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Locating Gene/Protein Information September 26, 2013 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System.

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Presentation on theme: "Locating Gene/Protein Information September 26, 2013 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System."— Presentation transcript:

1 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

2 Topics Literature Informatics Gene / Protein Information Gateways Search Engine for MolBio / Bioinformatics Databases and Software http://www.hsls.pitt.edu/molbio

3 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

4 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

5 Medical Subject Heading (MESH) http://www.hsls.pitt.edu/guides/genetics

6 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

7 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

8 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

9 MeSH Indexing http://www.hsls.pitt.edu/guides/genetics Source: NLM

10 MeSH Indexing http://www.hsls.pitt.edu/guides/genetics Genes/Chemicals MeSH Terms

11 PubMed Query Using MeSH http://www.ncbi.nlm.nih.gov/mesh http://www.hsls.pitt.edu/guides/genetics

12 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

13 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

14 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

15 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

16 Topic-Specific PubMed Queries http://www.nlm.nih.gov/bsd/special_queries.html http://www.hsls.pitt.edu/guides/genetics

17 Research on Optimal Search Strategies http://www.hsls.pitt.edu/guides/genetics

18 PubMed Special Topic Queries http://www.hsls.pitt.edu/guides/genetics

19 Search Filters http://www.hsls.pitt.edu/guides/genetics

20 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

21 PubMed Search Result Display http://www.hsls.pitt.edu/guides/genetics

22 Latest Innovations in Literature Searching GoPubMed Display search results sorted into meaningful topics and subtopics http://www.hsls.pitt.edu/guides/genetics

23 GoPubMed http://www.hsls.pitt.edu/guides/genetics www.gopubmed.com

24 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

25 GoPubMed Search Result http://www.hsls.pitt.edu/guides/genetics

26 GoPubMed Search Result Analysis http://www.hsls.pitt.edu/guides/genetics

27 GoPubMed Search Result Analysis http://www.hsls.pitt.edu/guides/genetics

28 Latest Innovations in Literature Searching http://www.hsls.pitt.edu/guides/genetics

29 PubMed driven Web Tools http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/

30 Literature to Gene List GLAD4U  http://bioinfo.vanderbilt.edu/glad4u/ http://bioinfo.vanderbilt.edu/glad4u/ http://www.hsls.pitt.edu/guides/genetics

31 Gene list to common functions http://www.hsls.pitt.edu/guides/genetics

32 Literature to Gene list http://www.hsls.pitt.edu/guides/genetics http://www.quertle.info/

33 NIH Grant Applications to Gene List http://www.hsls.pitt.edu/guides/genetics

34 Curated Molecular Databases http://www.hsls.pitt.edu/guides/genetics

35 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

36 Growth of Molecular Databases Source: Nodal Point Blog 2008: 1078 http://www.hsls.pitt.edu/guides/genetics 2011: 1330

37 GWA Studies Catalog http://www.hsls.pitt.edu/guides/genetics

38 GWA Studies Catalog http://www.hsls.pitt.edu/guides/genetics http://www.genome.gov/gwastudies/

39 Search Engine Just for Human Genetics CDC HuGENavigator : http://hugenavigator.net/http://hugenavigator.net/ http://www.hsls.pitt.edu/guides/genetics

40 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

41 Search Engine Just for Human Genetics http://www.hsls.pitt.edu/guides/genetics

42 Search Engine Just for Human Genetics CDC HuGENavigator : http://hugenavigator.net/http://hugenavigator.net/ http://www.hsls.pitt.edu/guides/genetics

43 Search Engine Just for Human Genetics http://hugenavigator.net/HuGENavigator/huGEPedia.do http://www.hsls.pitt.edu/guides/genetics

44 Search Engine Just for Human Genetics CDC HuGENavigator : http://hugenavigator.net/http://hugenavigator.net/ http://www.hsls.pitt.edu/guides/genetics

45 Find Disease Causing SNPs What SNPs are associated with “Schizophrenia”? http://hugenavigator.net/HuGENavigator/gWAHitStartPage.do http://www.hsls.pitt.edu/guides/genetics

