Microarray data analysis

Pmcid: pmc3089881microarray data analysis and mining toolssaravanakumar selvaraj and jeyakumar natarajan*data mining and text mining laboratory, department of bioinformatics, bharathiar university, coimbatore - 641 046, india*jeyakumar natarajan: @r information ► article notes ► copyright and license information ►received 2011 feb 2; accepted 2011 feb ght © 2011 biomedical informaticsthis is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium,For non-commercial purposes, provided the original author and source are article has been cited by other articles in ctmicroarrays are one of the latest breakthroughs in experimental molecular biology that allow monitoring the expression levels of tens of thousands of aneously. In this paper we concentrate on discussing various bioinformatics tools used for microarray data mining tasks with ying algorithms, web resources and relevant reference. We emphasize this paper mainly for digital biologists to get an aware about the plethora of tools ms available for microarray data analysis. First, we report the common data mining applications such as selecting differentially expressed genes, clustering,And classification. Next, we focused on gene expression based knowledge discovery studies such as transcription factor binding site analysis, pathway analysis,Protein- protein interaction network analysis and gene enrichment ds: microarrays, gene expression, microarray data analysis, bioinformatics toolsbackgroundmicroarray is one such technology which enables the researchers to address issues which were once thought to be non traceable by simultaneous measurement of the expression levels of thousands of genes. Microarray is simply a glass slide on which dna molecules are an ordered manner at specific locations called spots or printed on the glass slide by different technologies such ithography to robot spotting. A typical microarray platform and its architecture and flow ential design and data analysis perspective are illustrated microarrays one can analyze the expression of many genes in a on quickly and in an efficient manner. The core principle rrays is hybridization between two dna strands, the property mentary nucleic acid sequences to specifically pair with each other g hydrogen bonds between complementary nucleotide base r, with the generation of large amounts of microarray data, it increasingly important to address the challenges of data quality rdization related to this technology [4]. Recent advancement of rray technology has allowed for a very high resolution mapping somal aberrations with the use of their tiling array ational data analysis tasks such as data mining which fication and clustering used to extract useful knowledge from . In addition, relating gene expression data with other ation; it will provide kind of biological discoveries such as biding site analysis, pathway analysis, and protein- protein k analysis.

In the present paper focus was given on biologist'ctive to get knowledge about the several tools and programs available rray data mining tasks. With this motivation at the end of each task, we provided the list the commonly available tools with ying algorithms, web resources and relevant 1(a) a typical microarray platform and its architecture (b) flow of typical microarray experimental design and data analysis perspectivesmicroarray data analysismicroarray data sets are commonly very large, and analytical precision nced by a number of variables. Clustering is the unsupervised approaches to classify data into groups of genes or similar patterns that are characteristic to the group. There are several univariate statistical methods later to determine either the expression or relative expression of a normalized microarray data, including t tests. Analysisclustering is the most popular method currently used in the first step of sion data matrix analysis. The number and size of expression a data set can be estimated quickly, although the division of the tree clusters is often performed visually. Means clustering is a data mining/machine learning algorithm used to ations into groups of related observations without any prior those relationships [16]. The general data mining and ng application tools are used for classification tasks are illustrated in 3 (see table 3). Discovery with microarray dataclassification, clustering and identification of differential genes can ered as basic microarray data analysis tasks with gene es alone. Some of applications that addressed with gene expression data with ical information are discussed fication of transcription factor binding sitesthe identification of functional elements such as transcription-factor (tfbs) on a whole-genome level is the next challenge for es and gene-regulation studies.

