ArticlePloS one2011
Average rank-based score to measure deregulation of molecular pathway gene sets.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Revealing hub pathway cross-talk for premature newborns with bronchopulmonary dysplasia by the integration of pathway analysis and Monte Carlo Cross-Validation.Experimental and therapeutic medicine · 2019Article
- Integrative Analysis with Monte Carlo Cross-Validation Reveals miRNAs Regulating Pathways Cross-Talk in Aggressive Breast Cancer.BioMed research international · 2015Article
- Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis.The Plant cell · 2014Article
- Beyond differential expression: the quest for causal mutations and effector molecules.BMC genomics · 2012Article
- Prediction of breast cancer metastasis by gene expression profiles: a comparison of metagenes and single genes.Cancer informatics · 2012Article
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Authors and funding
3 authors.
Funding
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Abstract
backgroundDeregulation 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.
resultsIn 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.
conclusionsThe 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.
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