title: Average rank-based score to measure deregulation of molecular pathway gene sets.
abstract: BACKGROUND
  Deregulation of biological pathways has been shown to be involved in the turmorigenesis of a variety of cancers. The co-regulation of pathways in tumor and normal tissues has not been studied in a systematic manner.
  
  
  RESULTS
  In this study we propose a novel statistic named AR-score (average rank based score) to measure pathway activities based on microarray gene expression profiles. We calculate and compare the AR-scores of pathways in microarray datasets containing expression profiles for a wide range of cancer types as well as the corresponding normal tissues. We find that many pathways undergo significant activity changes in tumors with respect to normal tissues. AR-scores for a small subset of pathways are capable of distinguishing tumor from normal tissues or classifying tumor subtypes. In normal tissues many pathways are highly correlated in their activities, whereas their correlations reduce significantly in tumors and cancer cell lines. The co-expression of genes in the same pathways was also significantly perturbed in tumors.
  
  
  CONCLUSIONS
  The co-regulation of genes in the same pathways and co-regulation of different pathways are significantly perturbed in tumors versus normal tissues. Our method provides a useful tool for better understanding the mechanistic changes in tumors, which can also be used for exploring other biological problems.
authors.affiliation: Department of Reproductive Endocrinology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China.
authors.forename: Huan
authors.initials: H
authors.lastname: Yang
authors.forename: Chao
authors.initials: C
authors.lastname: Cheng
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics / Q000502:physiology; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology
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