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NSC numbers 638850, 607097, 630176, 650426, and 649890, respectively. These compounds were selected for development in part because their patterns of activity in the screen were unlike those of any agent already in the clinic.
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1842347747
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Database resources currently available on the World Wide Web include the following. (i) http:// epnws1.ncifcrf.gov:2345/dis3d/cancer_screen/ stdmech.html: mechanism of action assignments and chemical structures for a set of 122 standard agents based on (6) and (8). Clicking on a mechanism of action displays a list of the relevant compounds. (ii) ftp://helix.nih.gov/ncidata/canscr/std-agnt.tar.Z: activity patterns for standard agents based on (6) and (8). (iii) http://epnws1.ncifcrf.gov: 2345/dis3d/itb/stdagnt.html: searching by chemical name or NSC number in a set of 175 standard agents. (iv) http://epnws1.ncifcrf.gov:2345/dis3d/ cancer_screen/nsc4.html: retrieval by NSC number of "mean graph" representations (2) of activity patterns and COMPARE lists for approximately 20,000 nonconfidential compounds. (v) http:// epnws1.ncifcrf.gov:2345/dis3d/cancer_screen/ cmpmatrix.html: generation of an A·A′ matrix (non-clustered) for any choice of nonconfidential compounds. (vi) http://epnws1.ncifcrf.gov:2345/dis3d/ itb/pubtarget.html: published molecular target measurements, along with the ability to use the measurements as seeds in COMPARE searches of the activity databases for synthetic compounds and for natural product extracts.
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CiP1/Waf1, Mdm2, H-Ras, K-Ras, N-Ras, Raf, Src, Nm23, Pgp/Mdr-1, Mdr-2, Rb, Mrp, Lrp, telomerase, telomere length, alkylguanine transferase, metallothionein, phosphoinositol 3-kinase, thioredoxin, aldehyde dehydrogenase, epidermal growth factor receptor, transforming growth factor-α, c-ErbB2, fibroblast growth factor receptor, vascular endothelial growth factor receptor, human growth factor receptor, transforming growth factor-β receptor type II, Bcl-2, Bax, Bcl-X, DNA methylation, DT diaphorase, p450 reductase, b5 reductase, thymidylate synthetase, mismatch repair defects, topoisomerase II, galectin, p15, p16, and glutathione transferase isoenzymes.
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All cluster analyses were performed by the average linkage method with Pearson correlation coefficient as metric. Other methods (single linkage, complete linkage, centroid-based algorithms) and metrics (Euclidean) also yield coherent patterns but emphasize different features. DISCOVERY uses SAS (Statistics Analysis Systems Institute, Carry, NC) or S-Plus (MathSoft, Seattle, WA) scripting and routines for some of these calculations. Neither the 60 cell lines nor the compounds tested represent random samples from defined underlying populations; hence, all of the statistical parameters used in this article should be considered as heuristic indices.
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This set appears to be mechanistically different from the well-known anticancer α-formylpyridine thiosemicarbazones, 3-HP and 5-HP (3-and 5-hydroxypyridine-2-carboxaldehyde thiosemicarbazone), which are ribonucleotide reductase inhibitors. The latter two compounds and four of their analogs appear side by side in a separate group (compounds 3037 to 3042). Two structural features distinguish the group of 72 from the HP family: Most are synthetically derived from α-acetyl (rather than α-formyl) heterocyclics and generally have a large, lipophilic moiety at the end distal to the imine linkage.
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Autocorrelation analysis was performed on a set of 43 consecutive screenings of doxorubicin (which is used as a routine control in each experiment) performed over a period of 8 months. The Pearson correlation coefficient for any pair of tests was essentially independent of time elapsed between the tests (36).
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The linear methods described here cannot capture nonlinear, interactive aspects of the biological phenomena. However, the matrix multiplication used to obtain Fig. 2 can be replaced by any chosen nonlinear mathematical operator, statistical operator, or artificial intelligence-based algorithm. The various matrices summarize patterns of information, but the robustness of correlations is also examined on a number-by-number basis, and nonparametric boot-strap confidence limits for the correlation coefficient estimates are calculated when desired.
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Hartwell, L.H.1
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See, for example, S. Friend, Science 265, 334 (1994); L. H. Hartwell and M. B. Kastan, ibid. 266, 1821 (1994); M. L. Smith and A. J. Fornace Jr., Mutat. Res. 340, 109 (1996); C. C. Harris, Carcinogenesis 17, 1187 (1996).
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Smith, M.L.1
Fornace Jr., A.J.2
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See, for example, S. Friend, Science 265, 334 (1994); L. H. Hartwell and M. B. Kastan, ibid. 266, 1821 (1994); M. L. Smith and A. J. Fornace Jr., Mutat. Res. 340, 109 (1996); C. C. Harris, Carcinogenesis 17, 1187 (1996).
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Carcinogenesis
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Harris, C.C.1
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55
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in preparation
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P. M. O'Connor et al., in preparation.
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O'Connor, P.M.1
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This finding is consistent with observations by S. Fan et al. [Cancer Res. 54, 5824 (1994)] in Burkitt's lymphoma cells. Interestingly, the small, highly Mdr-1 -susceptible subgroup seen in Fig. 2 as compounds 3043 to 3069 includes nine anthracyclines, among them doxorubicin, deoxydoxorubicin, daunomycin, and rubidazone. The apparent differences between antimitotics and DNA-damaging agents are increased somewhat by confounding correlations with Mdr-1, as indicated when cell lines high in Mdr-1 were excluded from the p53 analyses.
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Cancer Res.
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Fan, S.1
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58
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1842348690
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note
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One such set of criteria included the Pearson correlation coefficient and Wilcoxon P value (as defined for Fig. 4) with respect to p53 sequence, the median difference in sensitivity between p53 wild-type and p53-mutant cell lines, and the mean potency of the compound. Additional triage was done on the basis of availability of the compound for testing and uniqueness of activity pattern and molecular structure. To cite one example, a subset of the ellipticines scored well with respect to those criteria.
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The p53 isogenic sets used here include p53 wild-type parental cells, p53-disrupted derivatives, and control cells [see, for example, S. Fan et al., Cancer Res. 55, 1649 (1995)]. The results obtained can depend markedly on the cell type and genotypic context.
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(1995)
Cancer Res.
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Fan, S.1
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1842282607
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note
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Molecular characterization of clinical tumor cells is central to the NCI's recently announced Cancer Genome Anatomy Project (CGAP).
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61
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T. G. Myers and J. N. Weinstein, data not shown
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T. G. Myers and J. N. Weinstein, data not shown.
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1842266978
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in preparation
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K. Wosikowski et al., in preparation.
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Wosikowski, K.1
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1842398188
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note
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For continuing collaboration on the screening endeavors, we thank the staff of the DTP and SAIC NCI-FCRDC, especially J. Mayo, V. Narayanan, R. Schultz, R. Camalier, J. Johnson, K. Hite, A. Chiausa, P. Svetlik, and D. Segal. LMP was part of the DTP when much of this work was done. The molecular target data discussed here are the contributions of many others, including J. Jackman, I. Bae, M. Alvarez, and K. Wosikowski. We thank L. Muenz for critique of the statistical issues, and M. R. Boyd, R. Shoemaker, M. Alley, B. A. Chabner, G. Vande Woude, M. R. Grever, and S. A. Schepartz for developing the current screening program and supporting the molecular targets enterprise.
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