Archived Comments for:
Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information
The problem of post-translational modulation of MYC transcriptional activity was previously studied, using the conditional mutual information, in the same dataset used in this paper. See
Wang K, Banerjee N, Margolin AA, Nemenman I, Califano A, (2006) Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes, in Lecture Notes in Computer Science, Vol. 3909:348-362, Proceedings of the 10th Annual International Conference on Research in Computational Molecular Biology (RECOMB). http://www.springerlink.com/content/j1l2g05341g070w2/fulltext.pdf
genome-wide results from that analysis were used to predict oncogenic lesions and drug mechanism of action in:
Mani K, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, and Califano A, (2008) “A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas,” Molecular Systems Biology 4:169. http://www.nature.com/msb/journal/v4/n1/full/msb20082.html
Finally, a genome-wide analysis of the post-translational regulators of TF activity in mature human B cells was recently published in
Wang K, Alvarez M, Bisikirska BC, Linding R, Basso K, Dalla Favera R, and Califano A (2008) “Dissecting the Interface Between Signaling and Transcriptional Regulation in Human B Cells,” Pac Symp Biocomput. 2009,264:275 http://psb.stanford.edu/psb-online/proceedings/psb09/wang.pdf
previous work
17 March 2009
The problem of post-translational modulation of MYC transcriptional activity was previously studied, using the conditional mutual information, in the same dataset used in this paper. See
Wang K, Banerjee N, Margolin AA, Nemenman I, Califano A, (2006) Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes, in Lecture Notes in Computer Science, Vol. 3909:348-362, Proceedings of the 10th Annual International Conference on Research in Computational Molecular Biology (RECOMB). http://www.springerlink.com/content/j1l2g05341g070w2/fulltext.pdf
genome-wide results from that analysis were used to predict oncogenic lesions and drug mechanism of action in:
Mani K, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, and Califano A, (2008) “A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas,” Molecular Systems Biology 4:169. http://www.nature.com/msb/journal/v4/n1/full/msb20082.html
Finally, a genome-wide analysis of the post-translational regulators of TF activity in mature human B cells was recently published in
Wang K, Alvarez M, Bisikirska BC, Linding R, Basso K, Dalla Favera R, and Califano A (2008) “Dissecting the Interface Between Signaling and Transcriptional Regulation in Human B Cells,” Pac Symp Biocomput. 2009,264:275 http://psb.stanford.edu/psb-online/proceedings/psb09/wang.pdf
Competing interests
None declared