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After logging into the PFS web server, you will be greeted with your home page ( called "home page" afterwards and you can always get back to it by clicking "home" in any page ) as shown in Figure One.


Figure One ( Click to view full size image )

Demos For Our Key Features:

1. Enter related search terms accurately and efficiently.
2. Find rs No. of a particular SNP. (This function can now be accessed at the Handy Tool section)
3. Formulate a complex search with multiple criteria.
4. Use the integrated gene / pathway information in the query result.
5. Easily accessible supporting information helpful for understanding the query results and forming new hypothesis.
6. pfSNP only view that helps in function category enrichment analysis.
7. Deposit new SNP function into pfSNP database.

Quick Start:

I want to ...

1. Know the potential and reported function of a list of SNPs or pfSNPs in LD with the SNPs.

"Query pfSNP Database" in home page --> Type or paste the list of rs number into the rs number query criteria and tick the checkbox for rs Number --> Review the conditions --> Get a list of pfSNP or pfSNP in LD with SNPs of interest and check FAQ 1 if some rs numbers are missing.

2. Look out for SNPs with potential and reported function in specific chromosomal region or genes or responsible for certain diseases or drug metabolism.

"Query pfSNP Database" in home page --> Fill in appropreate criteria in right criteria category and tick the checkbox for that caterory --> Review the conditions --> Get a list of gene names with gene information sorted by number of pfSNPs they contain or a list of "intergenic" SNPs or a summary of the results stating how many pfSNP in each category with an option to view pfSNP in either category. Pick a gene or view "intergenic" SNPs --> A list of pfSNPs and check FAQ 1 if some rs numbers are missing.

3. Pick pfSNPs for gene-based association studies.

Same as last task but remember to specify population specific MAF cut off in the query interface if you want to get rid of "non-informative" SNPs in specific populations.

4. Contribute newly reported SNP function to PFS server.

"Submit published SNP info" in hame page or "Report New Function" in "Reported" column of query result page --> Fill in PMID, rs number and function


Detailed User Guide:


To query PFS database or get pfSNP for gene-based association study:

If you are a biologist who has a SNP or a list of SNPs of interest and wondering what potential function they may have, click on the "Query PFS Database" and it will bring you to the query interface where you can query the SNP(s) of interest by its (their) rs number ( Figure Two ).

Figure Two ( Click to view full size image )

It does not matter if you do not know the rs number though. The query interface also provide a nice feature that facilitates translating what you know about the SNP into corresponding rs number. As Figure Three shows, you can provide gene name that the SNP belongs to and the features commonly used by biologist to describe a SNP and the PFS will translate these information into corresponding rs number.

Figure Three ( Click to view full size image )

The query interface is very versatile in that it does not take rs number only but also accepts a range of other criterias and allows "mix and match" of these criterias with custom boolean logic ( Figure Four ).

Figure Four ( Click to view full size image )
This may come in handy for biologist who is interested in a list of genes or diseases and wondering which SNPs in these genes may affect gene function or which SNPs are behind the scene of certain diseases.

Indicating a query criteria in a criteria category does not mean this is included in the query. You have to tick the checkbox of the particular criteria category to get it in. This design is troublesome at first sight but will come in handy if you want to compare query results when you quickly toggle some of the criterias on and off.

Doing query in PFS is made more user-friendly ( or troublesome ) by allowing user to apply a number of commonly used filters to the query results ( Figure Five ).

Figure Five ( Click to view full size image )
1. "Display pfSNP only" limits the result to pfSNP only and it is usually the cause of "missing SNP in the query results" problem ( e.g: you submit a list of 10 rs numbers and the query results mysteriously return 8 rs numbers only ). Be sure you uncheck this option and re-run the query before you write to PFS administrator in fury about this famous problem.

2. "Display PFS information matching gene context" displays PFS information in the right gene context only. e.g: SNP a can be a coding SNP in gene A but also a promoter SNP 4kb upstream of another gene B. Querying pfSNP in gene A will return you PFS information saying SNP a will change TF binding which is out of the context of gene A. By using this filter, such inappropreate information will be masked out. However, if you remove this filter, you may be open up to new possibilities: SNP a was reported as a causal SNP of certain disease in the literature and people largely believe this is due to its effect as a coding SNP in gene A. However, the true story is that it changes TF binding and affects expression level of gene B. PFS server is able to pull out such valuable information for you and assists in new hypothesis formation.

3. "Hapmap genotyped SNPs" will limit the results to SNPs already genotyped by the latest Hapmap release. It's helpful to biologists who wants to pick pfSNP for association study by eliminating the problem of genotyping "un-informative" SNPs.

