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  • BIL gate: A step toward a biological computer

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  • Web Server Issue of Nucleic Acids Research presents new free Array Analysis tools

    Nucleic Acids Research devotes a single issue in July to papers describing web-based software resources of value to the biological community.

    The emphasis of the current issue is on network and pathway analysis, high-throughput sequencing data analysis and biological text mining.



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Nucleic Acids Research (NAR) dedicates a special issue in July to papers and contents describing web-based software reources of value to the biological community.

"The Web Server Issue contains papers describing software programs that run on the web and provide useful computations on DNA, RNA and protein sequences or structures; network and pathway analysis; biological text mining; analysis of high throuhput sequencing data, metagenomics data and microarray data; tools for synthetic biology and innovative visualizations".

Ninety-five new web-based genomic data-analysis resources are discussed in the special issue of NAR; here we describe five among tools featured in the new issue: ArrayAnalysis, a tool for microarray quality control and pre-processing; TMA Navigator, a web application for the analysis of tissue microarray data; PATHiWAYS, a pathway visualization system; Graphite Web, a tool for gene set analysis that exploits pathway topology; and PlantGSEA, a web server focused on plant organisms. 


A team of Maastricht University bioinformaticians created this ArrayAnalysis tool. In the NAR paper the authors describe that while quality control (QC) is crucial for any scientific method to produce data, adoption of algorithms for QC, pre-processing, and normalization of  Affymetrix expression chips (many of which are available through Bioconductor for use with the statistical interface R), on the other hand it has been "hampered by lack of integrative tools that can be used by users of any experience level".

The authors created ArrayAnalysis "to fill this gap by extending, integrating and harmonizing" the functionality of various Bioconductor package. The portal includes interpretation help and detailed technical documentation with the ultimate aim of "improving data quality and reuse, and adoption of standards".

Resource: Nucleic Acids Res. 2013 Jul 1; 41(W1): W71-W76. Epub 2013 Apr 24.

TMA Navigator

Bioinformaticians at the Institute of Genetics and Molecular Medicine of the University of Edinburgh developed a software tool called TMA Navigator. This tool is for scientists running tissue microarrays which allow multiplexed analysis of tissue samples and are frequently used to estimate biomarker protein expression in tumor biopsies. The major strenght of the TMA Navigator approach is that it allows "hypothesis-driven and exploratory analysis of TMA data in a non-biased, data-led manner". As authors also state, "Users need no specialist computational or statistical knowledge to use the service and the user guide provides guidance with interpretation".

Resource: Nucleic Acids Res. 2013 Jul 1; 41(Web Server issue): W562-8. doi:10.1093/nar/gkt529. Epub 2013 Jun 12


PATHiWAYS was developed in the lab of Joaquin Dopazo in the department of Computational Genomics at the Centro de Investigacion Principe Felipe in Valencia, Spain.

PATHiWAYS is a web-based signaling pathway visualization system, that infers changes in signaling that affect cell functionality by the measurements of gene-expression values in typical expression microarray case-control experiments.

"The PATHiWAYS algorithms transforms the abstract and context-less parameter of gene expression level into a meaningful value: the probability of signal transmission in a pathway or, in other words, the capability of the cell to trigger a funcionality ae response to a particular stimulus", Dopazo said.

Resource: Nucleic Acids Res. 2013 Jul 1; 41(Web Server issue): W213-7. doi: 10.1093/nar/gkt451. Epub 2013 Jun 8.

Graphite Web

The University of Padua developed Graphite Web, a web tool for pathway analyses and network visualization of gene expression data.

Graphite Web allows the analysis of both microarray and RNA-seq data. This tool is a public web server for pathway analysis on gene expression data that combines topological/multivariate pathway analysis with an efficient system of interactive network visualizations for easy results interpretation. Graphite Web implements five different gene set analyses on three model organisms and two pathway databases.

Resource: Nucleic Acids Res. 2013 Jul 1; 41(Web Server issue): W89-97. doi:10.1093/nar/gkt386. Epub 2013 May 10.


The Plant GeneSet Enrichment Analysis Toolkit (PlantGSEA) is an online web server for gene set enrichment analysis of plant organisms developed by Zhen Su Lab in China Agricultural University.

PlantGSEA is a powerful method for determining wheter a set of genes defined a priori shows statistically significant differences between two phenotypes. PlantGSEA is based on the GSEA method and mainly focuses on plant organisms; it relies on 20.290 defined gene sets derived from different resouces. The PlantGSEA currently supports gene locus IDs and Afflymetrix microarray probe set IDs from four plant model species (Arabidopsis thaliana, Oryza sativa, Zea mays and Gossypium raimondii).

Resource: Nucleic Acids Res. 2013 Jul 1; 41(Web Server issue): W98-W103. doi: 10.1093/nar/gkt281. Epub 2013 Apr 30.

By Sara Caragnulo, AllBioinformatics editorial staff on 03/07/2013

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