This article is part of the supplement: Eleventh International Conference on Bioinformatics (InCoB2012): Computational Biology

Open Access Proceedings

iLOCi: a SNP interaction prioritization technique for detecting epistasis in genome-wide association studies

Jittima Piriyapongsa1, Chumpol Ngamphiw1, Apichart Intarapanich2, Supasak Kulawonganunchai1, Anunchai Assawamakin1, Chaiwat Bootchai1, Philip J Shaw1 and Sissades Tongsima1*

Author Affiliations

1 National Center for Genetic Engineering and Biotechnology, Pathumthani, 12120, Thailand

2 National Electronics and Computer Technology Center, Pathumthani, 12120, Thailand

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BMC Genomics 2012, 13(Suppl 7):S2  doi:10.1186/1471-2164-13-S7-S2

Published: 13 December 2012

Additional files

Additional file 1:

The mathematical details of ρdiff value and its relation with LD (iLOCi_details.pdf). This file includes the mathematical details of iLOCi formula and its relationship with the allele-based LD calculation.

Format: PDF Size: 372KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 2:

Penetrance tables for dataset simulation (Penetrance_tables.pdf). This file includes the penetrance models used for dataset simulation of two-locus and high-order ineractions.

Format: PDF Size: 85KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 3:

Top 1000 SNP pairs from analyses of complete SNP set of WTCCC (TopPairs_Complete.xls). This file includes the list of top 1000 SNP pairs with their associated genes obtained from the iLOCi analyses of all SNPs passing the quality control step. The evidences for disease association of each identified gene as reported in WTCCC original paper and HuGE Navigator database are also shown. The genes identified as candidate disease genes from ToppGene prioritization are indicated with their rank numbers and P-values.

Format: XLS Size: 1.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 4:

Top 1000 SNP pairs from analyses of gene-only SNP set of WTCCC (TopPairs_GeneOnly.xls). This file includes the list of top 1000 SNP pairs with their associated genes obtained from the iLOCi analyses of gene-only SNPs. The evidences for disease association of each identified gene as reported in WTCCC original paper and HuGE Navigator database are also shown. The genes identified as candidate disease genes from ToppGene prioritization are indicated with their rank numbers and P-values.

Format: XLS Size: 1.6MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Pathway enrichment analysis of WTCCC datasets (Pathway_analysis.xls). This file includes the list of enriched biological pathways obtained from ToppGene program using the training sets of HuGE Navigator disease-associated genes. The pathway P-value is reported along with the list of iLOCi identified genes associated with such pathway. For each pathway, the number of genes previously reported in HuGE Navigator database, reported in WTCCC paper, and the novel disease genes, is shown.

Format: XLS Size: 175KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data