1. "Omics", Whole Genomes, Mutations and Other Databases

2. vtrevino@itesm.mx  The genome, is the whole hereditary information encoded in the DNA (RNA for some viruses), genomicsDNARNA  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. proteins  The transcriptome, the mRNA complement of an entire organism, tissue type, or cell; with its associated field transcriptomicstranscriptomemRNAtranscriptomics  The metabolome, the totality of metabolites in an organism; with its associated field metabolomicsmetabolomemetabolitesmetabolomics http://en.wikipedia.org/wiki/-omics

3. vtrevino@itesm.mx  The metallome, the totality of metal and metalloid species; with its associated field metallomicsmetallomemetalmetalloidmetallomics  The lipidome, the totality of lipids; with its associated field Lipidomicslipidomelipids 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.glycomeglycans Glycomics 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 biologyinteractomesystems biology  The spliceome (see spliceosome), the totality of the alternative splicing protein isoforms; with its associated field spliceomics.spliceomespliceosome alternative splicingisoforms  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.ORFeomecodon  Reactome: A knowledge base of biological processes. Reactomeknowledge base http://en.wikipedia.org/wiki/-omics

4. vtrevino@itesm.mx  The speechome. (BBC article on the Speechome Project)speechomeBBC article on the Speechome Project  The mechanome refers to the force and mechanical systems at work within an organism.mechanome  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.Phenome  The Exposome - the collection of an individual's environmental exposures.Exposome http://en.wikipedia.org/wiki/-omics

5. vtrevino@itesm.mx  Textome: The body of scientific literature which text mining can analyse. Textomics: The study of the textome.text miningtextome  Kinome: The totality of protein kinases in a cell. Kinomics: The study of the kinome. Kinomeprotein kinases  Physiome: Related to physiology. Physiomics: The associated field of study. Physiomephysiology  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.neurobiologist  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? http://en.wikipedia.org/wiki/-omics

6. vtrevino@itesm.mx  Pharmacogenomics  Physiomics http://en.wikipedia.org/wiki/-omics

7. vtrevino@itesm.mx 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. vtrevino@itesm.mx

9.  NCBI  EBI  TIGR (Venter)

10. vtrevino@itesm.mx  http://www.ncbi.nlm.nih.gov/sites/entrez?db=genom e http://www.ncbi.nlm.nih.gov/sites/entrez?db=genom e  genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps  Organized in Archaea, Bacteria, Eukaryotae, Viruses, Viroids, and PlasmidsArchaeaBacteriaEukaryotaeViruses ViroidsPlasmids  Includes complete chromosomes, organelles and plasmids as well as draft genome assemblies

11. vtrevino@itesm.mx  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. vtrevino@itesm.mx

13. ~4Mb

14. vtrevino@itesm.mx

16. slit2 Gene Searches

17. vtrevino@itesm.mx

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

19. vtrevino@itesm.mx  Viruses: 1466  Phages:419  Organelles:1337  Archea:51  Bacteria:580  Eukaryota:74

20. vtrevino@itesm.mx http://www.ebi.ac.uk/ensembl/index.html http://www.ebi.ac.uk/ensembl/genome.pdf Navigation Manual

22. vtrevino@itesm.mx  ~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. vtrevino@itesm.mx http://www.ncbi.nlm.nih.gov/genomes/static/links.html Lots of sites with specific genome projects  GOOGLE

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

25. vtrevino@itesm.mx Figure 1

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

27. vtrevino@itesm.mx  ("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

28. vtrevino@itesm.mx  ("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

29. vtrevino@itesm.mx http://www.ebi.ac.uk/integr8/ GAS TOP 10 (Genome Annotated Score)

30. vtrevino@itesm.mx  By 2D Gel Electrophoresis  By Antibody chips

31. vtrevino@itesm.mx  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. vtrevino@itesm.mx  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. vtrevino@itesm.mx  ("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

34. vtrevino@itesm.mx

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

36. vtrevino@itesm.mx

37. http://www.proteomicworld.org/DatabasePage.html http://bioinformatics.icmb.utexas.edu/OPD/

38. vtrevino@itesm.mx  By Mass Spectrometry

39. vtrevino@itesm.mx  By NMR (Nuclear Magnetic Resonace) 900MHz, 21.2 T NMR Magnet at HWB-NMR, Birmingham, UK being loaded with a sampleT

40. vtrevino@itesm.mx Fhien and Kind, Metabolomics Methods and Protocols (Methods in Molecular Biology vol 358), Wolfram Weckwerth, Humana Press

41. vtrevino@itesm.mx  Human Metabolome Database http://www.hmdb.ca/

42. vtrevino@itesm.mx

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 http://www.hmdb.ca/

44. vtrevino@itesm.mx  ("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 http://www.hmdb.ca/

45. vtrevino@itesm.mx  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 @ Feb 2008 CLASSROOM ACTIVITY: UPDATE THIS!

46. vtrevino@itesm.mx  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? @ Feb 2009 CLASSROOM ACTIVITY: UPDATE THIS!

47. vtrevino@itesm.mx  ("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)

48. vtrevino@itesm.mx  NCBI  EBI  PubMed (queries)  Google  Wiki