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Homologene What are its homologous genes? Entrez Gene Page: Link Homologene change Display settings http://www.hsls.pitt.edu/guides/genetics Video Tutorials
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Reagents How can I get its cDNA clone?..antibodies?.. siRNA ? Entrez Gene Page: TOC: Additional Links Research Materias Exact 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? http://www.kosmix.com/topic/uniprot? Tutorial Video: http://www.youtube.com/watch?v=TCF3qWn7siI&feature=youtube_gdata 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 PeptideMa ss PeptideCutt er Homolog ous Seq Entrez Gene Homologe ne Domain/patt ern 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: 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. structureevolvefoldedEF hand domaincalmodulin 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?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 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?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..PDB Viewer: Cn3D : a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.Entrez Rasmol: EBI First glance in j mol : A simple tool for macromolecular visualization. (More..)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.BLAST LinkEntrez Proteins 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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Gene Lists Microarrays Protein arrays CHIP-chip SNP arrays RNA Seq Literature Search http://www.hsls.pitt.edu/guides/genetics
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Gene Expression Databases NCBI Gene Expression Omnibus (GEO) EBI ArrayExpress http://www.hsls.pitt.edu/guides/genetics
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Use of GEO Data http://goo.gl/yD2hR http://goo.gl/yD2hR
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Gene Expression Databases NCBI Gene Expression Omnibus (GEO) EBI ArrayExpress http://www.hsls.pitt.edu/guides/genetics
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Array Express http://www.hsls.pitt.edu/guides/genetics
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Gene Expression Atlas http://www.ebi.ac.uk/gxa/ http://www.hsls.pitt.edu/guides/genetics
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NextBio https://hsls.nextbio.com http://www.hsls.pitt.edu/guides/genetics
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NextBio
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Thank you! Any questions? Carrie IwemaAnsuman Chattopadhyay iwema@pitt.eduansuman@pitt.edu 412-383-6887412-648-1297 http://www.hsls.pitt.edu/molbio
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