46 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

47 Search Engine for Bioinformatics Tools http://www.hsls.pitt.edu/guides/genetics

48 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

49 Search.HSLS.MolBio http://www.hsls.pitt.edu/guides/genetics http://www.hsls.pitt.edu/molbio

50 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

51 Search term: “phosphorylation” http://www.hsls.pitt.edu/guides/genetics

52 Molecular Databases and Software: search term: “Phosphorylation” http://www.hsls.pitt.edu/guides/genetics

53 Search Result Page http://www.hsls.pitt.edu/guides/genetics

54 Citation Trackers http://www.hsls.pitt.edu/guides/genetics

55 Searh PubMed Articles on Databases and Software : “phosphorylation” http://www.hsls.pitt.edu/guides/genetics

56 Articles on Databases and Software http://www.hsls.pitt.edu/guides/genetics

57 Articles on Prediction of Phosphorylation Sites http://www.hsls.pitt.edu/guides/genetics

58 Prediction of Phosphorylation Sites http://www.hsls.pitt.edu/guides/genetics

59 MetaPredPS http://www.hsls.pitt.edu/guides/genetics

60 Clustering Remix http://www.hsls.pitt.edu/guides/genetics

61 Genes/Proteins Info http://www.hsls.pitt.edu/guides/genetics

62 Entrez Gene http://www.hsls.pitt.edu/guides/genetics

63 BioBase Knowledge Library http://www.hsls.pitt.edu/guides/genetics

64 Protocols: http://www.hsls.pitt.edu/guides/genetics

65 Seminar Talks Video http://www.hsls.pitt.edu/guides/genetics

66 Seminar Talks Video http://www.hsls.pitt.edu/guides/genetics

67 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

68 Faculty of 1000 http://www.hsls.pitt.edu/guides/genetics

69 Recommended Articles http://www.hsls.pitt.edu/guides/genetics

70 Recommended Articles http://www.hsls.pitt.edu/guides/genetics

71 Gene/Protein Information Mining http://www.hsls.pitt.edu/guides/genetics

72 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

73 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

74 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

75 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

76 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

77 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

78 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

79 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

80 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

81 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

82 International Nucleotide Sequence Database Collaboration http://www.hsls.pitt.edu/guides/genetics

83 Primary Vs Derivative databases http://www.hsls.pitt.edu/guides/genetics

84 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

85 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

86 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

87 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

88 Video Tutorials http://www.hsls.pitt.edu/molbio/videos?c=3 http://www.hsls.pitt.edu/guides/genetics

89 Find mRNA Sequence for Reelin Gene. http://www.hsls.pitt.edu/guides/genetics

90 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

91 Gene Ontology (GO)GO  Controlled vocabulary tagging Function Biological Processes Cellular Component http://www.hsls.pitt.edu/guides/genetics

92 Gene Ontology (GO) and KEGG GO information page GO evidence codes KEGG  Information page Information page http://www.hsls.pitt.edu/guides/genetics

93 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

94 Alternative Splicing http://www.hsls.pitt.edu/guides/genetics

95 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

96 Neighboring Genes What are its neighboring genes? Entrez Gene Page:  Genomic context (TOC) http://www.hsls.pitt.edu/guides/genetics Video Tutorials

97 Chromosomal location http://www.hsls.pitt.edu/guides/genetics

98 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

99 Homologene What are its homologous genes? Entrez Gene Page: Link Homologene change Display settings http://www.hsls.pitt.edu/guides/genetics Video Tutorials

100 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

101 Protein Information Gateways http://www.hsls.pitt.edu/guides/genetics

102 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

103 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 ?

104 Uniprot Video Tutorial http://www.hsls.pitt.edu/molbio/videos/play?v=19 http://www.hsls.pitt.edu/guides/genetics

105 Protein Function from UniprotKB Uniprot Search: http://www.hsls.pitt.edu/guides/genetics Look under: general annotation_Function, ontologies_keywords, geneontology

106 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

107 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

108 Protein Domain Resources Protein Domain Databases: InterPro http://www.hsls.pitt.edu/guides/genetics

109 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

110 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

111 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

112 Protein Structure http://www.hsls.pitt.edu/guides/genetics NCBI

113 Finding Protein Structure http://www.hsls.pitt.edu/guides/genetics

114 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

115 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

116 Manipulating the Structure Viewer Window

117 Find Similar Structure: NCBI VAST http://www.hsls.pitt.edu/guides/genetics

118 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

119 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

120 Hands-on Protein Structure of Chronophin http://kb-dev.psi-structuralgenomics.org/KB/archives.jsp?pageshow=3 http://www.hsls.pitt.edu/guides/genetics

121 Sequence Alignment in Cn3D NCBI http://www.hsls.pitt.edu/guides/genetics

122 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

123 Licensed Tools for Gene/Protein Information http://www.hsls.pitt.edu/guides/genetics

124 HSLS Licensed Tools BioBase Metacore Ingenuity IPA http://www.hsls.pitt.edu/guides/genetics

125 Gene/Protein facts from Biobase http://www.hsls.pitt.edu/guides/genetics http://goo.gl/9wpwG

126 BioBase BioKnowledge Library http://www.hsls.pitt.edu/guides/genetics

127 Protein Function from IPA http://www.hsls.pitt.edu/guides/genetics

128 Gene Lists Microarrays Protein arrays CHIP-chip SNP arrays RNA Seq Literature Search http://www.hsls.pitt.edu/guides/genetics

129 Gene Expression Databases NCBI Gene Expression Omnibus (GEO) EBI ArrayExpress http://www.hsls.pitt.edu/guides/genetics

130 Use of GEO Data  http://goo.gl/yD2hR http://goo.gl/yD2hR

131 Gene Expression Databases NCBI Gene Expression Omnibus (GEO) EBI ArrayExpress http://www.hsls.pitt.edu/guides/genetics

132 Array Express http://www.hsls.pitt.edu/guides/genetics

133 Gene Expression Atlas http://www.ebi.ac.uk/gxa/ http://www.hsls.pitt.edu/guides/genetics

134 NextBio https://hsls.nextbio.com http://www.hsls.pitt.edu/guides/genetics

135 NextBio

136

137

138 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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