Gene expression profiles in normal and cancer cells

Science

Volumn 276, Issue 5316, 1997, Pages 1268-1272

  Zhang, Lin ^a   Zhou, Wei ^a   Velculescu, Victor E ^a   Kern, Scott E ^a   Hruban, Ralph H ^a   Hamilton, Stanley R ^a   Vogelstein, Bert ^a   Kinzler, Kenneth W ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER CELL CULTURE; GASTROINTESTINAL TUMOR; GENE EXPRESSION REGULATION; GENETIC ANALYSIS; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROGNOSIS; TRANSCRIPTION REGULATION;

COLORECTAL NEOPLASMS; COMPUTER SIMULATION; DIGESTIVE PHYSIOLOGY; GASTROINTESTINAL NEOPLASMS; GENE EXPRESSION; HUMANS; REFERENCE VALUES; TUMOR CELLS, CULTURED;

EID: 0030962307     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.276.5316.1268     Document Type: Article

References (44)

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9. To minimize individual variation, approximately equal numbers of tags (30,000) were derived from two different patients for each tissue. For primary tumors (two CR carcinomas and two pancreatic adenocarcinomas), RNA was isolated from portions of tumors judged by histopathology to contain 60 to 90% tumor cells. The cells grown in vitro were derived from CR (SW837 and Caco2) and pancreatic (ASPC-1 and PL45) cancer cell lines. CR epithelial cells were isolated from sections of normal colon mucosa from two patients with the use of EDTA as described [S. Nakamura, I. Kino, S. Baba, Gut 34, 1240 (1993)). Histopathology confirmed that the isolated cells were >90% epithelial. Isolation of polyadenylate RNA and SAGE was performed as described (2). SAGE data were analyzed with SAGE software and GenBank Release 94 as described (2).
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15. To minimize the number of assumptions and to account for the large number of comparisons being made, we used Monte Carlo analysis to determine statistical significance. The null hypothesis was that the level, kind, and distribution of transcripts were the same for cancer and normal cells. For each transcript, we performed 100,000 simulations to determine the relative likelihood, due to chance atone (p-chance), of obtaining a difference in expression equal to or greater than the observed difference, given the null hypothesis. We converted this likelihood to an absolute probability value by simulating 40 expenments in which a representative number of transcripts (27,993 transcripts in each experiment) were identified and compared. We derived the distribution of transcripts used for these simulations from the average level of expression observed in the original samples. We then compared the distribution of the p-chance scores obtained in the 40 simulated experiments (false positives) with those obtained experimentally. On the basis of this comparison, a maximum value of 0.0005 was chosen for p-chance. This yielded a false-positive rate that was no higher than 0.01 for the least significant p-chance value below the cutoff.
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44. We thank K. Polyak and P. J. Morin for providing colon cancer cell lines; G. M. Nadasdy for providing pancreatic primary tumors; and J. Floyd, C. R. Robinson, and Y. Beazer-Barclay for technical assistance. Supported by the Clayton Fund and by NIH grants GM07309, CA57345, and CA62924. B.V. is an investigator of the Howard Hughes Medical Institute.