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Network-based prediction of polygenic disease genes involved in cell motility.


ABSTRACT:

Background

Schizophrenia and autism are examples of polygenic diseases caused by a multitude of genetic variants, many of which are still poorly understood. Recently, both diseases have been associated with disrupted neuron motility and migration patterns, suggesting that aberrant cell motility is a phenotype for these neurological diseases.

Results

We formulate the POLYGENIC DISEASE PHENOTYPE Problem which seeks to identify candidate disease genes that may be associated with a phenotype such as cell motility. We present a machine learning approach to solve this problem for schizophrenia and autism genes within a brain-specific functional interaction network. Our method outperforms peer semi-supervised learning approaches, achieving better cross-validation accuracy across different sets of gold-standard positives. We identify top candidates for both schizophrenia and autism, and select six genes labeled as schizophrenia positives that are predicted to be associated with cell motility for follow-up experiments.

Conclusions

Candidate genes predicted by our method suggest testable hypotheses about these genes’ role in cell motility regulation, offering a framework for generating predictions for experimental validation.

SUBMITTER: Bern M 

PROVIDER: S-EPMC6584515 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Network-based prediction of polygenic disease genes involved in cell motility.

Bern Miriam M   King Alexander A   Applewhite Derek A DA   Ritz Anna A  

BMC bioinformatics 20190620 Suppl 12


<h4>Background</h4>Schizophrenia and autism are examples of polygenic diseases caused by a multitude of genetic variants, many of which are still poorly understood. Recently, both diseases have been associated with disrupted neuron motility and migration patterns, suggesting that aberrant cell motility is a phenotype for these neurological diseases.<h4>Results</h4>We formulate the POLYGENIC DISEASE PHENOTYPE Problem which seeks to identify candidate disease genes that may be associated with a ph  ...[more]

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