Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Export

@article{Butt00, abstract = {In an effort to find gene regulatory networks and clusters of genes that affect cancer susceptibility to anticancer agents, we joined a database with baseline expression levels of 7,245 genes measured by using microarrays in 60 cancer cell lines, to a database with the amounts of 5,084 anticancer agents needed to inhibit growth of those same cell lines. Comprehensive pair-wise correlations were calculated between gene expression and measures of agent susceptibility. Associations weaker than a threshold strength were removed, leaving networks of highly correlated genes and agents called relevance networks. Hypotheses for potential single-gene determinants of anticancer agent susceptibility were constructed. The effect of random chance in the large number of calculations performed was empirically determined by repeated random permutation testing; only associations stronger than those seen in multiply permuted data were used in clustering. We discuss the advantages of this methodology over alternative approaches, such as phylogenetic-type tree clustering and self-organizing maps.}, address = {Children's Hospital Informatics Program and Division of Endocrinology, Department of Medicine, Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA. atul\_butte@harvard.edu}, author = {Butte, A. J. and Tamayo, P. and Slonim, D. and Golub, T. R. and Kohane, I. S.}, citeulike-article-id = {577105}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.220392197}, citeulike-linkout-1 = {http://www.pnas.org/content/97/22/12182.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/97/22/12182.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/11027309}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=11027309}, day = {24}, doi = {10.1073/pnas.220392197}, issn = {0027-8424}, journal = {Proc Natl Acad Sci U S A}, keywords = {cancer, networks, senior-project}, month = {October}, number = {22}, pages = {12182--12186}, posted-at = {2008-11-12 20:38:31}, priority = {2}, title = {Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks.}, url = {http://dx.doi.org/10.1073/pnas.220392197}, volume = {97}, year = {2000} }

TY - JOUR ID - Butt00 L3 - citeulike-article-id:577105 N2 - In an effort to find gene regulatory networks and clusters of genes that affect cancer susceptibility to anticancer agents, we joined a database with baseline expression levels of 7,245 genes measured by using microarrays in 60 cancer cell lines, to a database with the amounts of 5,084 anticancer agents needed to inhibit growth of those same cell lines. Comprehensive pair-wise correlations were calculated between gene expression and measures of agent susceptibility. Associations weaker than a threshold strength were removed, leaving networks of highly correlated genes and agents called relevance networks. Hypotheses for potential single-gene determinants of anticancer agent susceptibility were constructed. The effect of random chance in the large number of calculations performed was empirically determined by repeated random permutation testing; only associations stronger than those seen in multiply permuted data were used in clustering. We discuss the advantages of this methodology over alternative approaches, such as phylogenetic-type tree clustering and self-organizing maps. IS - 22 JF - Proc Natl Acad Sci U S A SN - 0027-8424 AD - Children's Hospital Informatics Program and Division of Endocrinology, Department of Medicine, Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA. atul_butte@harvard.edu EP - 12186 TI - Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. VL - 97 SP - 12182 KW - cancer KW - networks KW - senior-project AU - Butte, AJ AU - Tamayo, P AU - Slonim, D AU - Golub, TR AU - Kohane, IS PY - 2000/10/24/ UR - http://dx.doi.org/10.1073/pnas.220392197 ER -