Dataset Information

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data.

ABSTRACT:

Background

Analysis of High Throughput (HTP) Data such as microarray and proteomics data has provided a powerful methodology to study patterns of gene regulation at genome scale. A major unresolved problem in the post-genomic era is to assemble the large amounts of data generated into a meaningful biological context. We have developed a comprehensive software tool, WholePathwayScope (WPS), for deriving biological insights from analysis of HTP data.

Result

WPS extracts gene lists with shared biological themes through color cue templates. WPS statistically evaluates global functional category enrichment of gene lists and pathway-level pattern enrichment of data. WPS incorporates well-known biological pathways from KEGG (Kyoto Encyclopedia of Genes and Genomes) and Biocarta, GO (Gene Ontology) terms as well as user-defined pathways or relevant gene clusters or groups, and explores gene-term relationships within the derived gene-term association networks (GTANs). WPS simultaneously compares multiple datasets within biological contexts either as pathways or as association networks. WPS also integrates Genetic Association Database and Partial MedGene Database for disease-association information. We have used this program to analyze and compare microarray and proteomics datasets derived from a variety of biological systems. Application examples demonstrated the capacity of WPS to significantly facilitate the analysis of HTP data for integrative discovery.

Conclusion

This tool represents a pathway-based platform for discovery integration to maximize analysis power. The tool is freely available at http://www.abcc.ncifcrf.gov/wps/wps_index.php.

SUBMITTER: Yi M

PROVIDER: S-EPMC1388242 | biostudies-literature | 2006 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data.

Yi Ming M Horton Jay D JD Cohen Jonathan C JC Hobbs Helen H HH Stephens Robert M RM

BMC bioinformatics 20060119

<h4>Background</h4>Analysis of High Throughput (HTP) Data such as microarray and proteomics data has provided a powerful methodology to study patterns of gene regulation at genome scale. A major unresolved problem in the post-genomic era is to assemble the large amounts of data generated into a meaningful biological context. We have developed a comprehensive software tool, WholePathwayScope (WPS), for deriving biological insights from analysis of HTP data.<h4>Result</h4>WPS extracts gene lists w ...[more]

PMID: 16423281

Similar Datasets

Project description:BackgroundBisulfite sequencing is one of the most widely used technologies in analyzing DNA methylation patterns, which are important in understanding and characterizing the mechanism of DNA methylation and its functions in disease development. Efficient and user-friendly tools are critical in carrying out such analysis on high-throughput bisulfite sequencing data. However, existing tools are either not scalable well, or inadequate in providing visualization and other desirable functionalities.ResultsIn order to handle ultra large sequencing data and to provide additional functions and features, we have developed BSPAT, a fast online tool for bisulfite sequencing pattern analysis. With a user-friendly web interface, BSPAT seamlessly integrates read mapping/quality control/methylation calling with methylation pattern generation and visualization. BSPAT has the following important features: 1) instead of using multiple/pairwise sequence alignment methods, BSPAT adopts an efficient and widely used sequence mapping tool to provide fast alignment of sequence reads; 2) BSPAT summarizes and visualizes DNA methylation co-occurrence patterns at a single nucleotide level, which provide valuable information in understanding the mechanism and regulation of DNA methylation; 3) based on methylation co-occurrence patterns, BSPAT can automatically detect potential allele-specific methylation (ASM) patterns, which can greatly enhance the detection and analysis of ASM patterns; 4) by linking directly with other popular databases and tools, BSPAT allows users to perform integrative analysis of methylation patterns with other genomic features together within regions of interest.ConclusionBy utilizing a real bisulfite sequencing dataset generated from prostate cancer cell lines, we have shown that BSPAT is highly efficient. It has also reported some interesting methylation co-occurrence patterns and a potential allele-specific methylation case. In conclusion, BSPAT is an efficient and convenient tool for high-throughput bisulfite sequencing data analysis that can be broadly used.

Project description:BackgroundNext-generation sequencing (NGS) has been widely used in both clinics and research. It has become the most powerful tool for diagnosing genetic disorders and investigating disease etiology through the discovery of genetic variants. Variants identified by NGS are stored in variant call format (VCF) files. However, querying and filtering VCF files are extremely difficult for researchers without programming skills. Furthermore, as the mutation data are increasing exponentially, there is an urgent need to develop tools to manage these variant data in a centralized way.MethodsThe VCF-Server was developed as a web-based visualization tool to support the interactive analysis of genetic variant data. It allows researchers and medical geneticists to manage, annotate, filter, query, and export variants in a fast and effective way.ResultsIn this study, we developed the VCF-Server, a powerful and easily accessible tool for researchers and medical geneticists to perform variant analysis. Users can query VCFs, annotate, and filter variants without knowing programming code. Once the VCF file is uploaded, VCF-Server allows users to annotate the VCF with commonly used databases or user-defined variant annotations (including variant blacklist and whitelist). Variant information in the VCF is shown visually via the interactive graphical interface. Users can filter the variants with flexible filtering rules, and the prioritized variants can be exported locally for further analysis. As VCF-Server adopts a web file system, files in the VCF-Server can be stored and managed in a centralized way. Moreover, VCF-Server allows direct web-based analysis (accessible through either desktop computers or mobile devices) as well as local deployment.ConclusionsWith an easy-to-use graphical interface, VCF-Server allows researchers with little bioinformatics background to explore and mine mutation data, which may broaden the application of NGS technology in clinics and research. The tool is freely available for use at https://www.diseasegps.org/VCF-Server?lan = eng.

Project description:BACKGROUND: As microbial ecologists take advantage of high-throughput sequencing technologies to describe microbial communities across ever-increasing numbers of samples, new analysis tools are required to relate the distribution of microbes among larger numbers of communities, and to use increasingly rich and standards-compliant metadata to understand the biological factors driving these relationships. In particular, the Earth Microbiome Project drives these needs by profiling the genomic content of tens of thousands of samples across multiple environment types. FINDINGS: Features of EMPeror include: ability to visualize gradients and categorical data, visualize different principal coordinates axes, present the data in the form of parallel coordinates, show taxa as well as environmental samples, dynamically adjust the size and transparency of the spheres representing the communities on a per-category basis, dynamically scale the axes according to the fraction of variance each explains, show, hide or recolor points according to arbitrary metadata including that compliant with the MIxS family of standards developed by the Genomic Standards Consortium, display jackknifed-resampled data to assess statistical confidence in clustering, perform coordinate comparisons (useful for procrustes analysis plots), and greatly reduce loading times and overall memory footprint compared with existing approaches. Additionally, ease of sharing, given EMPeror's small output file size, enables agile collaboration by allowing users to embed these visualizations via emails or web pages without the need for extra plugins. CONCLUSIONS: Here we present EMPeror, an open source and web browser enabled tool with a versatile command line interface that allows researchers to perform rapid exploratory investigations of 3D visualizations of microbial community data, such as the widely used principal coordinates plots. EMPeror includes a rich set of controllers to modify features as a function of the metadata. By being specifically tailored to the requirements of microbial ecologists, EMPeror thus increases the speed with which insight can be gained from large microbiome datasets.

Dataset Information

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data.

Background

Result

Conclusion

Publications

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets