ArticlePloS one2008
SLEPR: a sample-level enrichment-based pathway ranking method -- seeking biological themes through pathway-level consistency.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Article
- Clinical cancer research : an official journal of the American Association for Cancer Research · 2018Article
- Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples.BMC genomics · 2015Article
- ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion.Nucleic acids research · 2015Article
- Systems analysis utilising pathway interactions identifies sonic hedgehog pathway as a primary biomarker and oncogenic target in hepatocellular carcinoma.IET systems biology · 2013Article
- Silencing of miR-148a in cancer-associated fibroblasts results in WNT10B-mediated stimulation of tumor cell motility.Oncogene · 2013Article
- Comparison of methods to identify aberrant expression patterns in individual patients: augmenting our toolkit for precision medicine.Genome medicine · 2013Article
- Perturbation of Rb, p53, and Brca1 or Brca2 cooperate in inducing metastatic serous epithelial ovarian cancer.Cancer research · 2012Article
- Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types.Genome medicine · 2012Article
- Associations between HIV and human pathways revealed by protein-protein interactions and correlated gene expression profiles.PloS one · 2012Article
- The role of miR-31 and its target gene SATB2 in cancer-associated fibroblasts.Cell cycle (Georgetown, Tex.) · 2010Article
- Functional analysis: evaluation of response intensities--tailoring ANOVA for lists of expression subsets.BMC bioinformatics · 2010Article
- Pandora, a pathway and network discovery approach based on common biological evidence.Bioinformatics (Oxford, England) · 2010Article
- Evidence for gender-specific transcriptional profiles of nigral dopamine neurons in Parkinson disease.PloS one · 2010Article
- Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis.BMC bioinformatics · 2009Article
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2 authors.
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Abstract
Analysis of microarray and other high throughput data often involves identification of genes consistently up or down-regulated across samples as the first step in extraction of biological meaning. This gene-level paradigm can be limited as a result of valid sample fluctuations and biological complexities. In this report, we describe a novel method, SLEPR, which eliminates this limitation by relying on pathway-level consistencies. Our method first selects the sample-level differentiated genes from each individual sample, capturing genes missed by other analysis methods, ascertains the enrichment levels of associated pathways from each of those lists, and then ranks annotated pathways based on the consistency of enrichment levels of individual samples from both sample classes. As a proof of concept, we have used this method to analyze three public microarray datasets with a direct comparison with the GSEA method, one of the most popular pathway-level analysis methods in the field. We found that our method was able to reproduce the earlier observations with significant improvements in depth of coverage for validated or expected biological themes, but also produced additional insights that make biological sense. This new method extends existing analyses approaches and facilitates integration of different types of HTP data.
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