4. "Regions" will limit the results to SNPs in specific region only. This may come in handy if you are doing gene-based association study and wants to pick gene region pfSNP for such task.

Once you specified the query criterias together with right filtering conditions, click on "Submit Query" for a summary of your query conditions ( Figure Six ).

Figure Six ( Click to view full size image )
Anything in red require your immediate attention because you have included a specific query condition without providing a proper query criteria. Read the page carefully before proceed since some of the criteria may be the ones that "sneak" into the list because you are trying to re-formulate a new query by "Retain my query criteria" from the previous one.

Depends on the query criteria and results, you may be directly shown the query result page or a page summarizing how many of pfSNP in a list of genes or in "intergenic" regions ( Figure Seven ). Choose a gene or "intergenic" region to view if you get an option.

Figure Seven ( Click to view full size image )

Finally, you are at the query result page. ( Figure Eight )

Figure Eight ( Click to view full size image )
You can adjust a few display options like whether to freeze the table title or how many SNP per page (Tip: The more SNPs per page you specify, the longer it takes to load the result into your browser.) before it takes some time to load the results from the PFS server. Detailed PFS information together with reference is just a click away from the hyperlinks in the table. You can also opt to download the table in EXCEL format with all the links preserved. If you find the results not as expected, you can always do a "New Query" with "Retain my query criteria"

To contribute to PFS server with SNP function information:


We understand that we can never exhaust the ever-growing literature for reported SNP functions and thus depends largely on the user-community of PFS server to contribute in new SNP function or SNP - disease association information. You can do so through 2 ways. One is to click on "Submit published SNP info" in your home page ( Figure Nine ) and the other is to do so "On-The-Fly" when you obtain PFS query results ( Figure Ten ). In either case, you will be redirected to the page as shown in Figure Eleven.You will be asked to provide PubMed ID for reference. You can search for PMID by clicking "Search for PubMed ID" and provide some article information and PFS server will return you titles for the first 20 articles matching your criteria. Pick the right title or redo the query by giving more information if you found the title is not in the list. Please provide other information required as well before submitting.

Figure Nine ( Click to view full size image )

Figure Ten ( Click to view full size image )

Figure Eleven ( Click to view full size image )


FAQs


1. Some of the SNPs I queried for is missing from the final query result SNP list.

They are probably non-pfSNPs. If you DO want to see them in the list, un-check "Display pfSNP only" in the filter section of query criteria page and re-run the query.

2. My query returned nothing. ( And you are pretty sure there should be something there in the results )

If this happened when you did a fresh query, check FAQ 4.If this does not solve your problem, please contact PFS administrator.

If this happened when you re-formulated a query by "Retain my query criteria" from the query result page, you probably "inherited" extra query conditions into your current query by forgetting to untick some of the query condition checkboxes. You probably also consider the query criteria summary page annoying and click the proceed button straight away whenever you see this page. Solution: Give the query criteria summary page some respect and read it carefully next time.

3. Some of the SNPs are in alien genes that are not in the list of genes I've provided.

Congratulations! You've just discovered some SNPs residing in two or more genes.

4. I've typed in what I want in a text box without selecting respective values from the Prompt-As-You-Type suggestion list. However, PFS server seems to be mulfunctioning after that ....

Please select values from the Prompt-As-You-Type suggestion box whenever you see them. This will keep our PFS server behave as designed. For those wondering why it's compulsory to do so, it's simply because .... IT'S BY DESIGN. :)

5. When I try getting rs number by keying in its gene location (e.g: ABCB1, Coding, Location 2677), I saw 2 entries of "2677" in the Prompt-As-You-Type suggestion box.

This means there are two distinct rs numbers pointing to the same gene location. Feel free to pick either entry and information about these 2 rs numbers will be shown in the result page.

6. I saw some rs number with mRNA location information but its gene name column is empty.

These genes are discontinued by NCBI and no longer available in the downloaded version of gene ID file.

7. In the query result summary page, it reported that 10 SNPs in one gene satisfid my query criteria. However, when I clicked on "View this gene", the next page reported 13 (more) SNPs satisfied my criteria.

There are multiple rs numbers pointing to the same gene location. The query result summary page avoids this redundancy by reporting unique gene location counts. The detailed query result page, however, shows all the rs numbers so as to avoid the "Why my rs number is not in the list?" problem.

8. When I try opening the downloaded query result in EXCEL format, EXCEL reports that the file may be corrupted and takes forever to open it.

The file is not in native EXCEL format and EXCEL has to do a lot of work to FORMAT IT ( combine rows, set background color, render all the hyper-links etc ) so it can be presented nicely.
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