Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: A meta-analysis of three microarray studies

Bioinformatics

Volumn 20, Issue 17, 2004, Pages 3166-3178

  Wang, J ^a   Coombes, K R ^a   Highsmith, W E ^b   Keating, M J ^a   Abruzzo, L V ^a  

^a UNIVERSITY OF TEXAS   (United States)

^b MAYO CLINIC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GLASS; NYLON;

ARTICLE; B CELL LEUKEMIA; B LYMPHOCYTE; BAYES THEOREM; BIOTECHNOLOGY; CANCER RESEARCH; CHRONIC LYMPHATIC LEUKEMIA; CLINICAL ARTICLE; CLINICAL TRIAL; CONTROLLED CLINICAL TRIAL; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE NUMBER; GENE TARGETING; GENETIC DIFFERENCE; GENETIC IDENTIFICATION; GENETIC MARKER; HUMAN; META ANALYSIS; PRIORITY JOURNAL; PROGNOSIS; STATISTICAL ANALYSIS;

EID: 10244224128     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth381     Document Type: Article

References (49)

1. Aalto,Y, El-Rifa,W., Vilpo,L., Ollila,J., Nagy,B., Vihinen,M., Vilpo,J. and Knuutila,S. (2001) Distinct gene expression profiling in chronic lymphocytic leukemia with 11q23 deletion. Leukemia, 15, 1721-1728.
2. Abts,H., Jucker,M., Diehl,V. and Tesch,H. (1991) Human chronic lymphocytic leukemia cells regularly express mRNAs of the protooncogenes lck and c-fgr. Leuk. Res., 15, 987-997.
3. Alizadeh,A.A., Eisen,M.B., Davis,R.E., Ma,C., Lossos,I.S., Rosenwald,A., Boldrick,J.C., Sabet,H., Tran,T., Yu,X. et al. (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, 403, 503-511.
4. Baggerly,K.A., Coombes,K.R., Hess,K.R., Stivers,D.N., Abruzzo,L.V. and Zhang,W. (2001) Identifying differentially-expressed genes in cDNA microarray experiments. J. Comput. Biol., 8, 639-659.
5. Baldi,P. and Long,A.D. (2001) A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics, 17, 509-519.
6. Baldini,L., Cro,L., Cortelezzi,A., Calori,R., Nobili,L., Maiolo,A.T. and Polli,E.E. (1990) Immunophenotypes in " classical" B-cell chronic lymphocytic leukemia. Correlation with normal cellular counterpart and clinical findings. Cancer, 66, 1738-1742.
7. Borgers,M., Verhaegen,H., De Brabander,M., De Cree,J., De Cock,W., Thone,F. and Geuens,G. (1978) Purine nucleoside phosphorylase in chronic lymphocytic leukemia (CLL). Blood, 52, 886-895.
8. Box,G.E. and Tiao,G.C. (1992) Bayesian Inference in Statistical Analysis. John Wiley and Sons, Inc., New York.
9. Brazma,A., Hingamp,P., Quackenbush,J., Sherlock,G., Spellman,P., Stoeckert,C., Aach,J., Ansorge,W., Ball,C.A., Causton,H.C. et al. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet., 29 365-371.
10. Broet,P., Richardson,S. and Radvanyi,F. (2002) Bayesian hierarchical model for identifying changes in gene expression from microarray experiments. J. Comput. Biol., 9, 671-683.
11. Coombes,K.R., Highsmith,W.E., Krogmann,T.A., Baggerly,K.A., Stivers,D.N. and Abruzzo,L.V. (2002) Identifying and quantifying sources of variation in microarray data using high-density cDNA membrane arrays. J. Comput. Biol., 9, 655-669.
12. Damle,R.N., Wasil,T., Fais,F., Ghiotto,F., Valetto,A., Allen,S.L., Buchbinder,A., Budman,D., Dittmar,K., Kolitz,J., et al. (1999) IgV gene mutation status and CD38 expression as novel prognostic indicators in chronic lymphocytic leukemia. Blood, 94, 1840-1847.
13. Dohner,H., Stilgenbauer,S., Dohner,K., Bentz,M. and Lichter,P. (1999) Chromosome aberrations in B-cell chronic lymphocytic leukemia: reassessment based on molecular cytogenetic analysis. J. Mol. Med., 77, 266-281.
14. Dudoit,S., Yang,Y.H., Callow,M.J. and Speed,T.P. (2002) Statistical methods for identifying differentially-expressed genes in replicated cDNA microarray experiments. Stat. Sin., 12, 111-139.
