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Two way clustering of microarray data using a hybrid approach

Raul Malutan, Bogdan Belean, Pedro Gomez Vilda, Monica Borda
2011 2011 34th International Conference on Telecommunications and Signal Processing (TSP)  
In this paper a hybrid approach is used to obtain a two way unsupervised clustering for a corrected microarray data.  ...  The Microarray technique is rather powerful, as it allows to test up thousands of genes at a time, but this produces an overwhelming set of data files containing huge amounts of data, which is quite difficult  ...  Other supervised and unsupervised methods are planned to be used in a hybrid approach to microarray data. i x belongs to one of the component densities.  ... 
doi:10.1109/tsp.2011.6043698 dblp:conf/tsp/MalutanBVB11 fatcat:o5jtzflo3ndojp2ps2magxboxm

DNA microarrays for functional plant genomics [chapter]

Asaph Aharoni, Oscar Vorst
2001 Functional Genomics  
DNA microarrays are currently fabricated and assayed by two main approaches involving either in situ synthesis of oligonucleotides ('oligonucleotide microarrays') or deposition of pre-synthesized DNA fragments  ...  The value of microarray technology to our understanding of living processes will depend both on the amount of data to be generated and on its clever exploration and integration with other biological knowledge  ...  Acknowledgements We would like to thank Robert Hall and Ruud de Maagd for critical reading of the manuscript.  ... 
doi:10.1007/978-94-010-0448-0_7 fatcat:avk4ml3wpbbhlduz66k4layf2i

Microarray data analysis and mining

Silvia Saviozzi, Giovanni Iazzetti, Enrico Caserta, Alessandro Guffanti, Raffaele A Calogero
2004 Methods in Molecular Medicine  
a hot topic in data mining.  ...  In this chapter an integrated approach of filtering and statistical validation to select trustable differentially expressed genes is described together with a brief introduction on data mining focusing  ...  Acknowledgments This work was partially supported by PRIN2001 2001057147 and FIRB RBAU01JTHS/ RBNEO157EH grants of the Italian Ministry of University and S&T Research-MIUR.  ... 
pmid:14959823 fatcat:qegmxpb4yfa6lhaqp3qqrkrj4u

A novel distance-based iterative sequential KNN algorithm for estimation of missing values in microarray gene expression data

Chandra Das, Shilpi Bose, Matangini Chattopadhyay, Samiran Chattopadhyay
2016 International Journal of Bioinformatics Research and Applications  
The estimation accuracy of the proposed clustering method is compared with the widely used KNNimpute, SKNNimpute and IKNNimpute methods on various microarray data sets with different rate of missing entries  ...  Based on this distance a modified K-means clustering algorithm is proposed to accurately predict missing values in microarray gene expression data.  ...  So, it is a new robust approach to estimate missing values in microarray gene expression data.  ... 
doi:10.1504/ijbra.2016.080719 fatcat:6x2mvljdlva77mppau4nfwvqqa

Statistical Challenges in Functional Genomics

Paola Sebastiani, Emanuela Gussoni, Isaac S. Kohane, Marco F. Ramoni
2003 Statistical Science  
This paper reviews the foundations of this technology and describes the statistical challenges posed by the analysis of microarray data.  ...  On February 12, 2001 the Human Genome Project announced that it had assembled a draft physical map of the human genome -the genetic blueprint for a human being.  ...  Acknowledgments This research was supported by NSF grant ECS-0120309, by NHLBI grant HL-99-024, and by the Genomics Core of Beth Israel Deaconess Medical Center, Boston, MA.  ... 
doi:10.1214/ss/1056397486 fatcat:da2v3h5vnbgv7od43ggee5qvwu

Computational approaches to analysis of DNA microarray data

J Quackenbush
2006 IMIA Yearbook of Medical Informatics  
To review the current state of the art in computational methods for the analysis of DNA microarray data.  ...  Methods for assaying gene expression levels by DNA microarray experiments produce considerably more data than other techniques, and require a wide variety of computational techniques for identifying patterns  ...  Clustering Approaches A useful first approach to the analysis of microarray data is to use an unsupervised method to explore expression patterns of that exist in the data.  ... 
pmid:17051302 fatcat:sx6nzpjtezbollzb34up5fnmoi

Section 7: Bioinformatics: Computational Approaches to Analysis of DNA Microarray Data

J. Quackenbush
2006 IMIA Yearbook of Medical Informatics  
, comparisons and predictions of gene expression from the data, their mechanistic analysis, related systems biology, and the application of clustering techniques.Functional genomics approaches have greatly  ...  analyses of biological systems.Methods for assaying gene expression levels by DNA microarray experiments produce considerably more data than other techniques, and require a wide variety of computational  ...  Clustering Approaches A useful first approach to the analysis of microarray data is to use an unsupervised method to explore expression patterns of that exist in the data.  ... 
doi:10.1055/s-0038-1638484 fatcat:gv7qh55aojdnxly4mc5vftlqnm

