Retrieval of gene information at NCBI

Transcription

1 Retrieval of gene information at NCBI

2 Some notes Slides are for presenting the main paper, should minimize the copy and paste from the paper, should write in your own language, give necessary reference, should be logic and slides are connected. Besides the main ideas in the paper, you can have yours from elsewhere. It is not expected for you to understand every detail or present everything in the paper. 3. Keep practicing programming.

3 What is a gene? From wiki 1. A gene is the molecular unit of heredity of a living organism. It is used extensively by the scientific community as a name given to some stretches of deoxyribonucleic acids (DNA) and ribonucleic acids (RNA) that code for a polypeptide or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains. Genes hold the information to build and maintain an organism's cells and pass genetic traits to offspring Bioinformatics is indispensible for biological research. 2. A modern working definition of a gene is "a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence regions.

4 Given a gene name, if you want to know what is known about this gene, you can find answers at NCBI By choosing gene in the search menu and inputting the gene name.

5 An example: STAT1 Gene ID Gene ID, also called Entrez ID or locus link previously, corresponds to the systematic feature qualifier used by the international sequence collaboration (DDBJ/EMBL/GenBank), and can be assigned by sequence submitters as a unique, systematic gene descriptor. When such a value is not available from submitted sequence, the identifier from a collaborating model organism database is used. Gene ID is often used to anchor a link to a database other than Entrez Gene.

6 An example: STAT1 HGNC HUGO Gene nomenclature Committee. For each known human gene the committee approves a gene name and symbol (shortform abbreviation). All approved symbols are stored in the HGNC database. Each symbol is unique and each gene is only given one approved gene symbol.

7 An example: STAT1 HPRD You can download all entries contained in HPRD including features of proteins such as post translational modifications, tissue expression, subcellular localization and protein protein interactions in tab delimited file format as per the users request. PhosphoMotif Finder contains known kinase/phosphatase substrate as well as binding motifs that are curated from the published literature. It reports the PRESENCE of any literaturederived motif in the query sequence.

8 An example: STAT1 OMIM Online Mendelian Inheritance in Man. OMIM is a comprehensive and authoritative compendium of human genes and genetic phenotypes. The full text, referenced overviews in OMIM contain information on all known mendelian disorders and over 14,000 genes. OMIM focuses on the relationship between phenotype and genotype. It is updated daily, and the entries contain copious links to other genetics resources

9 An example: STAT1

10 cellular component, biological process and molecular function. A gene product might be associated with or located in one or more cellular components; it is active in one or more biological processes, during which it performs one or more molecular functions. For example, the gene product cytochrome c can be described by the molecular function term oxidoreductase activity, the biological process terms oxidative phosphorylation and induction of cell death, and the cellular component terms mitochondrial matrix and mitochondrial inner membrane.

11 Cellular component A cellular component is just that, a component of a cell, but with the proviso that it is part of some larger object; this may be an anatomical structure (e.g. rough endoplasmic reticulum or nucleus) or a gene product group (e.g. ribosome, proteasome or a protein dimer). See the documentation on the cellular component ontology for more details.

12 Biological process A biological process is series of events accomplished by one or more ordered assemblies of molecular functions. Examples of broad biological process terms are cellular physiological process or signal transduction. Examples of more specific terms are pyrimidine metabolism or alpha glucoside transport. It can be difficult to distinguish between a biological process and a molecular function, but the general rule is that a process must have more than one distinct steps. A biological process is not equivalent to a pathway; at present, GO does not try to represent the dynamics or dependencies that would be required to fully describe a pathway. Further information can be found in the process ontology documentation.

13 Molecular function Molecular function describes activities, such as catalytic or binding activities, that occur at the molecular level. GO molecular function terms represent activities rather than the entities (molecules or complexes) that perform the actions, and do not specify where or when, or in what context, the action takes place. Molecular functions generally correspond to activities that can be performed by individual gene products, but some activities are performed by assembled complexes of gene products. Examples of broad functional terms are catalytic activity, transporter activity, or binding; examples of narrower functional terms are adenylate cyclase activity or Toll receptor binding.

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16 Another example: OCT4 What is your example?

17 Summary Entrez gene IDs and HGNC IDs are standard. HPRD provide good PPI and PTM. Function terms and gene annotation by GO. OMIM provides Phenotype information.