共查询到20条相似文献,搜索用时 15 毫秒
1.
Background
High-throughput genotyping microarrays assess both total DNA copy number and allelic composition, which makes them a tool of choice for copy number studies in cancer, including total copy number and loss of heterozygosity (LOH) analyses. Even after state of the art preprocessing methods, allelic signal estimates from genotyping arrays still suffer from systematic effects that make them difficult to use effectively for such downstream analyses. 相似文献2.
Cheng Li 《BMC bioinformatics》2008,9(1):231
Background
During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, challenges arise when dChip users want to analyze large number of arrays automatically and share data analysis procedures and parameters. Improvement is also needed when the dChip user support team tries to identify the causes of reported analysis errors or bugs from users. 相似文献3.
4.
Roel GW Verhaak Frank JT Staal Peter JM Valk Bob Lowenberg Marcel JT Reinders Dick de Ridder 《BMC bioinformatics》2006,7(1):105-15
Background
Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RMA and MAS have been developed for this purpose. This study assesses the effect of applying different pre-processing methods on the results of analyses of large Affymetrix datasets. By focusing on practical applications of microarray-based research, this study provides insight into the relevance of pre-processing procedures to biology-oriented researchers. 相似文献5.
Background
Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed microarrays, which are composed of DNA from more than one organism, are more effective than conventional microarrays composed of DNA from a single organism. Selection of probes is a key factor in designing successful mixed microarrays because redundant sequences are inefficient and limited representation of diversity can restrict application of the microarray. We have developed a Java-based software tool, called PLASMID, for use in selecting the minimum set of probe sequences needed to classify different groups of plasmids or bacteria. 相似文献6.
Background
cDNA microarrays are a powerful means to screen for biologically relevant gene expression changes, but are often limited by their ability to detect small changes accurately due to "noise" from random and systematic errors. While experimental designs and statistical analysis methods have been proposed to reduce these errors, few studies have tested their accuracy and ability to identify small, but biologically important, changes. Here, we have compared two cDNA microarray experimental design methods with northern blot confirmation to reveal changes in gene expression that could contribute to the early antiproliferative effects of neuregulin on MCF10AT human breast epithelial cells. 相似文献7.
Paschall JE Oleksiak MF VanWye JD Roach JL Whitehead JA Wyckoff GJ Kolell KJ Crawford DL 《BMC genomics》2004,5(1):96
Background
While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. 相似文献8.
Background
Clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome sequence is not available. Since the generation of a genomic DNA library is a random process, it is beforehand uncertain which genes are represented. Nevertheless, the genome coverage of such an array, which depends on different variables like the insert size and the number of clones in the library, can be predicted by mathematical approaches. When applying the classical formulas that determine the probability that a certain sequence is represented in a DNA library at the nucleotide level, massive amounts of clones would be necessary to obtain a proper coverage of the genome. 相似文献9.
Background
The MAQC project demonstrated that microarrays with comparable content show inter- and intra-platform reproducibility. However, since the content of gene databases still increases, the development of new generations of microarrays covering new content is mandatory. To better understand the potential challenges updated microarray content might pose on clinical and biological projects we developed a methodology consisting of in silico analyses combined with performance analysis using real biological samples. 相似文献10.
Background
Functional analysis of data from genome-scale experiments, such as microarrays, requires an extensive selection of differentially expressed genes. Under many conditions, the proportion of differentially expressed genes is considerable, making the selection criteria a balance between the inclusion of false positives and the exclusion of false negatives. 相似文献11.
Background
An important goal of whole-genome studies concerned with single nucleotide polymorphisms (SNPs) is the identification of SNPs associated with a covariate of interest such as the case-control status or the type of cancer. Since these studies often comprise the genotypes of hundreds of thousands of SNPs, methods are required that can cope with the corresponding multiple testing problem. For the analysis of gene expression data, approaches such as the empirical Bayes analysis of microarrays have been developed particularly for the detection of genes associated with the response. However, the empirical Bayes analysis of microarrays has only been suggested for binary responses when considering expression values, i.e. continuous predictors. 相似文献12.
Hualing Li Changhong Ren Jinping Shi Xingyi Hang Feilong Zhang Yan Gao Yonghong Wu Langlai Xu Changsheng Chen Chenggang Zhang 《Proteome science》2010,8(1):49
Background
The nematode Caenorhabditis elegans is both sensitive and tolerant to hypoxic stress, particularly when the evolutionarily conserved hypoxia response pathway HIF-1/EGL-9/VHL is involved. Hypoxia-induced changes in the expression of a number of genes have been analyzed using whole genome microarrays in C. elegans, but the changes at the protein level in response to hypoxic stress still remain unclear. 相似文献13.
14.
Matthew N McCall Peter N Murakami Margus Lukk Wolfgang Huber Rafael A Irizarry 《BMC bioinformatics》2011,12(1):137
Background
Microarray technology has become a widely used tool in the biological sciences. Over the past decade, the number of users has grown exponentially, and with the number of applications and secondary data analyses rapidly increasing, we expect this rate to continue. Various initiatives such as the External RNA Control Consortium (ERCC) and the MicroArray Quality Control (MAQC) project have explored ways to provide standards for the technology. For microarrays to become generally accepted as a reliable technology, statistical methods for assessing quality will be an indispensable component; however, there remains a lack of consensus in both defining and measuring microarray quality. 相似文献15.
16.
Jun Wu Qingchao Qiu Lu Xie Joseph Fullerton Jian Yu Yu Shyr Alfred L George Yajun Yi 《BMC bioinformatics》2009,10(1):420
Background
Widespread use of high-throughput techniques such as microarrays to monitor gene expression levels has resulted in an explosive growth of data sets in public domains. Integration and exploration of these complex and heterogeneous data have become a major challenge. 相似文献17.
Background
The quality of microarray data can seriously affect the accuracy of downstream analyses. In order to reduce variability and enhance signal reproducibility in these data, many normalization methods have been proposed and evaluated, most of which are for data obtained from cDNA microarrays and Affymetrix GeneChips. CodeLink Bioarrays are a newly emerged, single-color oligonucleotide microarray platform. To date, there are no reported studies that evaluate normalization methods for CodeLink Bioarrays. 相似文献18.
Background
To provide a broad analysis of gene expression changes in developing embryos from a solanaceous species, we produced amplicon-derived microarrays with 7741 ESTs isolated from Solanum chacoense ovules bearing embryos from all developmental stages. Our aims were to: 1) identify genes expressed in a tissue-specific and temporal-specific manner; 2) define clusters of genes showing similar patterns of spatial and temporal expression; and 3) identify stage-specific or transition-specific candidate genes for further functional genomic analyses. 相似文献19.
Detecting variants with Metabolic Design,a new software tool to design probes for explorative functional DNA microarray development 总被引:1,自引:0,他引:1
Sébastien Terrat Eric Peyretaillade Olivier Gonçalves Eric Dugat-Bony Fabrice Gravelat Anne Moné Corinne Biderre-Petit Delphine Boucher Julien Troquet Pierre Peyret 《BMC bioinformatics》2010,11(1):478
Background
Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex environments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes. 相似文献20.
Alberto Biscontin Silvia Casara Stefano Cagnin Lucia Tombolan Angelo Rosolen Gerolamo Lanfranchi Cristiano De Pittà 《BMC molecular biology》2010,11(1):44