↓ Skip to main content

A sequence-based method to predict the impact of regulatory variants using random forest

Overview of attention for article published in BMC Systems Biology, March 2017
Altmetric Badge

Mentioned by

twitter
2 X users

Citations

dimensions_citation
13 Dimensions

Readers on

mendeley
43 Mendeley
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Title
A sequence-based method to predict the impact of regulatory variants using random forest
Published in
BMC Systems Biology, March 2017
DOI 10.1186/s12918-017-0389-1
Pubmed ID
Authors

Qiao Liu, Mingxin Gan, Rui Jiang

Abstract

Most disease-associated variants identified by genome-wide association studies (GWAS) exist in noncoding regions. In spite of the common agreement that such variants may disrupt biological functions of their hosting regulatory elements, it remains a great challenge to characterize the risk of a genetic variant within the implicated genome sequence. Therefore, it is essential to develop an effective computational model that is not only capable of predicting the potential risk of a genetic variant but also valid in interpreting how the function of the genome is affected with the occurrence of the variant. We developed a method named kmerForest that used a random forest classifier with k-mer counts to predict accessible chromatin regions purely based on DNA sequences. We demonstrated that our method outperforms existing methods in distinguishing known accessible chromatin regions from random genomic sequences. Furthermore, the performance of our method can further be improved with the incorporation of sequence conservation features. Based on this model, we assessed importance of the k-mer features by a series of permutation experiments, and we characterized the risk of a single nucleotide polymorphism (SNP) on the function of the genome using the difference between the importance of the k-mer features affected by the occurrence of the SNP. We conducted a series of experiments and showed that our model can well discriminate between pathogenic and normal SNPs. Particularly, our model correctly prioritized SNPs that are proved to be enriched for the binding sites of FOXA1 in breast cancer cell lines from previous studies. We presented a novel method to interpret functional genetic variants purely base on DNA sequences. The proposed k-mer based score offers an effective means of measuring the impact of SNPs on the function of the genome, and thus shedding light on the identification of genetic risk factors underlying complex traits and diseases.

X Demographics

X Demographics

The data shown below were collected from the profiles of 2 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 43 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 43 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 7 16%
Researcher 6 14%
Student > Ph. D. Student 6 14%
Student > Bachelor 5 12%
Professor 3 7%
Other 7 16%
Unknown 9 21%
Readers by discipline Count As %
Computer Science 10 23%
Biochemistry, Genetics and Molecular Biology 5 12%
Agricultural and Biological Sciences 5 12%
Medicine and Dentistry 4 9%
Mathematics 2 5%
Other 5 12%
Unknown 12 28%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 01 April 2017.
All research outputs
#18,540,642
of 22,962,258 outputs
Outputs from BMC Systems Biology
#836
of 1,144 outputs
Outputs of similar age
#235,070
of 307,953 outputs
Outputs of similar age from BMC Systems Biology
#22
of 32 outputs
Altmetric has tracked 22,962,258 research outputs across all sources so far. This one is in the 11th percentile – i.e., 11% of other outputs scored the same or lower than it.
So far Altmetric has tracked 1,144 research outputs from this source. They receive a mean Attention Score of 3.6. This one is in the 11th percentile – i.e., 11% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 307,953 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 12th percentile – i.e., 12% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 32 others from the same source and published within six weeks on either side of this one. This one is in the 25th percentile – i.e., 25% of its contemporaries scored the same or lower than it.