Bioinformatics Dr. Víctor Treviño vtrevino@itesm.mx A7-421 Ext. 4536-103 BT4007 13+/M A4- 4 04

1. "Omics", Whole Genomes, Mutations and Other Databases BioinformaticsDr. Víctor Treviñovtrevino@itesm.mxA7-421Ext. 4536-103BT400713+/MA4-404

2. The genome, is the whole hereditary information encoded in the DNA (RNA for some viruses), genomics The proteome is the entire complement of proteins expressed by a genome, cell, tissue or organism. Specifically, it is the expressed proteins at a given time point under defined conditions. The transcriptome, the mRNA complement of an entire organism, tissue type, or cell; with its associated field transcriptomics The metabolome, the totality of metabolites in an organism; with its associated field metabolomics Common "OMICS" http://en.wikipedia.org/wiki/-omics

3. The metallome, the totality of metal and metalloid species; with its associated field metallomics The lipidome, the totality of lipids; with its associated field Lipidomics The glycome, the totality of glycans, carbohydrate structures of an organism, a cell or tissue type. Glycomics: The associated field of study. See http://www.functionalglycomics.org. The interactome, the totality of the molecular interactions in an organism; a once proposed field of interactomics has generally become known as systems biology The spliceome (see spliceosome), the totality of the alternative splicing protein isoforms; with its associated field spliceomics. The ORFeome refers to the totality of DNA sequences that begin with the initiation codon ATG, end with a nonsense codon, and contain no stop codon. Such sequences may therefore encode part or all of a protein. Reactome: A knowledge base of biological processes. New "OMICS" http://en.wikipedia.org/wiki/-omics

4. The speechome. (BBC article on the Speechome Project) The mechanome refers to the force and mechanical systems at work within an organism. The Phenome - the organism itself. The Phenome is to the genome what the phenotype is to the genotype. Also, the complete list of phenotypic mutants available for a species. The Exposome - the collection of an individual's environmental exposures. Miscellaneous "OMICS" http://en.wikipedia.org/wiki/-omics

5. Textome: The body of scientific literature which text mining can analyse. Textomics: The study of the textome. Kinome: The totality of protein kinases in a cell. Kinomics: The study of the kinome. Physiome: Related to physiology. Physiomics: The associated field of study. Neurome: The complete neural makeup of an organism. A word which a neurobiologist might utter in the future. Neuromics: The study of the neurome. Note: Neurome and Neuromics are now the names of Biotech companies. The term 'Neurome' has been used by NeuronBank.org, which is an attempt to develop an approach to catalog the Neurome. Predictome: A complete set of predictions. Omeome: A complete set of "omes", Omeomics will be the cataloguing of all "omics" Come: Collection of all Comics?  Speculative "OMICS" http://en.wikipedia.org/wiki/-omics

6. Pharmacogenomics Physiomics Other "OMICS" http://en.wikipedia.org/wiki/-omics

7. "OMICS" Journal (Since 2000) OMICS: A Journal of Integrative Biology is the only peer-reviewed journal to span all the OMICS-es to date, including: * genomics (the quantitative study of genes, regulatory and non-coding sequences) * transcriptomics (RNA and gene expression) * proteomics (protein expression) * metabolomics (metabolites and metabolic networks) Additionally, the Journal explores advances in the era of post-genomic biology and medicine, including: * pharmacogenomics (the quantitative study of how genetics affects hosts' responses to drugs) * physiomics (physiological dynamics and functions of whole organisms) The Journal covers the integration of many areas of biology and reports on the latest omics research, developments, and discoveries such as: * Physical mapping and sequencing * Gene and protein expression * Peptide identifications * Bacterial coding capabilities * Developments in plant research * Spectral analysis methods http://www.liebertpub.com/publication.aspx?pub_id=43

8. "OMICS" Journals

9. NCBI EBI TIGR (Venter) GENOMIC Databases

10. http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps Organized in Archaea, Bacteria, Eukaryotae, Viruses, Viroids, and Plasmids Includes complete chromosomes, organelles and plasmids as well as draft genome assemblies NCBI Genome Database

11. NCBI Genome Databases • Virus: 2483 • Phages: 465 • Viroids: 48 • Plasmids: 1224 • Bacteria: 1734 • Chr:636 • Plasmid:1096 • Draft: 458 • Archea: 100 • Eukaryots: 1966 • Completed: 20 • Maps: • Vertebrates: 15 • Invertebrates: 7 • Protozoa: 7 • Plants: 42 • Fungi: 16 • Organelles:1460 • Plasmids:22 @ Feb 7 2008

12. NCBI Genome Databases

13. NCBI Genome Databases ~4Mb

14. NCBI Genome Databases

15. NCBI Genome Databases

16. NCBI Genome Databases Gene Searches slit2

17. NCBI Genome Databases

18. EBI – EMBL - Genomes http://www.ebi.ac.uk/genomes/

19. EBI - Genomes • Viruses: 1466 • Phages:419 • Organelles:1337 • Archea:51 • Bacteria:580 • Eukaryota:74

20. EBI – Genome Browser http://www.ebi.ac.uk/ensembl/index.html Navigation Manual http://www.ebi.ac.uk/ensembl/genome.pdf

