In case of three lists, click on the or Another buttons and either copy the “Add Another List” “Add File” third list or upload it. The result layout is same except that there is a 3 circle venn diagram to illustrate the overlaps and the table contains entries for all possible combinations of overlaps between the 3 lists. Steps for simple are exactly the same except that has to be selected as input “SNP Overlap” “rsID” option and overlap type is “SNPs”. Simple SNP overlap 2 sets – The result interface is similar to gene overlap screenshots from above. Simple SNP overlap 2 sets – Enriched pathway overlap To find overlap using select the appropriate input option and “enriched pathways”, “KEGG as the desired overlap type. Pathways(Enriched)” Pathway overlap analysis query Since enrichment is involved in the overlap type, one has to select the appropriate “Correction for multiple testing correction and enter the to be used in the analysis. Procedure” “Significance Cut-off” Either copy the the gene lists in the text-areas or upload the files and click “Submit” The result interface displays a Venn diagram plot showing the overlap levels between the lists. Enriched pathway overlap analysis result 2 sets – Result screen also contains a table in which the filenames are listed in the first row. The table also contains an entry which indicates the of enriched pathways from each list. “intersection” Unique enriched pathways belonging to each list (including the intersection entries) can be downloaded by clicking on these names. In the scenario where NO pathways are enriched, the overlaps are found among ALL the pathways mapped to the list instead of just using the enriched ones and a suitable message is displayed. Enriched pathway overlap analysis result 2 sets – In case of three lists the steps are the same as described above. Use the Another or “Add List” “Add Another buttons to enter or upload the third list and click File” “Submit” The result screen contains a three circle venn diagram to show the overlap levels.
In case of three lists, click on the “Add Another List” or “Add Another File” buttons and either copy the third list or upload it. The result layout is same except that there is a 3 circle venn diagram to illustrate the overlaps and the table contains entries for all possible combinations of overlaps between the 3 lists. Steps for simple “SNP Overlap” are exactly the same except that “rsID” has to be selected as input option and overlap type is “SNPs”. Simple SNP overlap – 2 sets The result interface is similar to gene overlap screenshots from above. Simple SNP overlap – 2 sets Enriched pathway overlap To find overlap using “enriched pathways”, select the appropriate input option and “KEGG Pathways(Enriched)” as the desired overlap type. Pathway overlap analysis query Since enrichment is involved in the overlap type, one has to select the appropriate “Correction Procedure” for multiple testing correction and enter the “Significance Cut-off” to be used in the analysis. Either copy the the gene lists in the text-areas or upload the files and click “Submit” The result interface displays a Venn diagram plot showing the overlap levels between the lists. Enriched pathway overlap analysis result – 2 sets Result screen also contains a table in which the filenames are listed in the first row. The table also contains an entry which indicates the “intersection” of enriched pathways from each list. Unique enriched pathways belonging to each list (including the intersection entries) can be downloaded by clicking on these names. In the scenario where NO pathways are enriched, the overlaps are found among ALL the pathways mapped to the list instead of just using the enriched ones and a suitable message is displayed. Enriched pathway overlap analysis result – 2 sets In case of three lists the steps are the same as described above. Use the “Add Another List” or “Add Another File” buttons to enter or upload the third list and click “Submit” The result screen contains a three circle venn diagram to show the overlap levels.
GENEASE_Manual.docx