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Supplemental Material
Supplemental Figure 1. PheGenI search order strategy. Phenotype searches are linked to the
association results from dbGaP and the GWAS catalog. The rs numbers, and genes mapped to
those rs numbers, are subsequently used to query dbSNP, NCBI Gene, and GTEx in a series of
parallel searches. Similar searches can be performed for chromosomal location, gene, or SNP,
and results are filtered accordingly.
Supplemental Figure 2. Association results returned by PheGenI after executing a search for
celiac disease trait and limiting p-value to 1 X 10-8. These data can be downloaded as tab
delimited text. For better viewing, only the first 25 of 33 association results are shown.
Supplemental Text. Linking to PheGenI Records.
To link to PheGenI, the base URL is http://www.ncbi.nlm.nih.gov/gap/PheGenI and is case
sensitive. A link to a particular search requires a query string to be appended to the URL and
this begins with a question mark (?) followed by name=value pairs used as search parameters
and separated with an ampersand (&). The name=value pairs may contain some nonalphanumeric characters replaced by a percent sign (%) followed by two hexadecimal digits
representing the ASCII code of the original character. The following two encoded characters are
used in the provided examples:
%20 - 20 hex, 32 decimal, ASCII space
%0A - 0A hex, 10 decimal, new line or line feed
This overview is for constructing the most basic parameters and it is shown in three sections:
Phenotype search, Location search, and Other parameters. The minimum requirement is to
specify at least one trait (phenoTrait) or one of the three location specifications. Both a trait and
a location can be specified. A parameter named tab must be specified in order for any search to
be performed. This determines which, if any location search is to be performed.
Following are the three options for the tab parameter
tab=0 - location search
tab=1 - gene search
tab=2 - SNP search
This also determines which tab will be displayed in the form on the web page. If no genotype
search is to be specified, then tab=0 is recommended. If the tab parameter is omitted, then the
other parameters will be used to fill in the search form, but no search will be performed until the
user clicks on the "Search" button.
Phenotype search
Parameter: phenoTrait
Value: the exact name of a trait.
This is case sensitive and more than 1 trait can be specified, but with a separate phenoTrait
parameter for each. Following is an example with two traits specified:
http://www.ncbi.nlm.nih.gov/gap/PheGenI?tab=0&phenoTrait=Celiac%20Disease&phenoTrait=
Arthritis,%20Rheumatoid
Location search
The location search has three options, Chromosome location, Gene Search, or SNP Search. Only
one of these options can be implemented.
Chromosome location
Parameter: tab
Value: 0 - for chromosome location.
Parameter: chr - chromosome
Value: an integer from 1 to 22 or X, Y, or MT
Parameter: from
Value: integer, the minimum number location in base pairs within the specified chromosome.
This is required if not searching for a phenotype trait.
Parameter: to
Value: integer, the maximum number location in base pairs within the specified chromosome.
This is required if not searching for a phenotype trait and must be greater than the “from”
parameter.
Here are two examples. The first is a search by location on chr. 6 and 20-40 Mbp, and the
second is a phenotype and location search for "Diabetes Mellitus, Type 1" on chromosome 6.
http://www.ncbi.nlm.nih.gov/gap/PheGenI?chr=6&from=30000000&to=40000000&tab=0
http://www.ncbi.nlm.nih.gov/gap/PheGenI?chr=6&phenoTrait=Diabetes%20Mellitus,%20Type
%201&tab=0
Gene search
Parameter: tab
Value: 1 for gene search
Parameter: gene
Value: one or more gene symbols or IDs separated by non-alphanumeric characters, i.e. spaces,
commas, etc.
Unlike the phenoTrait parameter, there should only be one gene parameter specified but the
value can contain multiple genes.
Following are some examples with more than one gene specified:
http://www.ncbi.nlm.nih.gov/gap/PheGenI?tab=1&gene=ABO%20DMD
http://www.ncbi.nlm.nih.gov/gap/PheGenI?tab=1&gene=28%201756
SNP search
Parameter: tab
Value: 2 for SNP search
Parameter: rs
Value: one or more rs numbers separated by non-numeric characters. The rs numbers can
optionally be prefixed with “rs.” For example searching for "328" or "rs328" are equivalent.
Like the "gene" parameter specified above, only one rs parameter can be specified but the value
can contain multiple rs numbers.
Following is an example with three rs numbers:
http://www.ncbi.nlm.nih.gov/gap/PheGenI?tab=2&rs=rs579459%0A507666%0A10521971
Other parameters:
Parameter: pv – integer, p-value exponent
Value: a positive integer that represents the minimum acceptable P-value for association and
eQTL results. For example, if pv=10, then the minimum p-value is 1 x 10-10. The value
specified is positive but represent the negative power of 10.
The following example is a modified example of the SNP example search with a p-value
specified:
http://www.ncbi.nlm.nih.gov/gap/PheGenI?tab=2&rs=rs579459%0A507666%0A10521971&pv
=10
Parameter: fxn
Value: one of the following: exon, intron, neargene, UTR. This is case sensitive.
This parameter specifies the SNP function class and more than one can be specified but the
parameter name must be specified for each value. For example fxn=exon&fxn=intron is valid,
but fxn=exon%20intron is not because two values are specified for one parameter.
Following is an example which searches for "Diabetes Mellitus, Type 1" on chr 6 but only with
SNPs that have a function class:
http://www.ncbi.nlm.nih.gov/gap/PheGenI?tab=0&chr=6&phenoTrait=Diabetes%20Mellitus,%2
0Type%201&fxn=exon&fxn=neargene&fxn=UTR&fxn=intron