Dataset Information

Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses.

ABSTRACT: Differential expression experiments or other analyses often end in a list of genes. Pathway enrichment analysis is one method to discern important biological signals and patterns from noisy expression data. However, pathway enrichment analysis may perform suboptimally in situations where there are multiple implicated pathways - such as in the case of genes that define subtypes of complex diseases. Our simulation study shows that in this setting, standard overrepresentation analysis identifies many false positive pathways along with the true positives. These false positives hamper investigators' attempts to glean biological insights from enrichment analysis. We develop and evaluate an approach that combines community detection over functional networks with pathway enrichment to reduce false positives. Our simulation study demonstrates that a large reduction in false positives can be obtained with a small decrease in power. Though we hypothesized that multiple communities might underlie previously described subtypes of high-grade serous ovarian cancer and applied this approach, our results do not support this hypothesis. In summary, applying community detection before enrichment analysis may ease interpretation for complex gene sets that represent multiple distinct pathways.

SUBMITTER: Harrington LX

PROVIDER: S-EPMC5760988 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses.

Harrington Lia X LX Way Gregory P GP Doherty Jennifer A JA Greene Casey S CS

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 20180101

Differential expression experiments or other analyses often end in a list of genes. Pathway enrichment analysis is one method to discern important biological signals and patterns from noisy expression data. However, pathway enrichment analysis may perform suboptimally in situations where there are multiple implicated pathways - such as in the case of genes that define subtypes of complex diseases. Our simulation study shows that in this setting, standard overrepresentation analysis identifies ma ...[more]

PMID: 29218878

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Project description:BACKGROUND:Non-alcoholic fatty liver disease (NAFLD) is a common chronic liver illness with a genetically heterogeneous background that can be accompanied by considerable morbidity and attendant health care costs. The pathogenesis and progression of NAFLD is complex with many unanswered questions. We conducted genome-wide association studies (GWASs) using both adult and pediatric participants from the Electronic Medical Records and Genomics (eMERGE) Network to identify novel genetic contributors to this condition. METHODS:First, a natural language processing (NLP) algorithm was developed, tested, and deployed at each site to identify 1106 NAFLD cases and 8571 controls and histological data from liver tissue in 235 available participants. These include 1242 pediatric participants (396 cases, 846 controls). The algorithm included billing codes, text queries, laboratory values, and medication records. Next, GWASs were performed on NAFLD cases and controls and case-only analyses using histologic scores and liver function tests adjusting for age, sex, site, ancestry, PC, and body mass index (BMI). RESULTS:Consistent with previous results, a robust association was detected for the PNPLA3 gene cluster in participants with European ancestry. At the PNPLA3-SAMM50 region, three SNPs, rs738409, rs738408, and rs3747207, showed strongest association (best SNP rs738409 p?=?1.70?×?10-?20). This effect was consistent in both pediatric (p?=?9.92?×?10-?6) and adult (p?=?9.73?×?10-?15) cohorts. Additionally, this variant was also associated with disease severity and NAFLD Activity Score (NAS) (p?=?3.94?×?10-?8, beta?=?0.85). PheWAS analysis link this locus to a spectrum of liver diseases beyond NAFLD with a novel negative correlation with gout (p?=?1.09?×?10-?4). We also identified novel loci for NAFLD disease severity, including one novel locus for NAS score near IL17RA (rs5748926, p?=?3.80?×?10-?8), and another near ZFP90-CDH1 for fibrosis (rs698718, p?=?2.74?×?10-?11). Post-GWAS and gene-based analyses identified more than 300 genes that were used for functional and pathway enrichment analyses. CONCLUSIONS:In summary, this study demonstrates clear confirmation of a previously described NAFLD risk locus and several novel associations. Further collaborative studies including an ethnically diverse population with well-characterized liver histologic features of NAFLD are needed to further validate the novel findings.

Dataset Information

Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses.

Publications

Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses.

Similar Datasets

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