21. EBI – Genome Browser

22. Genomes TIGR – JCVIhttp://www.tigr.org/ , http://www.jcvi.org/ • ~16 plants • 3 parasites • other 4 eukaryotes • 5 Fungi • ? • Archea:28 • Bacteria:370 • Viruses:3 • ? http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenomesSortedByTaxonomy.cgi?crumbs=genomes

23. Genome Centres and Databases Lots of sites with specific genome projects  GOOGLE http://www.ncbi.nlm.nih.gov/genomes/static/links.html

24. Bioinformatics Links Directory • DNA  Mapping and Assembly • at least 16 sites • Organism-Specific Genome Databases Genome Databases Lots of sites with specific genome projects  GOOGLE http://bioinformatics.ca/links_directory/?subcategory_id=64 http://restools.sdsc.edu/biotools/biotools10.html

25. FG - Transcriptomics Figure 1

26. NCBI – GEO (http://www.ncbi.nlm.nih.gov/geo) EBI – ArrayExpress (http://www.ebi.ac.uk/Databases/microarray.html) SMD – Stanford (http://genome-www5.stanford.edu/) Celcius M-Chips (http://www.dkfz-heidelberg.de/mchips/) Oncomine (http://www.oncomine.org/) CGDCP(http://ncicb.nci.nih.gov/projects/cgdcp) FG – Transcriptomics Databases

27. ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (microarrays OR microarray) • 512 FG – Transcriptomics Databases

28. ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (microarrays[TI] OR microarray[TI]) • 205 FG – Transcriptomics Databases

29. EBI – Integr8 - Proteomes GAS TOP 10 (Genome Annotated Score) http://www.ebi.ac.uk/integr8/

30. By 2D Gel Electrophoresis By Antibody chips FG - Proteomics

31. FG - Proteomics • Cut out Spots and Identify Proteins by Tandom Mass Spectroscopy • Each peptide could be broken into many possible smaller fragments • Each ion will have its own mass to charge ratio • The real spectrum is compared to all possible spectra for a given species and the peptide sequence is identified

32. FG - Proteomics • Cut out Spots and Identify Proteins by Tandom Mass Spectroscopy • Each peptide could be broken into many possible smaller fragments • Each ion will have its own mass to charge ratio • The real spectrum is compared to all possible spectra for a given species and the peptide sequence is identified

33. ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (Proteomic OR Proteomics) • 468 FG - Proteomics Databases

34. FG - Proteomics Databases

35. ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (Proteomic[TI] OR Proteomics[TI]) • 114 FG - Proteomics Databases

36. FG - Proteomics Databases

37. FG - Proteomics Databases http://bioinformatics.icmb.utexas.edu/OPD/ http://www.proteomicworld.org/DatabasePage.html

38. By Mass Spectrometry FG - Metabolomics

39. By NMR (Nuclear Magnetic Resonace) FG - Metabolomics 900MHz, 21.2 T NMR Magnet at HWB-NMR, Birmingham, UK being loaded with a sample

40. FG - Metabolomics Fhien and Kind, Metabolomics Methods and Protocols (Methods in Molecular Biology vol 358), Wolfram Weckwerth, Humana Press

41. Human Metabolome Database Metabolomics Databases http://www.hmdb.ca/

42. Metabolomics Databases

43. ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (Metabolic OR Metabolomics OR Metabonome OR Metabonomics) • 816 Metabolomics Databases http://www.hmdb.ca/

44. ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (Metabolic[TI] OR Metabolomics[TI] OR Metabonome[TI] OR Metabonomics[TI]) • 75 Metabolomics Databases http://www.hmdb.ca/

45. Other Databases(using MESH [MAJR] and [TI]) • miRNA = 23 • snRNA+snoRNA = 14 • rRNA = 14 • piRNA = 0 (49) • SNP = 66 • mutation(s) = 222 • compound(s) = 70 [TI] not used • sugars = 127 • lipids = 74 • membrane = 180 CLASSROOM ACTIVITY: UPDATE THIS! @ Feb 2008

46. Other Databases(using MESH [MAJR] and [TI]) • miRNA = 46 • snRNA+snoRNA = 16 • rRNA = 40 • piRNA = 1 (49) • SNP = 97 • mutation(s) = 468 • compound(s) = 76..90 [TI] not used • sugars = 239 • lipids = 74? • membrane = 180? CLASSROOM ACTIVITY: UPDATE THIS! @ Feb 2009

47. ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (Metabolic[TI] OR Metabolomics[TI] OR Metabonome[TI] OR Metabonomics[TI]) ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (mirna[TI] OR mirnas[TI] OR microRNA) ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (snRNA[TI] OR snRNA[TI] OR snoRNA[TI] OR small nuclear RNA) ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (rRNA[TI]) ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (SNP[TI] OR SNPs[TI]) ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (piRNA[TI]) ("Software"[MAJR]) AND (piRNA[TI]) ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (mutation[TI] OR mutations[TI]) ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (compound[TI] OR compounds[TI]) ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (sugars) ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (lipids) ("Database "[Publication Type] OR "Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (membrane) Other Databases(using MESH [MAJR] and [TI])

48. NCBI EBI PubMed (queries) Google Wiki Tons of other Databases