Protein interaction network and pathway analysisprotein-protein interactions (ppi) are useful tools for investigating the ons of genes. Several databases that have been store protein interactions such as the biomolecular interaction se of interacting proteins (dip) [27], intact. Combining well as interacting genes in the same cluster several tions related to gene functions, evolutionary prelateships and sly, the next promising method for rray data is pathway analysis as it involves the cascade of ctions. Analyzing the microarray data in a pathway perspective could a higher level of understanding of the system [32]. Integrates the normalized array data and their annotations, such as metabolic pathways ontology and functional classifications. Metabolic pathway analysis fy more subtle changes in expression than the gene lists that result iate statistical analysis [33]. There are several web based tools ic softwares are available to predict protein interactions and microarray data and are tabulated in table 5 (see table 5). Set enrichment analysisgene set enrichment analysis (gsea) is a computational method ines whether a set of genes shows statistically significant and ences between two biological states. However, innovative statistical techniques ing software are essential for the successful analysis of microarray review shows the current bioinformatics tools and the ations for analyzing data from microarray experiments. The various is perspectives and softwares mentioned in the paper will help ical expertise as a good foundation for computational analysis s:article | pubreader | epub (beta) | pdf (736k) | rray analysis wikipedia, the free to: navigation, has been suggested that this article be merged with gene chip analysis and significance analysis of microarrays.

Discuss) proposed since may e of an approximately 40,000 probe spotted oligo microarray with enlarged inset to show rray analysis techniques are used in interpreting the data generated from experiments on dna, rna, and protein microarrays, which allow researchers to investigate the expression state of a large number of genes - in many cases, an organism's entire genome - in a single experiment. Citation needed] such experiments can generate very large volumes of data, allowing researchers to assess the overall state of a cell or organism. These large data amount can be difficult to analyze, especially in the absence of good gene annotation. Changing any one of the steps will change the outcome of the analysis, so the maqc project[1] was created to identify a set of standard strategies. Microarray manufacturers, such as affymetrix and agilent,[3] provide commercial data analysis software with microarray equipment such as plate ound correction[edit]. A variety of tools for background correction and further analysis are available from tigr,[4] agilent (genespring),[5] and ocimum bio solutions (genowiz). Arrays may have obvious flaws detectable by visual inspection, pairwise comparisons to arrays in the same experimental group, or by analysis of rna degradation. 7] results may improve by removing these arrays from the analysis identification of local artifacts, such as printing or washing defects, may likewise suggest the removal of individual spots. 8] a common method for evaluating how well normalized an array is, is to plot an ma plot of the affy data contains about twenty probes for the same rna target. Analysis for robust microarray summarization (farms)[13] is a model-based technique for summarizing array data at perfect match probe level.

It is based on a factor analysis model for which a bayesian maximum a posteriori method optimizes the model parameters under the assumption of gaussian measurement noise. Systems for gene network analysis such as ingenuity[17] and pathway studio[18] create visual representations of differentially expressed genes based on current scientific literature. Non-commercial tools such as funrich,[19] genmapp and moksiskaan also aid in organizing and visualizing gene network data procured from one or several microarray experiments. A wide variety of microarray analysis tools are available through bioconductor written in the r programming language. The frequently cited sam excel module and other microarray tools[20] are available through stanford university. Software tools for statistical analysis to determine the extent of over- or under-expression of a gene in a microarray experiment relative to a reference state have also been developed to aid in identifying genes or gene sets associated with particular phenotypes. One such method of analysis, known as gene set enrichment analysis (gsea), uses a kolmogorov-smirnov-style statistic to identify groups of genes that are regulated together. 22] this third-party statistics package offers the user information on the genes or gene sets of interest, including links to entries in databases such as ncbi's genbank and curated databases such as biocarta[23] and gene ontology. Protein complex enrichment analysis tool (compleat) provides similar enrichment analysis at the level of protein complexes. Related system, paint[25] and scope[26] performs a statistical analysis on gene promoter regions, identifying over and under representation of previously identified transcription factor response elements.

