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Curvature Based Clustering for DNA Microarray Data Analysis [chapter]

Emil Saucan, Eli Appleboim
2005 Lecture Notes in Computer Science  
( 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

Jacques Rougemont, Pascal Hingamp
2003 BMC Bioinformatics  
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

S.S. Ray, S. Bandyopadhyay, P. Mitra, S.K. Pal
2005 IEE Proceedings - Circuits Devices and Systems  
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?

Peter D. Wentzell, Tobias K. Karakach
2005 The Analyst  
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

Yu Wang, Maia Angelova, Akhtar Ali
2013 Journal of Biosciences and Medicines  
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

Ruijie Liu, Ana-Teresa Maia, Roslin Russell, Carlos Caldas, Bruce A. Ponder, Matthew E. Ritchie
2012 Bioinformatics  
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 ( 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

John N. Weinstein, Uwe Scherf, Jae K. Lee, Satoshi Nishizuka, Fuad Gwadry, Ajay Kim Bussey, S. Kim, Lawrence H. Smith, Lorraine Tanabe, Samuel Richman, Jessie Alexander, Hosein Kouros-Mehr (+2 others)
2001 Cytometry  
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

Jaak Vilo, Katja Kivinen
2001 European Neuropsychopharmacology  
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]

Jizhong Zhou, Dorothea K Thompson
2004 Advances in Agronomy  
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

Sean Thomas, Amanda Green, Nancy R Sturm, David A Campbell, Peter J Myler
2009 BMC Genomics  
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

Hiroto Hatakeyama, Erika Ito, Momoko Yamamoto, Hidetaka Akita, Yasuhiro Hayashi, Kazuaki Kajimoto, Noritada Kaji, Yoshinobu Baba, Hideyoshi Harashima
2011 Molecular Therapy  
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

Sacha Lucchini, Gary Rowley, Martin D. Goldberg, Douglas Hurd, Marcus Harrison, Jay C. D. Hinton
2006 PLoS Pathogens  
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

Todd T Eckdahl, Adam D Brown, Steven N Hart, Kelly J Malloy, Martha Shott, Gloria Yiu, Laura Hoopes, Laurie J Heyer
2008 BMC Genomics  
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

Daniel C Eastwood, Andrew Mead, Martin J Sergeant, Kerry S Burton
2008 BMC Molecular Biology  
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

Derrick K Rollins, Dongmei Zhai, Alrica L Joe, Jack W Guidarelli, Abhishek Murarka, Ramon Gonzalez
2006 BMC Bioinformatics  
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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