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Curvature Based Clustering for DNA Microarray Data Analysis
[chapter]
2005
Lecture Notes in Computer Science
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( 2 ) 2 Curvature Based Clustering for DNA Microarray Data Analysis, with Eli Appleboim, IbPRIA 2005 -2nd Iberian Conference on Pattern Recognition and Image Analysis, June 7-9, 2005; Estoril, Portugal ...
Theoretical Computer Science/Applied Mathematics
( 1 ) 1 Curvature Based Clustering for DNA Microarray Data Analysis, with Eli Appleboim, Lecture Notes in Computer Science, IbPRIA 2005, 3523, pp. 405 ...
doi:10.1007/11492542_50
fatcat:lney3vpjbzggza4cgcnqfbqheu
DNA microarray data and contextual analysis of correlation graphs
2003
BMC Bioinformatics
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Their analysis requires efficient and reliable algorithms for dimensional reduction, classification and annotation. We study networks of co-expressed genes obtained from DNA microarray experiments. ...
We provide a method for automatically determining relevant gene clusters among the many genes monitored with microarrays. ...
Moses for useful comments on earlier versions of the program and for detailed explanations of their results. Part of this research was supported by the Temblor project EU grant QLRT-2001-00015. ...
doi:10.1186/1471-2105-4-15
pmid:12720549
pmcid:PMC156617
fatcat:synwan3f65g2peyujmmq7i5hnm
Bioinformatics in neurocomputing framework
2005
IEE Proceedings - Circuits Devices and Systems
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Different bioinformatics tasks like gene sequence analysis, gene finding, protein structure prediction and analysis, gene expression with microarray analysis and gene regulatory network analysis are described ...
Different neural network based algorithms to address the aforesaid tasks are then presented. Finally some limitations of the current research activity are provided. ...
Base pair effects in determining the extent of DNA curvature has been developed. ...
doi:10.1049/ip-cds:20045051
fatcat:mcu56pkgjbbcblspl46ft66ahe
DNA microarrays: is there a role for analytical chemistry?
2005
The Analyst
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for microarray data. ...
Analytical chemistry, through the subdiscipline of chemometrics, is ideally suited to make valuable contributions to the analysis of DNA microarray data. ...
doi:10.1039/b508677a
pmid:16172653
fatcat:52kqhjf6vze4rfnd4bb2r5ed3i
Fuzzy clustering of time series gene expression data with cubic-spline
2013
Journal of Biosciences and Medicines
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Data clustering techniques have been applied to extract information from gene expression data for two decades. ...
The discrete values of radius of curvature are used to compute the similarity between spline curves. ...
To address this feature, fuzzy clustering is applied for gene expression data analysis [11] . ...
doi:10.4236/jbm.2013.13004
fatcat:fuzl7bgzxbdslmlbwlkbb332xy
Allele-specific expression analysis methods for high-density SNP microarray data
2012
Bioinformatics
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We investigate the application of SNP microarrays to this task, exploring data obtained from both celllines and primary tissue for which both RNA and DNA profiles are available. ...
Availability and Implementation: Analysis was carried out in R (http://www.R-project.org/) using existing functions. ...
that of the Cluster method for the full data set (Figure 5C ). ...
doi:10.1093/bioinformatics/bts089
pmid:22355082
fatcat:pnyzpoohmvghplvnuvb7cogc4u
The bioinformatics of microarray gene expression profiling
2001
Cytometry
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A red point (high positive Pearson correlation coefficient)
Table 1 1 Tasks in the Analysis of Microarray-Based Gene Expression Data1. ...
The former include, for example, techniques based on regression, discrimination, or prediction; the latter on techniques such as clustering (5, 6, 9, 10, 13) , principal components analysis, or multidimensional ...
doi:10.1002/cyto.10041
pmid:11774349
fatcat:oopxxovssbhc7ibwzlnx7tp6vy
Regulatory sequence analysis: application to the interpretation of gene expression
2001
European Neuropsychopharmacology
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Microarray technologies for measuring mRNA abundances in cells allow monitoring of gene expression levels for tens of thousands of genes in parallel. ...
The prerequisite for this kind of analysis is the existence of genomic DNA sequence, knowledge about gene locations, and experimental gene expression measurements for a variety of conditions. ...
in each of these, in order to cluster data aspects of the data analysis. ...
doi:10.1016/s0924-977x(01)00117-1
pmid:11704417
fatcat:qpnzkd45ivflvpqybbo6icafwy
Microarray Technology and Applications in Environmental Microbiology
[chapter]
2004
Advances in Agronomy
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After removing poor slides, poor quality spots, outliers and background, the microarray data are ready for further normalization and data analysis.