Microarrays: handling the deluge of data and extracting reliable information

Kenneth R Hess, Wei Zhang, Keith A Baggerly, David N Stivers, Kevin R Coombes, Wei Zhang
2001 Trends in Biotechnology  
An alternative approach is to use a large number (≥75) of housekeeping genes.  ...  Rigorous standardization and validation of microarray data is required before such a data repository would be useful.  ...  Great progress has been made with the two main approaches of protein engineering: rational design and combinatorial synthesis.  ... 
doi:10.1016/s0167-7799(01)01792-9 pmid:11602311 fatcat:64oelxznlnavzfqnxt6jfkqisu

A glance at DNA microarray technology and applications

Amir Ata Saei, Yadollah Omidi
2011 BioImpacts  
be used in preprocessing and/or data mining of microarray data.  ...  Studying the regulation patterns of genes in groups, using clustering and classification methods helps us understand different pathways in the cell, their functions, regulations and the way one component  ...  Acknowledgement Authors are grateful to the Ministry of Health, Care and Medical Education for the financial support.  ... 
doi:10.5681/bi.2011.011 pmid:23678411 pmcid:PMC3648957 fatcat:4ywgkf6i2zaxtg7z6lvzvhfjn4

Gene Ontology Analysis of 3D Microarray Gene Expression Data using Hybrid PSO Optimization

Triclustering approach identifies a coherent pattern in the 3D gene expression data using Mean Correlation Value (MCV).  ...  Triclustering is a simultaneously clustering of subset of Gene (G), subset of Sample (S), and over a subset of Time point (T).  ...  This literature study clearly depicts that PSO or Hybrid PSO based approaches mainly used for one and two dimensional clustering of GST i.e. 3D microarray data.  ... 
doi:10.35940/ijitee.k1261.0981119 fatcat:fkyxjfic4bbh5a5z56o7vj75ti

LTR: Linear Cross-Platform Integration of Microarray Data

Paul C. Boutros
2010 Cancer Informatics  
LTR was tested on a new benchmark dataset of 20 samples hybridized to different Affymetrix microarray platforms.  ...  One experimental control is the replicate hybridization of a subset of samples at each site or on each platform to learn the relationship between the two platforms.  ...  Funding for this study was provided by a grant from the Canadian Institutes of Health Research to PCB and Dr. Allan B. Okey (MOP-57903).  ... 
doi:10.4137/cin.s5756 pmid:20838609 pmcid:PMC2935818 fatcat:ao5doetynrbqvo4md3kwabgjum

Microarray Technology and Applications in Environmental Microbiology [chapter]

Jizhong Zhou, Dorothea K Thompson
2004 Advances in Agronomy  
For this, two aliquots of the two RNA samples (A and B) are labeled with Cy3 or Cy5 separately, and then hybridized with two microarrays.  ...  Depending on the way in which the data are clustered, cluster analysis can be divided into hierarchical clustering and non-hierarchical clustering. (i) Hierarchical clustering.  ... 
doi:10.1016/s0065-2113(03)82004-7 fatcat:mrkm4hlo2nbbfev6efao6j3vb4

Survey on different Methods for Classifying Gene Expression using Microarray Approach

Emad Mohamed, Enas M., Khaled Tawfik, Akram Ibrahim
2016 International Journal of Computer Applications  
There are two principal ways of achieving this. The first one, cluster analysis, is exclusively data driven, the second one, annotation analysis, is knowledge-driven [7] .  ...  K.Sathishkumar, et al [29] proposed a new method using cluster analysis approach. The idea is to use an algorithm that can reduce and solve the problem of high dimensionality.  ... 
doi:10.5120/ijca2016911441 fatcat:mpjihtmerzdexbe7gtiaomw2ju

Community Dynamics of Bacteria in Sourdough Fermentations as Revealed by Their Metatranscriptome

S. Weckx, R. Van der Meulen, J. Allemeersch, G. Huys, P. Vandamme, P. Van Hummelen, L. De Vuyst
2010 Applied and Environmental Microbiology  
The lactic acid bacterial (LAB) community dynamics of two wheat and two spelt sourdough fermentations that were daily back-slopped were monitored during a period of 10 days by hybridizing time-related  ...  Consequently, metatranscriptome hybridization data obtained using an LAB functional gene microarray was shown to be an interesting alternative to microbiological analysis of the community dynamics of complex  ...  The identification as revealed by the microarray hybridization data was in agreement with the outcome of a combined culture-dependent and culture-independent identification approach.  ... 
doi:10.1128/aem.00570-10 pmid:20581179 pmcid:PMC2918950 fatcat:s6v6s4rc7rgxpbnng3psvi5fci

Impacts of DNA Microarray Technology in Gene Therapy [chapter]

Jaleh Barar, Amir Ata, Yadollah Omidi
2011 Gene Therapy - Developments and Future Perspectives  
For implementation of this technology, however, one needs to be familiar with the different methods used in microarray data analyses and the ways for more efficient applications of such methods to enhance  ...  Impacts of DNA Microarray Technology in Gene Therapy Reverse engineering of regulatory networks can be fulfilled using two methods, one of which is "time-series data" and second one is "steady-state data  ...  This source will make our doctors become comfortable with the common problems of gene therapy and inspire others to delve a bit more deeply into a topic of interest.  ... 
doi:10.5772/18979 fatcat:alzlo5wyjfe4to3ehgmoqveyei
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