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This web page is Online Supplementary Information for
Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Model on Massively Parallel Computers
Yoshinori Tamada, Seiya Imoto, Hiromitsu Araki, Masao Nagasaki, Cristin Print, D. Stephen Charnock-Jones, and Satoru Miyano
published in IEEE/ACM Transactions on Computational Biology and Bioinformatics.
Contact: Yoshinori Tamada <tamadasatpimsadotsu-tokyoadotmacsdotsjp>a(replace "at" with "@", "dot" with ".")
Go to the web page for this paper on Journal's web site. (Abstract & PDF available)
Last Update: September 29 2010.
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Random DAG with 10,000 nodes Network Structure: RDAG-10k.txt (Tab separated parent and child list)
Random DAG with 10,000 nodes Simulated Numerical Data: RDAG-10k-500.txt (Tab separated matrix file. Each column corresponds to a sample)
Sparse Random DAG with 10,000 nodes Network Structure: RDAG-10kSP.txt (Tab separated parent and child list)
Sparse Random DAG with 10,000 nodes Simulated Numerical Data: RDAG-10kSP-500.txt (Tab separated matrix file)
ALARM DAG with 10,027 nodes Network Structure: ALARM-10k.txt (Tab separated parent and child list)
ALARM DAG with 10,027 nodes Simulated Numerical Data: ALARM-10k-500.txt (Tab separated matrix file)
Gene Network with 10,540 nodes Network Structure: GN-10k.txt (Tab separated parent and child list)
Gene Network with 10,540 nodes Simulated Numerical Data: GN-10k-500.txt (Tab separated matrix file)
Gene Network with 21,080 nodes Network Structure: GN-20k.txt (Tab separated parent and child list)
Gene Network with 21,080 nodes Simulated Numerical Data: GN-20k-500.txt (Tab separated matrix file)
Estimated HUVEC Genome-Wide Gene Network with 13,731 nodes: HUVEC-GWGN.csml.gz (Gzipped CSML file that can be opened in Cell Illustrator Online 5.0 (CIO 5.0). HUVEC-GWGN.CIO4.csml.gz (Gzipped CSML file that can be opened in Cell Illustrator Online 4.0 (CIO 4.0). Note that this requires a huge amount of memory to open in CIO), HUVEC-GWGN.txt (Tab separated parent and child list)
HUVEC Genome-Wide Gene Network Hub Gene List: HUVEC-GWGN-hubs.txt (Tab separated hub node list)
Estimated HUVEC Gene Network with 527 genes: HUVEC-527GN.csml (for CIO 5), HUVEC-527GN.CIO4.csml (for CIO 4), HUVEC-527GN.txtThe original gene lists of the 527 genes extracted separately for all the time points are available at PSB 2009 Supplementary Information Site.
Fig. S1. A very high resolution figure (24,942 x 15,436 pixels) of the HUVEC Genome-Wide Gene Network by the BFL layout algorithm in T.B. Hashimoto, M. Nagasaki, K. Kojima, S. Miyano, BFL: a node and edge betweenness based fast layout algorithm for large scale networks. BMC Bioinformatics 10:19, 2009: FigS1-HUVEC-GWGN.jpg (If an error occurs, please download the file in your PC first. At least Firefox for Mac OS X could not open this because it is too large.)
Fig. S2. Distribution of overlapped edges within distance 6 between the 527 network and the randomly substituted genome-wide network: FigS2.pdf