VI. MICROARRAY DATA ANALYSIS A. ...
For microarray data analysis, genes or experiments can be considered as variables. ...
doi:10.1016/s0065-2113(03)82004-7
fatcat:mrkm4hlo2nbbfev6efao6j3vb4
Histone acetylations mark origins of polycistronic transcription in Leishmania major
2009
BMC Genomics
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with DNA obtained through chromatin immunoprecipitation (ChIP-chip). ...
Results: The chromosomal location of TATA-binding protein (TBP or TRF4), Small Nuclear Activating Protein complex (SNAP 50 ), and H3 histones were assessed in Leishmania major using microarrays hybridized ...
Acknowledgements The authors would like to thank Patricia Respuela for advice on selecting antibodies to target histone H3 and acetylated H3 in L. major. ...
doi:10.1186/1471-2164-10-152
pmid:19356248
pmcid:PMC2679053
fatcat:3eixx63ctbdv5cai5vgvtg5bte
A DNA Microarray-based Analysis of the Host Response to a Nonviral Gene Carrier: A Strategy for Improving the Immune Response
2011
Molecular Therapy
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These findings indicate that a carrier design based on microarray analysis and the manipulation of intracellular trafficking constitutes a rational strategy for reducing the host immune response to NPs ...
Based on the microarray and a pathway analysis, we hypothesize that PEGylation inhibited the endosomal escape of NP, and extended the interaction of TLR9 with CpG-DNA accompanied by the production of type ...
Materials and Methods
Materials
Data analysis Microarray data were analyzed using GeneSpring software version 7.3 (Agilent, Foster City, CA, USA). ...
doi:10.1038/mt.2011.24
pmid:21386823
pmcid:PMC3149170
fatcat:qfzip2dvsvgofcnvubxqp4q56u
H-NS Mediates the Silencing of Laterally Acquired Genes in Bacteria
2006
PLoS Pathogens
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SL analyzed the data. DH and MH contributed reagents/materials/ analysis tools. SL and JCDH wrote the paper. Funding. This work was funded by the BBSRC core strategic grant to JCDH. ...
We are grateful to Dave Ussery for assistance in making the Genome Atlas which gave a new perspective to our H-NS and RNA polymerase binding data by adding structural factors; an interactive version of ...
Data acquisition and analysis. The microarray slides were scanned using a GenePix 4000A scanner (Axon Instruments, Union City, California, United States). ...
doi:10.1371/journal.ppat.0020081
pmid:16933988
pmcid:PMC1550270
fatcat:ab5yny7dpzb43l7z5jkcmzl34y
Microarray analysis of the in vivo sequence preferences of a minor groove binding drug
2008
BMC Genomics
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Results: Here we describe the use of microarray analysis to discover yeast genes that are affected by treatment with the MGBD berenil, thereby allowing the investigation of its sequence requirements for ...
There is a need to extend knowledge of the sequence requirements for MGBDs from in vitro DNA binding studies to living cells. ...
Anderson for valuable advice and discussions. ...
doi:10.1186/1471-2164-9-32
pmid:18215295
pmcid:PMC2254601
fatcat:vekaotzg2barlbj4isuz5gwdpi
Statistical modelling of transcript profiles of differentially regulated genes
2008
BMC Molecular Biology
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Previous studies have summarised gene expression profiles using simple descriptive statistics, basic analysis of variance (ANOVA) and the clustering of genes based on simple models fitted to their expression ...
The vast quantities of gene expression profiling data produced in microarray studies, and the more precise quantitative PCR, are often not statistically analysed to their full potential. ...
Acknowledgements Funding was provided by the UK Government Department for Food and Rural Affairs (DEFRA) project HH2116SMU. ...
doi:10.1186/1471-2199-9-66
pmid:18651954
pmcid:PMC2525656
fatcat:iogygymfcnh47b4ihd2h6kain4
A novel data mining method to identify assay-specific signatures in functional genomic studies
2006
BMC Bioinformatics
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The strengths of the PM are demonstrated using a simulation study, and two studies of real DNA microarray data--a study of classification of human tissue samples and a study of E. coli cultures with different ...
This article proposes a new and powerful PCA-based method for the identification of assay-specific gene signatures in FG studies. The proposed method (PM) is unique for several reasons. ...
Ingram for making available their data sets. ...
doi:10.1186/1471-2105-7-377
pmid:16907975
pmcid:PMC1599756
fatcat:wmhecm5hxnagng3j4bu3dmt6jy
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