ArrayFusion

Category Genomics>Genetic Data Analysis/Tools

Abstract ArrayFusion is a web-based application that can be used for the multi-dimensional analysis of Comparative Genomic Hybridization (CGH), Single Nucleotide Polymorphism (SNP) and microarray data.

ArrayFusion annotates conventional CGH results and various types of microarray data from a range of platforms (cDNA, expression, exon, SNP, array-CGH and ChIP-on-chip) and converts them into standard formats which can be visualized in genome browsers (Affymetrix TM Integrated Genome Browser and GBrowse from the HapMap Project).

Converted files can then be imported simultaneously into a single genome browser to benefit a collective interpretation between different array results.

Implementation of ArrayFusion -- ArrayFusion is built via Java Server Pages (JSP) by the implementation of Struts Action Framework and uses Apache Tomcat as the back-end serve-let container.

The MVC (Model-View-Controller) Model 2 architecture was chosen as the manufacturers design pattern with the intention of utilizing and separating each module into independent pieces, hence the whole system is flexible to grow and maintain.

Powered by the MySQL database server, ArrayFusion maintains and comprises annotations from public databases [HUGO Gene Nomenclature Committee (HGNC) and National Center for Biotechnology Information (NCBI)] and different chip suppliers (Affymetrix and Agilent TM).

The genome assembly for all human arrays is based on NCBI build data.

To ensure that users can continuously analyze different datasets under the same assembly, the manufacturer includes a function to support the conversion between different human genome assemblies.

This is achieved by the LiftOver's chain conversion files from University of California, Santa Cruz (UCSC).

The manufacturer designed a database to store these chain files and developed a LiftOver-like module in Java to convert genome coordinates between assemblies.

Usage and Data Presentation of ArrayFusion --

ArrayFusion can be accessed online freely without registration.

A batch query function is available for NCBI cytological locations, HGNC gene symbols, GenBank or RefSeq mRNA accessions, Ensembl Gene IDs or commercial probe IDs. The required file format should contain IDs separated by a new line.

Users can copy-and-paste gene or array identifiers in the text area or upload a file containing this data. Upon querying the database, annotations are generated by mapping queried IDs to their corresponding chromosomal locations.

In terms of gene symbol queries, the corresponding gene symbol may fall in either ‘Approved Symbol’, ‘Previous Symbols’ or ‘Aliases’ columns in the HGNC database. ArrayFusion will search sequentially until the corresponding gene symbol is found.

After being identified, ArrayFusion maps the genes to represent the RefSeq IDs. The mapping procedure follows the HGNC database design, starting from manually curated RefSeq IDs and then the Entrez Gene mapped entries.

ArrayFusion also assigns the corresponding Affymetrix HG-U133 Plus 2.0 probe-set IDs for queried gene symbols, so that users may compare their cDNA array data with Affymetrix results.

The output file formats include:

(1) a TXT tab-delimited annotation file, which includes combined information for queried IDs.

For Affymetrix exon array annotations, ArrayFusion additionally parses the original ‘Gene Assignment’ columns from the NetAffx Analysis Center and splits them into separate but handy columns;

(2) an EGR format file for the Affymetrix Integrated Genome Browser (IGB); Data viewed in Affymetrix IGB can be further redirected to the UCSC Genome Browser (see G6G Abstract Number 20197), which in turn expands the usage of ArrayFusion;

(3) a GFF format file for the Generic Genome Browser (GBrowse); applied by the HapMap project, for the UCSC Genome Browser, and for the Ensembl's KaryoView.

In addition to chromosome location information, haplotype information from the HapMap public database can also be considered together, thereby helping the interpretation of microarray data and the formation of new hypotheses.

The manufacturer recommends users to use IGB and/or GBrowse to start their analysis.

System Requirements

ArrayFusion is designed to run on Apache Tomcat 5.5.x and requires J2SE 5.0 and later.

Manufacturer

Manufacturer Web Site ArrayFusion

Price Contact manufacturer.

G6G Abstract Number 20319

G6G Manufacturer Number 102873