How to use eSNPO Database
Query:

  Each entry can be retrieved by SNP name or GO term ID.

  1. Search by SNP name.

  Example: If you want to query the GO functions for rs2732660 in "Brain", you should select "Brain" in the pull-down menu for tissues and input rs2732660 in the SNP section and press "Search" button (Figure 1).

Figure 1 Search by SNP name

  The total number of results in eSNPO is shown in the top. Clicking the SNP name, you can turn to NCBI dbSNP for more information about this SNP. The results are listed for 100 entries in a page, you can turn to other pages using the page number button in the bottom. For each entry, you can get the related GO ID, GO term name and the tissue type. Clicking a GO ID, you can turn to the search results in all tissues for this GO term with the related SNPs in eSNPO. (Figure 2)

Figure 2 The search results of rs2732660

  2. Search by GO ID.

  Example: If you want to query the SNPs related to GO:0010819 in "Brain", you should select "Brain" in the pull-down menu for tissues and input GO:0010819 in the GO ID section and press "Search" button (Figure 3).

Figure 3 Search by GO ID

  The total number of results in eSNPO is shown in the top. Clicking the GO term ID, you can turn to Gene Ontology for more information about this term. The results are listed for 100 entries in a page, you can turn to other pages using the page number button in the bottom. For each entry, you can get the related GO term name, SNPs and the tissue type. Clicking a SNP, you can turn to the search results in all tissues for this SNP with the related GO terms in eSNPO. (Figure 4)

Figure 4 The search results of GO:0010819

SNP Enrichment Analysis:

  The SNP enrichment analysis is performed using fisher exact test. The p values can be adjusted through 7 methods.

  First you should choose the tissue type and p value adjustment method. There are 12 tissue types. If you select "All" in tissue type, you will get results using data in all these 12 tissues. The p values are adjusted by p.adjust() function in R. The adjustment methods include the Bonferroni correction ("bonferroni") in which the p values are multiplied by the number of comparisons. Less conservative corrections are also included by Holm (1979) ("holm"), Hochberg (1988) ("hochberg"), Hommel (1988) ("hommel"), Benjamini & Hochberg (1995) ("BH" or its alias "fdr"), and Benjamini & Yekutieli (2001) ("BY"), respectively.

  The input SNPs should be in format of dbSNP reference records (rs#). The SNPs list should be separated by newline character. In other words, there should be one SNP in a line only. There is a sample data with 100 Parkinson's (PD) SNPs on the web. Click “e.g.”, you can see the input style. Click “e.g.txt”, you can open a seprate website to see the input style. Click “reset”, the input block will be cleared. Click “submit”, the input data will be submitted to calculate the enrichment analysis.

  We input 100 Parkinson's Disease (PD) related SNPs in Brain tissue as an example. (Figure 5)

Figure 5 Inputs of enrichment analysis for 100 SNPs in Brain

  If you select "All" in tissue type, the computation may take minutes, please don’t close the IE window while waiting for results.

  In the title of the results, you can get the number of SNPs with annotation in eSNPO and the enrichment analysis results. In this example, there are 46 SNPs with annotation in eSNPO and 71 enrichment analysis results.

  In the results, you can get these information: GO ID, GO term, count, %, p value and q value. The count is the number of input SNPs with annotations in this GO term; the % is the percent of annotated SNPs in this GO term; the p value is calculated by fisher exact test and the q value is calculated using "qvalue" package in R. We haven't performed any screening for p values or q values.

  You can download the results with a text format file. In this file, you can get the SNPs with annotation in each GO term.


Figure 6 Results of enrichment analysis for 100 SNPs in Brain