Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Beißbarth, T.
Right arrow Articles by Vingron, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Beißbarth, T.
Right arrow Articles by Vingron, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 16 no. 11 2000
Pages 1014-1022
© 2000 Oxford University Press

Computing with Genetic Networks

Processing and quality control of DNA array hybridization data

T. Beißbarth 1,2, K. Fellenberg 1, B. Brors 1,3, R. Arribas-Prat 2, J. M. Boer 4, N. C. Hauser 3, M. Scheideler 3, J. D. Hoheisel 3, G. Schütz 2, A. Poustka 4 and M. Vingron 1,

1 Abt. Theoretische Bioinformatik
2 Abt. Molekularbiologie der Zelle I
3 Abt. Funktionelle Genomanalyse
4 Abt. Molekulare Genomanalyse, Deutsches Krebsforschungszentrum, INF 280, D–69120 Heidelberg, Germany

Received on October 11, 1999 ; revised on June 1, 2000 ; accepted on June 1, 2000

Motivation: The technology of hybridization to DNA arrays is used to obtain the expression levels of many different genes simultaneously. It enables searching for genes that are expressed specifically under certain conditions. However, the technology produces large amounts of data demanding computational methods for their analysis. It is necessary to find ways to compare data from different experiments and to consider the quality and reproducibility of the data.

Results: Data analyzed in this paper have been generated by hybridization of radioactively labeled targets to DNA arrays spotted on nylon membranes. We introduce methods to compare the intensity values of several hybridization experiments. This is essential to find differentially expressed genes or to do pattern analysis. We also discuss possibilities for quality control of the acquired data.

Availability: http://www.dkfz.de/tbi

Contact: M.Vingron{at}dkfz-heidelberg.de

To whom correspondence should be addressed.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
A. Hassibi, H. Vikalo, J. L. Riechmann, and B. Hassibi
Real-time DNA microarray analysis
Nucleic Acids Res., November 1, 2009; 37(20): e132 - e132.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L.-H. Ding, Y. Xie, S. Park, G. Xiao, and M. D. Story
Enhanced identification and biological validation of differential gene expression via Illumina whole-genome expression arrays through the use of the model-based background correction methodology
Nucleic Acids Res., June 1, 2008; 36(10): e58 - e58.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. E. Ritchie, J. Silver, A. Oshlack, M. Holmes, D. Diyagama, A. Holloway, and G. K. Smyth
A comparison of background correction methods for two-colour microarrays
Bioinformatics, October 15, 2007; 23(20): 2700 - 2707.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
O. N. Reva, C. Weinel, M. Weinel, K. Bohm, D. Stjepandic, J. D. Hoheisel, and B. Tummler
Functional Genomics of Stress Response in Pseudomonas putida KT2440
J. Bacteriol., June 1, 2006; 188(11): 4079 - 4092.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
S. S. Chatterjee, H. Hossain, S. Otten, C. Kuenne, K. Kuchmina, S. Machata, E. Domann, T. Chakraborty, and T. Hain
Intracellular Gene Expression Profile of Listeria monocytogenes
Infect. Immun., February 1, 2006; 74(2): 1323 - 1338.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C. H. Busold, S. Winter, N. Hauser, A. Bauer, J. Dippon, J. D. Hoheisel, and K. Fellenberg
Integration of GO annotations in Correspondence Analysis: facilitating the interpretation of microarray data
Bioinformatics, May 15, 2005; 21(10): 2424 - 2429.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
G. K. Smyth, J. Michaud, and H. S. Scott
Use of within-array replicate spots for assessing differential expression in microarray experiments
Bioinformatics, May 1, 2005; 21(9): 2067 - 2075.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
M. Bey, K. Stuber, K. Fellenberg, Z. Schwarz-Sommer, H. Sommer, H. Saedler, and S. Zachgo
Characterization of Antirrhinum Petal Development and Identification of Target Genes of the Class B MADS Box Gene DEFICIENS
PLANT CELL, December 1, 2004; 16(12): 3197 - 3215.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
U. Steidl, S. Bork, S. Schaub, O. Selbach, J. Seres, M. Aivado, T. Schroeder, U.-P. Rohr, R. Fenk, S. Kliszewski, et al.
Primary human CD34+ hematopoietic stem and progenitor cells express functionally active receptors of neuromediators
Blood, July 1, 2004; 104(1): 81 - 88.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
O. Modlich, H.-B. Prisack, G. Pitschke, U. Ramp, R. Ackermann, H. Bojar, T. A. Vogeli, and M.-O. Grimm
Identifying Superficial, Muscle-Invasive, and Metastasizing Transitional Cell Carcinoma of the Bladder: Use of cDNA Array Analysis of Gene Expression Profiles
Clin. Cancer Res., May 15, 2004; 10(10): 3410 - 3421.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. Konig, D. Baldessari, N. Pollet, C. Niehrs, and R. Eils
Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design
Nucleic Acids Res., February 13, 2004; 32(3): e29 - e29.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Weiner III, C.-U. Zimmerman, H. W. H. Gohlmann, and R. Herrmann
Transcription profiles of the bacterium Mycoplasma pneumoniae grown at different temperatures
Nucleic Acids Res., November 1, 2003; 31(21): 6306 - 6320.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
A. Lagorce, N. C. Hauser, D. Labourdette, C. Rodriguez, H. Martin-Yken, J. Arroyo, J. D. Hoheisel, and J. Francois
Genome-wide Analysis of the Response to Cell Wall Mutations in the Yeast Saccharomyces cerevisiae
J. Biol. Chem., May 23, 2003; 278(22): 20345 - 20357.
[Abstract] [Full Text] [PDF]

