My Microarray Software Comparison - Data
Annotation Software
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Definition of data
annotation software
Suggested readings
Data
annotation software (in alphabetical order)
[ ARROGANT | DAVID | DRAGON
(Database Referencing of Array Genes ONline) | EASE | FANTOM (Functional
Annotation of Mouse) | GoMiner | MatchMiner | Onto-Express | RESOURCERER ]
Referencing database
[ GenBank | Gene
Ontology | SWISS-PROT ]
Definition of data
annotation software
Annotation software annotates the genes on the array by
cross-referencing to public databases like Gene Ontology. This type of
software as well as a lot of turnkey
systems and comprehensive
software provide different levels of annotation functions.
Suggested readings
- Jenssen TK, Laegreid A, Komorowski J, Hovig E. A literature
network of human genes for high-throughput analysis of gene expression.
Nat Genet. 2001 May;28(1):21-28. [PubMed]
Data
annotation software (in alphabetical order)
- ARROGANT - Array
Organizing Tool (ARROGANT) is a software tool developed to facilitate
the identification, annotation and comparison of large collections of
genes or clones. ARROGANT enables users to compile gene/clone
collections from a variety of different databases, to devise
experiments
and analyze the collections as well as associated experimental data in
an efficient manner. Reference [PubMed]
- DAVID
- DAVID is a web-based, client/server application that allows
users to access a relational database of functional annotation.
Functional annotations are derived primarily from LocusLink at the
National Center for Biotechnology Information (NCBI). DAVID uses
LocusLink accession numbers to link gene accessioning systems like
Genbank, Unigene, and Affymetrix identifiers to biological annotations
including gene names and aliases, functional summaries, Gene
Ontologies, protein domains, and biochemical and signal transduction
pathways. Annotation pedigrees are provided via direct links to
the primary sources of annotation, which also provide additional gene
specific information. Reference [PubMed][pdf]
- DRAGON (Database
Referencing of Array Genes ONline) - Dragon lets you upload
your microarray data, annotate and visualize the position and
expression
level of genes in cellular pathways. Reference [PubMed]
- EASE - EASE
is a customizable, standalone software application that facilitates the
biological interpretation of gene lists derived from the results of
microarray, proteomic, and SAGE experiments. EASE provides
statistical methods for discovering enriched biological themes within
gene lists, generates gene annotation tables, and enables automated
linking to online analysis tools. Reference [PubMed][pdf]
- FANTOM (Functional
Annotation of Mouse) - The FANTOM is a collection of
functional annotations for the RIKEN full-length cDNA clones.
- GoMiner -
GoMiner batch-processes and organizes lists of thousands or tens of
thousands of genes and provides two fluent, robust visualizations of
the
genes in the framework of the Gene Ontology hierarch. Reference [PubMed][pdf]
- MatchMiner
- a set of tools that enables
the user to translate between disparate ids for the same gene. It uses
data from the UCSC, LocusLink, Unigene and OMIM data sources to
determine how different ids relate. Supported id types include, gene
symbols and names, IMAGE and FISH clones, GenBank accession numbers
and UniGene cluster ids. Reference [PubMed][pdf]
- Onto-Express
- automatically translate differentially regulated genes into
functional
profiles (using Gene Ontology terms) characterizing the impact of the
condition studied. Reference 1 [PubMed],
Reference 2 [PubMed]
- RESOURCERER
- provides annotation based on the TIGR
Gene Indices (TGI) for commonly available microarray resources
Referencing database
- GenBank
- Gene Ontology - The
objective of GO is to provide controlled vocabularies for the
description of the molecular function, biological process and cellular
component of gene products.These terms are to be used as attributes of
gene products by collaborating databases, facilitating uniform queries
across them.
- SWISS-PROT - SWISS-PROT
is a curated protein sequence database which strives to provide a high
level of annotations (such as the description of the function of a
protein, its domains structure, post-translational modifications,
variants, etc.), a minimal level of redundancy and high level of
integration with other databases
last updated: 20 Jul 2003
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