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

BIOINFORMATICSDR. VÍCTOR TREVIÑOVTREVINO@ITESM.MXA7-421EXT. 4536-103BT400713+/MA4-404

"Omics", Whole Genomes, Mutations and Other Databases

vtrevino@itesm.mxCOMMON "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

vtrevino@itesm.mxNEW "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

vtrevino@itesm.mxMISCELLANEOUS "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

vtrevino@itesm.mxSPECULATIVE "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

vtrevino@itesm.mxOTHER "OMICS" Pharmacogenomics Physiomics

http://en.wikipedia.org/wiki/-omics

vtrevino@itesm.mx

"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

vtrevino@itesm.mx

"OMICS" JOURNALS

vtrevino@itesm.mx

GENOMIC DATABASES NCBI EBI TIGR (Venter)

vtrevino@itesm.mx

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

vtrevino@itesm.mx

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

vtrevino@itesm.mx

NCBI GENOME DATABASES

vtrevino@itesm.mx

NCBI GENOME DATABASES

~4Mb

vtrevino@itesm.mx

NCBI GENOME DATABASES

vtrevino@itesm.mx

NCBI GENOME DATABASES

vtrevino@itesm.mxNCBI GENOME DATABASES

slit2

Gene Searches

vtrevino@itesm.mxNCBI GENOME DATABASES

vtrevino@itesm.mx

EBI – EMBL - GENOMES

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

vtrevino@itesm.mx

EBI - GENOMES Viruses: 1466 Phages:419 Organelles:1337

Archea:51 Bacteria:580 Eukaryota:74

vtrevino@itesm.mxEBI – GENOME BROWSER

http://www.ebi.ac.uk/ensembl/index.html

http://www.ebi.ac.uk/ensembl/genome.pdf Navigation Manual

EBI – GENOME BROWSER

vtrevino@itesm.mx

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

vtrevino@itesm.mxGENOME CENTRES AND DATABASES

http://www.ncbi.nlm.nih.gov/genomes/static/links.html

Lots of sites with specific genome projects GOOGLE

vtrevino@itesm.mx

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

vtrevino@itesm.mx

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

vtrevino@itesm.mx

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)

vtrevino@itesm.mx

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

vtrevino@itesm.mx

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

vtrevino@itesm.mx

EBI – INTEGR8 - PROTEOMES

http://www.ebi.ac.uk/integr8/

GAS TOP 10(Genome Annotated Score)

vtrevino@itesm.mx

FG - PROTEOMICS By 2D Gel Electrophoresis By Antibody chips

vtrevino@itesm.mx

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

vtrevino@itesm.mx

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

vtrevino@itesm.mxFG - 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

vtrevino@itesm.mxFG - PROTEOMICS DATABASES

vtrevino@itesm.mxFG - 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

vtrevino@itesm.mxFG - PROTEOMICS DATABASES

vtrevino@itesm.mxFG - PROTEOMICS DATABASES

http://www.proteomicworld.org/DatabasePage.html

http://bioinformatics.icmb.utexas.edu/OPD/

vtrevino@itesm.mx

FG - METABOLOMICS By Mass Spectrometry

vtrevino@itesm.mx

FG - METABOLOMICS By NMR (Nuclear Magnetic Resonace)

900MHz, 21.2 T NMR Magnet at HWB-NMR, Birmingham, UK being loaded with a sample

vtrevino@itesm.mx

FG - METABOLOMICS

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

vtrevino@itesm.mx

METABOLOMICS DATABASES Human Metabolome Database

http://www.hmdb.ca/

vtrevino@itesm.mx

METABOLOMICS DATABASES

vtrevino@itesm.mx

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/

vtrevino@itesm.mx

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/

vtrevino@itesm.mx

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!

vtrevino@itesm.mx

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!

vtrevino@itesm.mx

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)

vtrevino@itesm.mx

TONS OF OTHER DATABASES NCBI EBI PubMed (queries) Google Wiki