ARROGANT: an application to manipulate large gene collections.
ARROGANT (ARRay OrGANizing Tool) is a software tool developed to facilitate the identification, annotation and comparison of large collections of genes or clones. The objective is to enable users to compile gene/clone collections from different databases, allowing them to design experiments and analyze the collections as well as associated experimental data efficiently. ARROGANT can relate different sequence identifiers to their common reference sequence using the UniGene database, allowing for the comparison of data from two different microarray experiments. ARROGANT has been successfully used to analyze microarray expression data for colon cancer, to compile genes potentially related to cardiac diseases for subsequent resequencing (to identify single nucleotide polymorphisms, SNPs), to design a new comprehensive human cDNA microarray for cancer, to combine and compare expression data generated by different microarrays and to provide annotation for genes on custom and Affymetrix chips.
Kulkarni
Amit V
AV
Program in Biomedical Engineering, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.
Williams
Noelle Sevilir
NS
Lian
Yun
Y
Wren
Jonathan D
JD
Mittelman
David
D
Pertsemlidis
Alexander
A
Garner
Harold R
HR
D001483:Base Sequence; D003001:Cloning, Molecular; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D004282:Documentation / Q000379:methods*; D005786:Gene Expression Regulation / Q000235:genetics; D006331:Heart Diseases / Q000235:genetics; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D008969:Molecular Sequence Data; D009369:Neoplasms / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011110:Polymorphism, Genetic / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software