Overview[]
Figure 1. Breakdown of genes contained in Gene as of 9/7/2013 source
Gene (Often referred to as Entrez Gene) is a database included in the NCBI that catalogs all sequenced genes, and information about them including organism, location, size, phenotypic manifestation, modifications, and interactions. This is achieved through the use of specific "GeneID" numbers for every gene which are then used to track and organize genes based on the information cataloged by the database. Much of the information in Gene is compiled from collaborative projects such as RefSeq and GenBank.[1]
According to the current Gene statistics page (9/7/2014), Gene Contains a total of 13131 total taxa and 16348184 total genes broken down in Figure 1.
How to Use Gene[]
As with any database, the first step is to find a subject to search. For example, the gene that encodes the mammalian redox protein Thioredoxin. Depending on whether or not the gene name is known, the search can be conducted using either that or the name of the protein of interest. To find the specific gene in the organism of interest, in this case Homo sapiens, the results the search can be filtered using the top organisms sidebar to the right. The results will show a short summary of the gene including the name, GeneID, a description with the organism, location, and MIM number. Clicking on the gene will open the database page, in this case the page is for the gene TXN. Contained in this page is all of the currently available information about the gene. This includes chromosome, position, size, coding regions, transcript info, product info, phenotypes, variants, pathways, and interactions with links to other databases that go into these properties in more detail. These other databases contain nucleotide sequences, phenotypes, SNP variants, protein interactions, different isoforms, related sequences, and other relevant information for a genetic researcher. The process with some examples of other database links can be found in the following video.
Gene in Cancer Research[]
A map by Bonacci et al. from their paper detailing the modifications discovered in response to chemotheraputics [2]
Gene, along with other databases linked to it through the NCBI, has recently been used in a study conducted by Bonacci and co-workers (2014) who attempted to catalogue the post-translational modifications to ubiquitin-like proteins in an attempt to gain a better understanding of the cellular response to chemotherapy treatments for pancreatic ductal adenocarcinoma. In the study, human cancer cells were treated with the chemotherapy drug Gemcitabine,lysed, and proteins purified from the lysates were analyzed via mass spectrometry for post-translational modifications by ubiquitin-like proteins Ubiquitin, Nedd8 and Sumo1. Following the mass spec analysis, an extensive bioinformatic study was undergone to compare these modifications to those in cells untreated with Gemcitabine. The group was able to verify many of the suspected modifications by ubiquitin-like proteins in response to Gemcitabine, as well as identify a new target for chemotherapy agents in the Sumolation of transcriptional co-activator protein SNIP1 via SUMO1 protein which is involved in cell proliferation, oncogenic processes, and resistance mechanisms.[2]
Sources[]
- ↑ D. Maglott, J. Ostell, K.D. Pruitt, and T. Tatusova. (January 2011). Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res; 39(Database issue): D52–D57 Pubmed
- ↑ 2.0 2.1 T. Bonacci, S. Audebert, L. Camoin, E. Baudelet, G. Bidaut, M. Garcia, II. Witzel, N. Perkins, JP. Borg, JL. Iovanna, P. Soubeyran. (May 2014) Identification of new mechanisms of cellular response to chemotherapy by tracking changes in post-translational modifications by ubiquitin and ubiquitin-like proteins. J Proteome Res. 2;13(5):2478-94 Pubmed