Difference between revisions of "How to deal with multi-named genes"
| Line 27: | Line 27: | ||
| − | ===GeneCard=== | + | ===Using GeneCard to Search for Gene in Humans=== |
This is a little strange because the ''Drosophila'' ''OSCP'' page did not have a also known as section. | This is a little strange because the ''Drosophila'' ''OSCP'' page did not have a also known as section. | ||
You decide to get further confirmation that ''OSCP'' is ''ATP50''. You search "OSCP" on GeneCard, a database for human genes, and get "ATP50" as a hit. That seems promising. | You decide to get further confirmation that ''OSCP'' is ''ATP50''. You search "OSCP" on GeneCard, a database for human genes, and get "ATP50" as a hit. That seems promising. | ||
| Line 33: | Line 33: | ||
| − | ==='''Using Blast to | + | ==='''Using Blast to Compare Genes in All Organisms'''=== |
You decide you want to find the OSCP in other organism, but do not want to go through the hassel of searching all of NCBI for alternative names, like you did for Homo sapiens. You run the gene sequence of OSCP you found in drosophila against, all organisms and get lots of hits. The name of the protein the hit encodes is clearly shown, making it easy to detect whether or not you have discovered OSCP genes. | You decide you want to find the OSCP in other organism, but do not want to go through the hassel of searching all of NCBI for alternative names, like you did for Homo sapiens. You run the gene sequence of OSCP you found in drosophila against, all organisms and get lots of hits. The name of the protein the hit encodes is clearly shown, making it easy to detect whether or not you have discovered OSCP genes. | ||
Revision as of 01:40, 24 February 2011
One always must be leery of the possibility that a gene may have multiple names. When investigating a gene, information can be overlooked by assuming a gene only has one name across species. This tutorial demonstrates how to determine if a gene is referred to by multiple names across species.
Contents
Finding Your Gene of Interest
Say you just are sitting in Biology class and your teacher mentions ATP synthase has a subunit within its complex that is resistant to oligomyocin called Oligomyocin Sensitivity Conferring Protein, gene name OSCP. This sparks your interest, and you want to investigate this gene more. After class you immediately run home, and go to NCBI Gene and search for "OSCP."
Searching Among Species
Perfect! You get a hit for OSCP in Drosophila melanogaster. You review the page and realize you want to research OSCP in other organisms, including humans. You pubmed search "OSCP homo sapiens." You get hits, but none specifically say OSCP. The first hit is for a gene called ATP50.
Is It the Same Gene?
You scroll down to "General Protein Information," as see that gene does encode for oligomyocin sensitivity conferring protein. It must be the OSCP in humans, just referred to by another name.
You also notice that there "Also Known As" section, that indicates the gene goes by the names: ATPO; OSCP; ATP5O.
Using GeneCard to Search for Gene in Humans
This is a little strange because the Drosophila OSCP page did not have a also known as section. You decide to get further confirmation that OSCP is ATP50. You search "OSCP" on GeneCard, a database for human genes, and get "ATP50" as a hit. That seems promising.
Using Blast to Compare Genes in All Organisms
You decide you want to find the OSCP in other organism, but do not want to go through the hassel of searching all of NCBI for alternative names, like you did for Homo sapiens. You run the gene sequence of OSCP you found in drosophila against, all organisms and get lots of hits. The name of the protein the hit encodes is clearly shown, making it easy to detect whether or not you have discovered OSCP genes.
Summary
Gene may have one or more names across species. As in the case with OSCP on the Drosophila page, the alternative name for the gene are not alway listed. Utilize as many database such a NCBI, Pubmed, GeneCard and Blast to discover if there is variance in the names.