15. Edgar,R., Domrachev,M. and Lash,A.E. (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210.
16. Efron,B. and Tibshirani,R. (2002) Empirical Bayes methods and false discovery rates for microarrays. Genet. Epidemiol., 23, 70-86.
17. Friedman,N., Linial,M., Nachman,I. and Pe'er,D. (2000) Using Bayesian networks to analyze expression data. J. Comput. Biol., 7, 601-620.
18. Furman,R.R., Asgary,Z., Mascarenhas,J.O., Liou,H.C. and Schattner,E.J. (2000) Modulation of NF-kappa B activity and apoptosis in chronic lymphocytic leukemia B cells. J. Immunol., 164, 2200-2206.
19. Gagro,A., Dasic,G., Sabioncello,A., Rabatic,S., Reckzeh,B., Havemann,K., Kardum,I., Jacksic,B. and Vitale,B. (1997) Phenotypic analysis of receptor-ligand pairs on B-cells in B-chronic lymphocytic leukemia. Leuk. Lymphoma, 25, 301-311.
20. Hamblin,T.J., Davis,Z., Gardiner,A., Oscier,D.G. and Stevenson,F.K. (1999) Unmutated Ig VH genes are associated with a more aggressive form of chronic lymphocytic leukemia. Blood, 94, 1848-1854.
21. Hautaniemi,S., Edgren,H., Vesanen,R, Wolf,M., Jarvinen,A.K., Yli-Harja,O., Astola,J., Kallioniemi,O. and Monni,O. (2003) A novel strategy for microarray quality control using Bayesian networks. Bioinformatics, 19, 2031-2038.
22. Hughes,T.R., Mao,M., Jones,A.R., Burchard,J., Marton,M.J., Shannon,K.W., Lefkowitz,S.M., Ziman,M., Schelter,J.M., Meyer,M.R. et al. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol., 19, 342-347.
23. Ibrahim,S., Jilani,I., O'Brien,S., Rogers,A., Manshouri,T., Giles,F., Faderl,S., Thomas,D., Kantarjian,H., Keating,M. and Albitar,M. (2003) Clinical relevance of the expression of the CD31 ligand for CD38 in patients with B-cell chronic lymphocytic leukemia. Cancer, 97 1914-1919.
24. Jurlander,J., Lai,C.F., Tan,J., Chou,C.C., Geisler,C.H., Schriber,J., Blumenson,L.E., Narula,S.K., Baumann,H. and Caligiuri,M.A. (1997) Characterization of interleukin-10 receptor expression on B-cell chronic lymphocytic leukemia cells. Blood, 89, 4146-4152.
25. Klein,U., Tu,Y., Stolovitzky,G.A., Mattioli,M., Cattoretti,G., Husson,H., Freedman,A., Inghirmi,G., Cro,L., Baldini,L. et al. (2001) Gene expression profile of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells. J. Exp. Med., 194, 1625-1638.
26. Kuo,P.W., Jenssen,T.K., Butte,A.J., Ohno-Machado,L. and Kohane,I.S. (2002) Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics, 18, 405-412.
27. Larsson,L.G., Schena,M., Carlsson,M., Sallstrom,J. and Nilsson,K. (1991) Expression of the c-myc protein is down-regulated at the terminal stages during in vitro differentiation of B-type chronic lymphocytic leukemia cells. Blood, 77, 1025-1032.
28. Lee,M.L., Lu,W., Whitmore,G.A. and Beier,D. (2002) Models for microarray gene expression data. J. Biopharm. Stat., 12, 1-19.
29. Lee,K.E., Sha,N., Dougherty,E.R., Vannucci,M. and Mallick,B.K. (2003) Gene selection: a Bayesian variable selection approach. Bioinformatics, 19, 90-97.
30. Li,Y., Campbell,C. and Tipping,M. (2002) Bayesian automatic relevance determination algorithms for classifying gene expression data. Bioinformatics, 18, 1332-1339.
31. Matutes,E. and Polliack,A. (2000) Morphological and immunophenotypic features of chronic lymphocytic leukemia. Rev. Clin. Exp. Hematol., 4, 22-47.
32. McCarthy,H., Wierda,W.G., Barron,L.L., Cromwell,C.C., Wang,J., Coombes,K.R., Rangel,R., Elenitoba-Johnson,K.S., Keating,M.J. and Abruzzo,L.V. (2003) High expression of activation-induced cytidine deaminase (AID) and splice variants is a distinctive feature of poor prognosis chronic lymphocytic leukemia. Blood, 101, 4903-4908.
