Table 1

Default feature weights as result of the optimization process.

Section

Feature Name

Feature Weight


SNPs and Genes

MAF

0.3133

Localization

0.7052

Essential Genes

0.2665

Phylo

0.5797

Lamina associated domains

0.2444


Epigenetics and transcription regulations

Open Chromatin

0.1596

Chromatin Structure

0.7525

Methylation (seq regions)

0.4009

Methylation

0.3743

CpG Island

0.8992

DNase clusters

0.9558

TSS (eponine)

0.3705

CpG islands, promoters, first exons

0.9665

FOX2 CLIP-seq

0.5608

TAF1 binding sites

0.2468

Intergenic regulatory elements

0.4006

TSS (SwitchGear)

0.6773

Regulatory regions (OregAnno)

0.8818

TFBS (TRANSFAC)

0.8243

TXN factor ChIP-Seq

0.4477

Enhancers (VISTA)

0.9571


Translation regulations

Alternative Splicing

0.7032

miRNA binding regions

0.8358


Proteins

Hub protein

0.5796

Protein Domain

0.6316

PolyPhen

0.5678

SNPs 3D

0.5977

LS-SNP

0.3158

Protein Interactions

0.3728

PTM

0.5399


Disease

Pathologies OMIM

0.2904


The table presents the SNP features used by SNPranker 2.0 with their default weights, according to the optimization performed using the genetic algorithm (sensitivity = 0.814, specificity = 0.761 and accuracy = 0.761).

Merelli et al. BMC Bioinformatics 2013 14(Suppl 1):S9   doi:10.1186/1471-2105-14-S1-S9

Open Data