title: Comparison of univariate and multivariate gene set analysis in acute lymphoblastic leukemia.
abstract: BACKGROUND
  Gene set analysis (GSA) incorporates biological with statistical knowledge to identify gene sets which are differentially expressed that between two or more phenotypes.
  
  
  METHODS
  In this paper gene sets differentially expressed between acute lymphoblastic leukaemia (ALL) with BCR-ABL and those with no observed cytogenetic abnormalities were determined by GSA methods. The BCR-ABL is an abnormal gene found in some people with ALL.
  
  
  RESULTS
  The results of two GSAs showed that the Category test identified 30 gene sets differentially expressed between two phenotypes, while the Hotelling's T2 could discover just 19 gene sets. On the other hand, assessment of common genes among significant gene sets showed that there were high agreement between the results of GSA and the findings of biologists. In addition, the performance of these methods was compared by simulated and ALL data.
  
  
  CONCLUSIONS
  The results on simulated data indicated decrease in the type I error rate and increase the power in multivariate (Hotelling's T2) test as increasing the correlation between gene pairs in contrast to the univariate (Category) test.
authors.affiliation: Department of Epidemiology, Faculty of Public Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Khodakarim
authors.initials: K
authors.lastname: Soheila
authors.forename: Alavimajd
authors.initials: A
authors.lastname: Hamid
authors.forename: Zayeri
authors.initials: Z
authors.lastname: Farid
authors.forename: Rezaee-Tavirani
authors.initials: RT
authors.lastname: Mostafa
authors.forename: Dehghan-Nayeri
authors.initials: DN
authors.lastname: Nasrin
authors.forename: Tabatabaee
authors.initials: T
authors.lastname: Syyed-Mohammad
authors.forename: Tajalli
authors.initials: T
authors.lastname: Vahide
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D005500:Follow-Up Studies; D016044:Fusion Proteins, bcr-abl / Q000235:genetics*; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics* / Q000378:metabolism; D011379:Prognosis
chemical_list: D014408:Biomarkers, Tumor; D016044:Fusion Proteins, bcr-abl