AGRA: analysis of gene ranking algorithms

Simon Kocbek (Author), Rune Saetre (Author), Gregor Štiglic (Author), Jin-Dong Kim (Author), Igor Pernek (Author), Yoshimasa Tsuruoka (Author), Peter Kokol (Author), Sophia Ananiadou (Author), Jun-ichi Tsujii (Author)

Abstract

Often, the most informative genes have to be selected from different gene setsand several computer gene ranking algorithms have been developed to cope with the problem. To help researchers decide which algorithm to use, we developed the Analysis of Gene Ranking Algorithms (AGRA) system that offers a novel technique for comparing ranked lists of genes. The most important feature of AGRA is that no previous knowledge of gene ranking algorithms is needed for their comparison. Using the text mining system FACTA (Tsuruoka et al., 2008), AGRA defines what we call Biomedical Concept Space (BCS) for each gene list and offers comparison of the gene lists in six different BCS categories. The uploaded gene lists can be compared using two different methods. In the first method, the overlap between each pair of two gene lists of BCSs is calculated. The second method offers a text field where specific biomedical concept can be entered. AGRA searches for this concept in each genelistsć BCS, highlights the rank of the concept and offers a visual representation of concepts ranked above and below it.

Keywords

genetic algorithms;

Data

Language:	English
Year of publishing:	2011
Typology:	1.01 - Original Scientific Article
Organization:	UM FZV - Faculty of Health Sciences
UDC:	004.8:575
COBISS:	1676708
ISSN:	1367-4803
Views:	1620
Downloads:	113
Average score:	0 (0 votes)
Metadata:

Other data

Secondary language:	English
Secondary keywords:	genetski algoritmi;
URN:	URN:SI:UM:
Pages:	str. 1185-1186
Volume:	ǂVol. ǂ27
Issue:	ǂno. ǂ8
Chronology:	2011
Keywords (UDC):	science and knowledge;organization;computer science;information;documentation;librarianship;institutions;publications;znanost in znanje;organizacije;informacije;dokumentacija;bibliotekarstvo;institucije;publikacije;prolegomena;fundamentals of knowledge and culture;propaedeutics;prolegomena;splošne osnove znanosti in kulture;computer science and technology;computing;data processing;računalniška znanost in tehnologija;računalništvo;obdelava podatkov;artificial intelligence;umetna inteligenca;mathematics;natural sciences;naravoslovne vede;matematika;biological sciences in general;biologija;general genetics;general cytogenetics;splošna genetika;splošna citogenetika;
DOI:	10.1093/bioinformatics/btr097
ID:	14780