Supplementary Information for Tamada et al. (2005)

This web page is supplementary information of the paper submitted for publication.

Paper Title:

Utilizing evolutionary information and gene expression data for estimating gene networks with Bayesian network models

Yoshinori Tamada ^a, Hideo Bannai ^b, Seiya Imoto ^b, Toshiaki Katayama ^b, Minoru Kanehisa ^a and Miyano Satoru ^b
a Bioinformatics Center, Institute for Chemical Research, Kyoto University
^b Human Genome Center, Institute of Medical Science, The University of Tokyo

Contact: Yoshinori Tamada <tamadasatpimsadotsu-tokyoadotmacsdotsjp>a(replace "at" with "@", "dot" with ".")

List of genes in Experiment I

• S. cerevisiae (plain text, 91 bytes)
• H. sapiens (plain text, 108 bytes)
• List of orthologous gene pairs (TAB-separated text file, 286 bytes. The first column is S. cerevisiae's genes. The following columns are genes of H. sapiens that are orthologous to the genes at the first column)

Estimated networks in Experiment I

• S. cerevisiae (TAB-separated text file, 694 bytes. The first column is the genes in the dataset. The following columns are child genes of the genes at the first column.)
• H. sapiens (TAB-separated text file, 555 bytes. The format is the same as the above file.)
• S. cerevisiae: newly estimated edges by the proposed method. (plain text, 797 bytes)
• H. sapiens: newly estimated edges by the proposed method. (plain text, 757 bytes)

List of genes in Experiment II

• S. cerevisiae (plain text, 273 bytes)
• H. sapiens (plain text, 368 bytes)
• List of orthologous gene pairs (TAB-separated text file, 1,289 bytes)

Estimated networks in Experiment II

• S. cerevisiae (TAB-separated text file, 1,968 bytes)
• H. sapiens (TAB-separated text file, 1,629 bytes)
• S. cerevisiae: newly estimated edges by the proposed method. (plain text, 1,900 bytes)
• H. sapiens: newly estimated edges by the proposed method. (plain text, 1,601 bytes)

Additional Information

• S. cerevisiae GO annotations assigned to the estimated edges in Experiment II. (TAB-separated text file, 11,170 bytes)
• H. sapiens GO annotations assigned to the estimated edges in Experiment II. (TAB-separated text file, 7,845 bytes)

Meaning of GO annotations (e.g. GO:0005634) can be found at the Gene Ontology Consortium (http://www.geneontology.org/).

GO annotations of S. cerevisiae for our calculation were taken from SGD web site (http://www.yeastgenome.org/) on July 25 2004. GO annotations of H. sapiens were collected manually from the web site of the GO Consortium (http://www.geneontology.org/) on July 25 2004.

Copyright © 2004 - 2005 Yoshinori Tamada, Human Genome Center, Institute of Medical Science, The University of Tokyo & Bioinformatics Center, Institute for Chemical Research, Kyoto University.