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

被引:399
作者
Butte, AJ
Tamayo, P
Slonim, D
Golub, TR
Kohane, IS
机构
[1] Childrens Hosp, Informat Program, Boston, MA 02115 USA
[2] Childrens Hosp, Dept Med, Div Endocrinol, Boston, MA 02115 USA
[3] Whitehead Inst Biomed Res, Cambridge, MA 02142 USA
[4] Dana Farber Canc Inst, Boston, MA 02115 USA
关键词
D O I
10.1073/pnas.220392197
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
引用
收藏
页码:12182 / 12186
页数:5
相关论文
共 28 条
  • [1] Butte A J, 2000, Pac Symp Biocomput, P418
  • [2] Human signaling protein 14-3-3ζ interacts with platelet glycoprotein Ib subunits Ibα and Ibβ
    Calverley, DC
    Kavanagh, TJ
    Roth, GJ
    [J]. BLOOD, 1998, 91 (04) : 1295 - 1303
  • [3] Activation of the 43 kDa inositol polyphosphate 5-phosphatase by 14-3-3 zeta
    Campbell, JK
    Gurung, R
    Romero, S
    Speed, CJ
    Andrews, RK
    Berndt, MC
    Mitchell, CA
    [J]. BIOCHEMISTRY, 1997, 36 (49) : 15363 - 15370
  • [4] STRUCTURE, CHROMOSOMAL LOCALIZATION, AND EXPRESSION OF 12 GENES OF THE MAGE FAMILY
    DEPLAEN, E
    ARDEN, K
    TRAVERSARI, C
    GAFORIO, JJ
    SZIKORA, JP
    DESMET, C
    BRASSEUR, F
    VANDERBRUGGEN, P
    LETHE, B
    LURQUIN, C
    BRASSEUR, R
    CHOMEZ, P
    DEBACKER, O
    CAVENEE, W
    BOON, T
    [J]. IMMUNOGENETICS, 1994, 40 (05) : 360 - 369
  • [5] DeRisi J, 1996, NAT GENET, V14, P457
  • [6] Cluster analysis and display of genome-wide expression patterns
    Eisen, MB
    Spellman, PT
    Brown, PO
    Botstein, D
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (25) : 14863 - 14868
  • [7] Frederick MJ, 1996, CANCER RES, V56, P138
  • [8] Discovery and analysis of inflammatory disease-related genes using cDNA microarrays
    Heller, RA
    Schena, M
    Chai, A
    Shalon, D
    Bedilion, T
    Gilmore, J
    Woolley, DE
    Davis, RW
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, 94 (06) : 2150 - 2155
  • [9] Increased expression of T-plastin gene in cisplatin-resistant human cancer cells: Identification by mRNA differential display
    Hisano, T
    Ono, M
    Nakayama, M
    Naito, S
    Kuwano, M
    Wada, M
    [J]. FEBS LETTERS, 1996, 397 (01) : 101 - 107
  • [10] The transcriptional program in the response of human fibroblasts to serum
    Iyer, VR
    Eisen, MB
    Ross, DT
    Schuler, G
    Moore, T
    Lee, JCF
    Trent, JM
    Staudt, LM
    Hudson, J
    Boguski, MS
    Lashkari, D
    Shalon, D
    Botstein, D
    Brown, PO
    [J]. SCIENCE, 1999, 283 (5398) : 83 - 87