Though we cannot provide universal MR threshold, most success cases used strong coexpression having MR<20.
https://www.ncbi.nlm.nih.gov/pubmed/20383554
The actual procedure of NetworkDrawer is as follows:
- (1) Searching additional genes.
- (1-1) Checking coexpressed (Top 3 MR) genes from query genes.
- (1-2) Checking PPI genes from query genes. [option]
- (1-3) Summarizing genes with at least two edges to the query genes.
- (2) Making gene network of the genes to draw.
We used "neato" function from Graphviz as follows:
- (1) Prepare a dot file with following parameters.
- overlap=orthoxy;
- model=shortpath;
- start="[regular][1]";
- splines=true;
- fontname=Helvetica;
- node [height=.45, width=.4, fontname=Helvetica];
- (2) Create a postscript file of gene network.
- (3) Parse the postscript file for 2 purposes: (a) to decorate the network easy to see, and (b) to annotate it with KEGG annotation.
- (For small network A)
- (A-4) Convert the postscript fil to PNG file.
- (A-5) Make clickable map on html.
- (For google map network B)
- (B-4) Convert the postscript fil to PNG files with various sizes.
- (B-5) Split each of the PNG files into small rectangle PNG files with 256 x 256 picels.
- (B-6) Use Google Maps API.
Sorry. We do not prepare such function.
Yes. Many coexpression databases are available.
- Gene-to-gene correlation
- ACT: Arabidopsis
- Bio Array Resource: Arabidopsis, poplar
- Cop: Arabidopsis, soybean, poplar
- CORNET: Arabidopsis
- COXPRESdb: human, mouse, rat, chicken, zebra fish, fly, nematoda
- CressExpress: Arabidopsis
- CSB.DB: Arabidopsis, E. coli, S. cerevisiae
- GeneCAT: Arabidopsis, poplar, barley, rice
- Oryza_Express: rice
- STARNET 2: human, mouse, rat, chicken, zebra fish, fly, nematoda, S. cerevisiae, Arabidopsis, rice
- RiceArrayNet: rice
- Rice Array Database: rice
- Sample-to-sample correlation
