Gene Cloud (genecloud.org
) is a novel tool presenting gene-gene associations based on the scientific literature. It was developed by the Knockout Mouse Repository (www.komp.org
) to help our customers find products related to other products they chose.
We have built a detailed graph model of gene-gene associations based on how many times two genes are cited in the same article. If two genes are cited in many papers together, they are considered strongly connected.
Each instance of Gene Cloud is centered around a specific gene. A list of the top most related genes is plotted as a branching structure from the center.
A secondary branch can occur if a gene in the graph is more related a non-central gene than it is to the center gene.
The font size of a branched gene indicates the relative strength of connection--always to the center gene. The distribution of genes in space is randomized each time Gene Cloud is run so a different picture will result for the same central gene.
Color is used to indicate the availability of Knockout Mouse products at the KOMP Repository. If a gene is colored green in the graph there are products (mutant ES cells, sperm, embryos, or mice) ready to be ordered. Blue colored genes do not yet have products available, but you can follow the links back to the KOMP Repository and register interest to be alerted when products do become available.
At this time the length of an edge connecting two genes does not contain any information, but we are interested in pursuing this avenue in the future.
A user can re-center Gene Cloud by clicking on any gene symbol or by starting a new cloud using the Search form at the top of the page.
You can share Gene Cloud graphs with others by simply sending the complete link (e.g., http://genecloud.org/#87909
Gene Cloud is driven by a database of gene-gene associations that currently contains 82,000 genes and other biotypes, 113,000 annotated publications, and 467 million connections. The latest gene symbols, names and gene-publication annotation information is updated daily from the Mouse Genome Informatics
database. The graphing is accomplished through the use of a modified version of jsViz
We would love to hear your questions, comments, and feedback! Let us know at email@example.com