Another statistical analysis tool is rank sum statistics for gene set collections (rssgsc), which uses rank sum probability distribution functions to find gene sets that explain experimental data. Genevestigator is a public tool to perform contextual meta-analysis across contexts such as anatomical parts, stages of development, and response to diseases, chemicals, stresses, and icance analysis of microarrays. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias". The microarray quality control (maqc) project shows inter- and intraplatform reproducibility of gene expression measurements". Retrieved xplorer - compare microarray side by side to find the one that best suits your research - factor analysis for robust microarray summarization, an r package —rray - online microarray analysis services —h - perform gene set enrichment analysis —ries: microarraysbioinformatics algorithmshidden categories: articles to be merged from may 2017all articles to be mergedall articles with unsourced statementsarticles with unsourced statements from february logged intalkcontributionscreate accountlog pagecontentsfeatured contentcurrent eventsrandom articledonate to wikipediawikipedia out wikipediacommunity portalrecent changescontact links hererelated changesupload filespecial pagespermanent linkpage informationwikidata itemcite this a bookdownload as pdfprintable page was last edited on 11 september 2017, at 10: is available under the creative commons attribution-sharealike license;. In microarray experiments, collected from each spot is used to estimate the expression level of . A microarray contains thousands of dna spots, covering almost every first high-throughput technology for gene expression is rna-sequencing. Both of them can monitor expression levels of thousands number of published ing to microarray -seq (in their titles sion data expression data y presented in an expression matrix. Each rectangle represents t of the expression chical chical clustering is the most popular method expression data analysis. Template expression y a template expression ate correlation template and each gene in the data for genes with similar expression pattern to the template (te matching is particularly useful when cher is searching for genes with a specific expression xperiment viewer (mev).

Use the file menu to open a new multiple array load data from the file menu the file-loading dialog. Color bar is displayed along the right side : k-means / k-medians of clusters = of iterations = nature genetics special issues rray analysis: the chipping forecast i, ii, s genetics article series of next generation date: february 17. K-means clustering method (euclidean ) to group the 16 samples into two r 1: sample 1, 3,5,7,9,11,13,r 2: sample 2,4,6,8,10,12,14, should be included in the email:Large scale gene expression data analysis cui (ycui2@). K-means clustering method (euclidean ) to group the 16 samples into two r 1: sample 1, 3,5,7,9,11,13,r 2: sample 2,4,6,8,10,12,14, should be included in the email:Popular genomics genotyping -human genotyping ation array ation array data analysis rray data studio rray probe for microarray expression array analysis. Microarray data rray software tools to ensure optimal rray data analysis and experimental ew of microarray microarray software offerings include tools that facilitate analysis of microarray data, and enable array experimental design and sample tracking. These solutions ensure optimal time-to-answer, so you can spend more time doing research, and less time designing probes, managing samples, and configuring complex microarray data analysis rray data analysis convert microarray data into meaningful results with these analysis tools:Genomestudio studio software enables you to visualize and analyze microarray data generated on illumina platforms. The software package is composed of discrete application modules that enable you to obtain a comprehensive view of the genome, gene expression, and gene genomestudio e software offers a direct path to reduce experimental microarray data size and facilitate data analysis for large experiments. As the size of array data sets increases, the time required to calculate sample statistics and visually interrogate clusters has become prohibitive. Beeline software addresses this bottleneck by enabling pre-filtering of large data sets prior to import into beeline design for array studio is an online software tool for designing custom illumina genotyping array probes. Create assays tailored directly to specific needs for applications such as targeted region genotyping and fine more about array probe for microarray illumina laboratory information management system (lims) provides positive array sample tracking and component verification.

It also enables project and data management, lab workflow management, and reporting for illumina genotyping array sted in receiving newsletters, case studies, and information on genomic analysis techniques? Enter your email to analyze microarray online training to learn how to analyze data with illumina microarray rray software array software user guides, downloads, and other technical array software zing genotyping microarray data out how to analyze genotyping array data more sion array data how to ascertain gene expression microarray data quality and identify outlier genotyping non-human genotyping gene expression array ation array analysis microarray data analysis.