EcoGene is a database that allows people to access the annotation of Escherichia coli K-12 strain MG1655(Seq). EcoGene helps users to better understand and give them a better knowledge of E. coli K-12. This database has been updated 3 times, making the most recent updated version EcoGene 3.0. On EcoGene there are many things available to the user. This includes; BLAST search, EcoArray, EcoTopics, EcoSearch, EcoTools, and the Gene Index.
E.coli K-12 is one of the most common model organisms. This organism shows no harm to humans or the environment, and grows very rapidly on lab media. These characteristics make it very helpful during experiments on the organism or perhaps on other organisms. Knowing the sequence of this model organism as well as information about each gene is a valuable tool in genetic research. It is possible to compare E.coli K-12 to an unknown organism and see the similiarities and differences between difference sequences or functional genes. E.coli K-12 is also used in industry for the production of specialty chemicals or for human drugs, such as insulin.
EcoSeq was the first database to show large sets of the DNA sequence for E.coli K-12. EcoSeq began as a collection of genomic sequence contigs of the organism, then these sequences were aligned and used to complete a genome restriction map for E.coli K-12. EcoGene was first made by accessing EcoSeq and using new methods to correctly re-annotate the gene content found. Then this re-annotating of the genome sequence was done again to make EcoGene into EcoGene 2.0 because there were differences found with the Genbank records and with EcoGenes information.
EcoGene 2.0 was recently updated to EcoGene 3.0. This update added new tools to look at E.coli K-12 as well as give the database a new layout.
When clicking on the BLAST search button on the EcoGene website it will bring you to a page that may look familiar. It doesn't redirect you to the BLAST website, however it uses the BLAST tool to search for certain sequences. It allows you to perform a BLAST search without ever having to leave the EcoGene website. This search will show a large box, where a known sequence can be typed in. Then you can hit search and it will give you every organism that may possibly have that sequence in its genome.
The EcoArray tab allows the user to search for EcoArray experiments. One can do this by typing in the Pubmed ID, the authors' name, and/or the experimental variables. The choice to select for the certain experimental type desired is also available. If someone doesn't know exactly what they're looking for under the search bars it shows a list of every experiment on E. coli K-12. There are almost 1000 experiments to choose from with easy to find titles. When the experiment needed is found on this list, one may click on it and it brings them to a Pubmed article related to that K-12 experiment.
EcoSearch is used to know more about the gene or protein that is of interest. It gives space to type what is known of the gene or protein. For instance; the name, the size, the location, etc. Then the database will give you a list of the results that your gene or protein matches. EcoGene uses a database called Gene Ontology (GO) to access the list of genes. This search is helpful because it simply shows the gene name, synonym, a short description, the centisome, the product seq, the EG ID, the b#, and the link to the references. It is a very simply way to know everything one may need to about the gene. If one needs to know more information about the gene they can click on the name and it will bring them to the GenePage for the E.coli K-12 gene. This page can also be found through the Gene Index tab.
The Gene Index tab shows an alphabetical index of the known genes in Escherichia coli K-12. When placing a cursor over a certain gene a drop-down list of the next 18 genes in alphabetical order appear. Once the certain gene of interest is found in this list it can be clicked and sends you to the GenePage. This GenePage is a very helpful collection of information about the gene. One can find on this page simple information, as in the gene name, the gene symbols, and locations. One can even find the gene and site maps of the gene on this page. It also shows smaller tabs which will send you to the DNA sequence, the Microarray experiment search results for that gene, the protein data, the PDF structure (if available), and possible references.
The EcoTools tab brings you to the newest additions to the EcoGene database. It shows titles of different pages with short summaries as to what the pages offer. This includes; EcoGene Database Table, a GeneSets Venn Diagram and Boolean Query, a Cross Reference Mapping and Download, a PrimerPairs Design, and a Gene Interval Update. The Database Table will bring you to a selectable list of different fields one would wish to download and select for. As soon as something is clicked a table below will show you the data you're looking for. Then you can hit download to save the information to your personal computer. GeneSets Venn Diagram and Boolean Query allows you to Upload GeneSets from EcoTopic, EcoArray or from a different file. After the GeneSet is uploaded, you must select the certain GeneSet then execute the boolean query on this GeneSet. When all of this is finished, clicking the Venn Diagram button will allow you to see the genes that are shared between the GeneSets and which are not. The Cross Reference Mapping and Download allows you to search different genes using different identifiers and then download and save the results. The PrimerPairs Design allows you to choose the type of DNA you're interested in, if you want to look at cloning or deletion, and then the exact fields you want to download. The Gene Interval Update will tell you if theres an update within the Original Interval System and the Target Interval System.
EcoGene Topics allows one to search for certain text or through Topic IDs. If you don't want to go through a search bar a list of Topics with their Topic ID is listed underneath. The list of topics includes the name, the topic ID, the gene set, the super topics, the sub topics, and the type of topic. Once a topic is selected it brings you to a page with the topic info, the reference, as well as a review.
- "Escherichia Coli K-12 Derivatives Final Risk Assessment." EPA. Environmental Protection Agency, Feb. 1997. Web. 9 Sept. 2013. <http://www.epa.gov/biotech_rule/pubs/fra/fra004.htm>.
- "Welcome to EcoGene 3.0." Welcome to EcoGene 3.0. University of Miami, 2011. Web. <http://www.ecogene.org/>.
- Zhou, Jindan, and Kenneth E. Rudd. "Abstract." National Center for Biotechnology Information. U.S. National Library of Medicine, 28 Nov. 2012. Web. 9 Sept. 2013. <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531124/>.