Using Genomic Tools
When researching a gene of interest, researchers often employ genomic tools - such as databases, alignments, previous literature, sequence analysis and many more. These tools can help the researcher develop a background knowledge which can be used to form creative hypotheses and further research. Listed below are some of the behind-the-scenes genomic tools used in the creation of this website.
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Lab for Course
Genomic Sequence and Entrez Homology and Phylogeny Motif and Domain Discovery Gene Ontology RNAi databases Chemical Genetics Microarrays Proteomics Protein Interaction Networks |
Genomic Tools
Familiarize yourself with genomic databases and gather background information on a gene of interest. Use homology programs, like Homologene and BLAST, to identify homologue candidates in other organisms. One can also use an alignment programs like ClustalOmega and T-coffee and compare trees calculated using different statistical methods. Identify domain structures in a known sequence by submitting them to sequence analysis, like Prosite or SMART. BLAST also identifies known protein motifs. Gene ontology can identify biological processes, molecular functions and cellular localizations associated with a gene of interest. RNAi, knock-out and other interference tools are specific to each model organism. These can provide a model system to observe your gene in low functionality or null. Small chemicals can be a useful method of inhibiting your target gene or protein by binding. Microarrays can measure gene expression on the genomic level or to genotype for a mutation. These could show widespread changes associated with lifestyle change, drug treatment, or increased symptoms. Proteomics is an umbrella category for many identifiers and resources. Some examples include post-translational modifications, and identifying sites that can be phosphorylated or ubiquitinated. Protein interaction networks can provide a global picture of how your protein interacts in the cell, what functions it may contribute to, and where it may localize. |
MEFV Discoveries
FASTA sequences for MEFV Homologues can be viewed for both MEFV gene and pyrin protein. Phylogenetic trees can be viewed for both MEFV gene and pyrin protein. Domain structures can be viewed for both MEFV gene and pyrin protein. See the gene ontology for MEFV. Mouse models inducing both loss of function and gain of function mutations in MEFV gene have been used in the literature. A common drug used in Familial Mediterranean Fever is colchicine. This inhibitor prevents colocalization of pyrin with actin. No microarray data was found for MEFV. No proteomic tools were used to analyze pyrin. Pyrin interaction networks can be viewed here. |
This website was created for the Genetics 677 course at UW Madison.