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" Omics ", Whole Genomes, Mutations and Other Databases. Bioinformatics Dr. Víctor Treviño [email protected] A7-421 Ext. 4536-103 BT4007 13+/M A4- 4 04. The genome , is the whole hereditary information encoded in the DNA ( RNA for some viruses), genomics - PowerPoint PPT Presentation
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BIOINFORMATICSDR. VÍCTOR TREVIÑ[email protected]. 4536-103BT400713+/MA4-404
"Omics", Whole Genomes, Mutations and Other Databases
[email protected] "OMICS" 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
http://en.wikipedia.org/wiki/-omics
[email protected] "OMICS" 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.http://en.wikipedia.org/wiki/-omics
[email protected] "OMICS" 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.
http://en.wikipedia.org/wiki/-omics
[email protected] "OMICS" 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? http://en.wikipedia.org/wiki/-omics
"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
NCBI GENOME DATABASE 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 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
[email protected] GENOME DATABASES
EBI - GENOMES Viruses: 1466 Phages:419 Organelles:1337
Archea:51 Bacteria:580 Eukaryota:74
[email protected] – GENOME BROWSER
http://www.ebi.ac.uk/ensembl/index.html
http://www.ebi.ac.uk/ensembl/genome.pdf Navigation Manual
EBI – GENOME BROWSER
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
[email protected] CENTRES AND DATABASES
http://www.ncbi.nlm.nih.gov/genomes/static/links.html
Lots of sites with specific genome projects GOOGLE
GENOME DATABASES 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
FG - TRANSCRIPTOMICS
mRNAExtraction
(and amplification)
Labelling
Hybridization
Scanning
StatisticalAnalysis
Image Analysis &Data Processing
PROCESS
Healty/Control Disease/TreatementREFERENCE TEST
Gene: A 1-1 B 1-0 C 3-3 D 0-3Gene: E 3-0 F 0-1 G 1-1 H 2-0Gene: I 2-2 J 0-0 K 3-0 L 2-1
Gene D 0.001Gene E 0.005Gene K 0.001
TWO-DYES
mRNA/cDNA
LabeledmRNA
DigitalImage
Microarray
Data
SelectedGenes
PRODUCTTEST
Gene: A 1 B 1 C 1 D 0Gene: E 4 F 1 G 1 H 2Gene: I 2 J 0 K 5 L 2
Sample
Gene D 0.001Gene E 0.005Gene K 0.001Gene J 0.003
ONE-DYE
FG – TRANSCRIPTOMICS DATABASES
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
("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
("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
EBI – INTEGR8 - PROTEOMES
http://www.ebi.ac.uk/integr8/
GAS TOP 10(Genome Annotated Score)
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
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
[email protected] - PROTEOMICS DATABASES
("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
[email protected] - PROTEOMICS DATABASES
[email protected] - PROTEOMICS DATABASES
("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
[email protected] - PROTEOMICS DATABASES
[email protected] - PROTEOMICS DATABASES
http://www.proteomicworld.org/DatabasePage.html
http://bioinformatics.icmb.utexas.edu/OPD/
FG - METABOLOMICS By NMR (Nuclear Magnetic Resonace)
900MHz, 21.2 T NMR Magnet at HWB-NMR, Birmingham, UK being loaded with a sample
FG - METABOLOMICS
Fhien and Kind, Metabolomics Methods and Protocols (Methods in Molecular Biology vol 358), Wolfram Weckwerth, Humana Press
METABOLOMICS DATABASES Human Metabolome Database
http://www.hmdb.ca/
METABOLOMICS DATABASES ("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/
METABOLOMICS DATABASES ("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/
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
@ Feb 2008
CLASSROOM ACTIVITY: UPDATE THIS!
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?
@ Feb 2009
CLASSROOM ACTIVITY: UPDATE THIS!
OTHER DATABASES(USING MESH [MAJR] AND [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 (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)