Home page
 CirculationHome page
B. Kaynak, A. von Heydebreck, S. Mebus, D. Seelow, S. Hennig, J. Vogel, H.-P. Sperling, R. Pregla, V. Alexi-Meskishvili, R. Hetzer, et al.
Genome-Wide Array Analysis of Normal and Malformed Human Hearts
Circulation, May 20, 2003; 107(19): 2467 - 2474.
[Abstract] [Full Text] [PDF]

Home page
 J. Cell Sci.Home page
T. Barz, K. Ackermann, G. Dubois, R. Eils, and W. Pyerin
Genome-wide expression screens indicate a global role for protein kinase CK2 in chromatin remodeling
J. Cell Sci., April 15, 2003; 116(8): 1563 - 1577.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
H. Yang, H. Haddad, C. Tomas, K. Alsaker, and E. T. Papoutsakis
A segmental nearest neighbor normalization and gene identification method gives superior results for DNA-array analysis
PNAS, February 4, 2003; 100(3): 1122 - 1127.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
E. I. Cline, S. Bicciato, C. DiBello, and M. W. Lingen
Prediction of in Vivo Synergistic Activity of Antiangiogenic Compounds by Gene Expression Profiling
Cancer Res., December 15, 2002; 62(24): 7143 - 7148.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. M. Talaat, S. T. Howard, W. Hale IV, R. Lyons, H. Garner, and S. A. Johnston
Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis
Nucleic Acids Res., October 15, 2002; 30(20): e104 - e104.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Diehl, B. Beckmann, N. Kellner, N. C. Hauser, S. Diehl, and J. D. Hoheisel
Manufacturing DNA microarrays from unpurified PCR products
Nucleic Acids Res., August 15, 2002; 30(16): e79 - e79.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
B. Fritz, F. Schubert, G. Wrobel, C. Schwaenen, S. Wessendorf, M. Nessling, C. Korz, R. J. Rieker, K. Montgomery, R. Kucherlapati, et al.
Microarray-based Copy Number and Expression Profiling in Dedifferentiated and Pleomorphic Liposarcoma
Cancer Res., June 1, 2002; 62(11): 2993 - 2998.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
M. Scheideler, N. L. Schlaich, K. Fellenberg, T. Beissbarth, N. C. Hauser, M. Vingron, A. J. Slusarenko, and J. D. Hoheisel
Monitoring the Switch from Housekeeping to Pathogen Defense Metabolism in Arabidopsis thaliana Using cDNA Arrays
J. Biol. Chem., March 15, 2002; 277(12): 10555 - 10561.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
U. Steidl, R. Kronenwett, U.-P. Rohr, R. Fenk, S. Kliszewski, C. Maercker, P. Neubert, M. Aivado, J. Koch, O. Modlich, et al.
Gene expression profiling identifies significant differences between the molecular phenotypes of bone marrow-derived and circulating human CD34+ hematopoietic stem cells
Blood, March 15, 2002; 99(6): 2037 - 2044.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
K. Fellenberg, N. C. Hauser, B. Brors, A. Neutzner, J. D. Hoheisel, and M. Vingron
Correspondence analysis applied to microarray data
PNAS, September 4, 2001; (2001) 181597298.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Endocrinol.Home page
N. Akutsu, R. Lin, Y. Bastien, A. Bestawros, D. J. Enepekides, M. J. Black, and J. H. White
Regulation of Gene Expression by 1{{alpha}},25-Dihydroxyvitamin D3 and Its Analog EB1089 under Growth-Inhibitory Conditions in Squamous Carcinoma Cells
Mol. Endocrinol., July 1, 2001; 15(7): 1127 - 1139.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
K. Fellenberg, N. C. Hauser, B. Brors, A. Neutzner, J. D. Hoheisel, and M. Vingron
Correspondence analysis applied to microarray data
PNAS, September 11, 2001; 98(19): 10781 - 10786.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
J. M. Boer, W. K. Huber, H. Sultmann, F. Wilmer, A. von Heydebreck, S. Haas, B. Korn, B. Gunawan, A. Vente, L. Fuzesi, et al.
Identification and Classification of Differentially Expressed Genes in Renal Cell Carcinoma by Expression Profiling on a Global Human 31,500-Element cDNA Array
Genome Res., November 1, 2001; 11(11): 1861 - 1870.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.