33. Medvedovic,M. and Sivaganesan,S. (2002) Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics, 18, 1194-1206.
34. Newton,M.A., Kendziorski,C.M., Richmond,C.S., Blattner,F.R. and Tsui,K.W. (2001) On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J. Comput. Biol., 8, 37-52.
35. Oba,S., Sato,M.A., Takemasa,I., Monden,M., Matsubara,K. and Ishii,S. (2003) A Bayesian missing value estimation method for gene expression profile data. Bioinformatics, 19, 2088-2096.
36. Rai,K.R. and Patel,D.V. (2000) Chronic lymphocytic leukemia. In Hoffman,R., Benz,E.J.,Jr, Shattil,S.J., Furie,B., Cohen,H.J., Silberstein,L.E. and McGlave,P. (eds), Hematology: Basic Principles and Practice, 3rd edn. Churchill Livingstone, New York, pp. 1350.
37. Ranheim,E.A., Cantwell,M.J. and Kipps,T.J. (1995) Expression of CD27 and its ligand, CD70, on chronic lymphocytic leukemia B cells. Blood, 85, 3556-3565.
38. Rosenwald,A., Alizadeh,A.A., WidhopfG., Simon,R., Davis,R.E., Yu,X., Yang,L., Pickeral,O.K., Rassenti,L.Z., Powell,J. et al. (2001) Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia. J. Exp. Med., 194, 1639-1647.
39. Savoie,C.J., Aburatani,S., Watanabe,S., Eguchi,Y., Muta,S., Imoto,S., Miyano,S., Kuhara,S. and Tashiro,K. (2003) Use of gene networks from full genome microarray libraries to identify functionally relevant drug-affected genes and gene regulation cascades. DNA Res., 10 19-25.
40. Schena,M., Larsson,L.G., Gottardi,D., Gaidano,G., Carlsson,M., Nilsson,K. and Caligaris-Cappio,F. (1992) Growth- and differentiation-associated expression of bcl-2 in B-chronic lymphocytic leukemia cells. Blood, 79, 2981-2989.
41. Sluka,J.P. (2002) Extracting knowledge from genomic experiments by incorporating the biomedical literature. In Lin,S.M. and Johnson,K.F. (eds), Methods of Microarray Data Analysis II. Kluwer Academic Publishers, Boston, MA, pp. 195-209.
42. Tabucchi,A., Carlucci,F., Rosi,F., Guerranti,R. and Marinello,E. (2001) Determination, activity and biological role of adenylosuccinate lyase in blood cells. Biomed. Pharmacother., 55 277-283.
43. Tobler,J.B., Molla,M.N., Nuwaysir,E.F., Green,R.D. and Shavlik,J.W. (2002) Evaluating machine learning approaches for aiding probe selection for gene-expression arrays. Bioinformatics, 18 (Suppl. 1), S164-S171.
44. Tung,R., Silber,R., Quagliata,F., Conklyn,M., Gottesman,J. and Hirschhorn,R. (1976) Adenosine deaminase activity in chronic lymphocytic leukemia. Relationship to B- and T-cell subpopulations. J. Clin. Invest., 57, 756-761.
45. Waage,A., Liabakk,N., Lien,E., Lamvik,J. and Espevik,T. (1992) p55 and p75 tumor necrosis factor receptors in patients with chronic lymphocytic leukemia. Blood, 80, 2577-2583.
46. Wolowiec,D., Ciszak,L., Kosmaczewska,A., Bocko,D., Teodorowska,R., Frydecka,I. and Kuliczkowski,K. (2001) Cell cycle regulatory proteins and apoptosis in B-cell chronic lymphocytic leukemia. Haematologica, 86, 1296-1304.
47. Yang,M.C., Ruan,Q.G., Yang,J.J., Eckenrode,S., Wu,S., McIndoe,R.A. and She,J.X. (2001) A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays. Physiol. Genomics, 7, 45-53.
48. Yuen,T., Wurmbach,E., Pfeffer,R.L., Ebersole,B.J. and Sealfon,S.C. (2002) Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res., 30, e48.
49. Zhou,X., Wang,X. and Dougherty,E.R. (2003) Missing-value estimation using linear and non-linear regression with Bayesian gene selection. Bioinformatics, 19, 2302-2307.