The multi-reference contrast method: facilitating set enrichment analysis.
Set enrichment analysis (SEA) is used to identify enriched biological categories/terms within high-throughput differential expression experiments. This is done by evaluating the proportion of differentially expressed genes against a background reference (BR). However, the choice of the "appropriate" BR is a perplexing problem and results will depend on it. Here, a visualization procedure that integrates results from several BRs and a stability analysis of enriched terms is presented as a tool to aid SEA. The multi-reference contrast method (MRCM) combines results from multiple BRs in a unique picture. The application of the proposed method was illustrated in one proteomic and three microarray experiments. The MRCM facilitates the exploration task involved in ontology analysis on proteomic/genomic experiments, where consensus terms were found to validate main experimental hypothesis. The use of more than one reference may provide new biological insights. The tool automatically highlights non-consensus terms assisting SEA.
BioScience Data Mining Group, Catholic University of Córdoba, Córdoba, Argentina.
Cristóbal
C
Fresno
Andrea S
AS
Llera
María R
MR
Girotti
María P
MP
Valacco
Juan A
JA
López
Osvaldo L
OL
Podhajcer
Mónica G
MG
Balzarini
Federico
F
Prada
Elmer A
EA
Fernández
D000818:Animals; D016000:Cluster Analysis; D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D015180:Electrophoresis, Gel, Two-Dimensional; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D008962:Models, Theoretical; D020411:Oligonucleotide Array Sequence Analysis; D040901:Proteomics; D009626:Terminology as Topic