What is meant by Criteria?

As part of an ongoing effort to summarise potential support for a biological feature (i.e. marker, gene, genetic locus or study) for a role in a particular phenotype, we have added the ability to compare diseases based on a set of criteria (see Criteria Descriptions section). Using a variety of electronic and manual methods (which we call Criteria) each feature is tagged using the set of phenotypes listed in the table below. This means that we can:

• Highlight visually which genes, markers, loci and studies may be important in one or more phenotypes.
• Provide better search by sorting terms based on an internal score derived from this tagging.
• Provide easy to access cross links between features by shared phenotype.

Supported Phenotypes in ImmunoBase

ImmunoBase supports the following disease phenotypes. The disease bar represents these 12 core diseases plus other diseases (‘OD’) of interest.

The results of these analyses are located in the top right corner of feature pages (see examples below). In each page, where they are displayed, there is a criteria section, allowing the user to “drill-down” and obtain the specific criteria met for that feature to have been tagged with a disease. A full description of all the criteria currently implemented, and their context is outlined in the Criteria Descriptions section.

Below are some examples of disease comparisons on this site.

Search:

10p15.1

Marker Page:

rs2476601

Gene Page:

PTPN22

Locus Page:

1p13.2

Study Page:

GDxHsS00004 (Barrett et al)

Criteria Descriptions

Marker Criteria Description

Criteria	Description
Marker is GW-Significant in a Study	A GW-significant marker in a study is defined as a marker detected in one of our curated studies that meets genome-wide (GW) significance in that study. The P value from the study is shown.
Marker is GW-Significant on the ImmunoChip	An Immunochip significant marker is defined as a marker that has been typed on the ImmunoChip Custom Genotype Array and reaches a significance level of P<5×10-08. The P value from the assay is shown.
Marker is in R²>0.8 with an index SNP	A marker is in R²>0.8 with an index SNP is defined as an index snp in a curated study being in R²>0.8 with this marker. The R² value between the 2 markers is shown.
Feature lies in MHC region	A feature lying in the MHC region is defined as any feature that is physically located within or overlaps the bounds of the Human MHC Region (chr6:25,000,000-35,000,000).
Marker is an index SNP in a Region	An index marker in a region is defined as a marker used to build a curated disease region.

Gene Criteria Description

Criteria	Description
Candidate Gene in a Study	A candidate gene in a study is defined as a gene cited in the principal paper of one of our curated studies.
Gene is located within a Region	A gene in a region is defined as a gene that is physically located within or overlaps the bounds of a region.
Candidate Gene in a Region	A gene in a region is defined as a gene that is physically located within or overlaps the bounds of a region.
Feature lies in MHC region	A feature lying in the MHC region is defined as any feature that is physically located within or overlaps the bounds of the Human MHC Region (chr6:25,000,000-35,000,000).
Exonic index SNP in this Gene	An exonic index snp in this gene shows genes which contain an index snp from one of our curated studies that lies within an exon of this gene.

Region Criteria Description

Criteria	Description
Feature overlaps a disease region	A feature overlaps a disease region is defined as a region that has has been curated and tagged with diseases.
Feature lies in MHC region	A feature lying in the MHC region is defined as any feature that is physically located within or overlaps the bounds of the Human MHC Region (chr6:25,000,000-35,000,000).

Study Criteria Description

Criteria	Description
Study for a Disease	A study for a disease is a curated study that covers a disease.