Datapunk Opus 23 Pro

Help Docs

Pop-ups

Pop-up windows are shown by clicking on genes links in maps, or where rs ID numbers are displayed with a link. Depending on the situation, pop-ups are also used to bring up context data such as PubMed abstracts. An important use of pop-ups is the ability to notate elements in Opus 23 Pro. Elements notated in Opus 23 Pro will appear in the Chart and Client Reports. The use of notations is discussed under its own section. Clicking on the 'X' in the upper right hand corner of the pop-up, or anywhere outside the pop-up window, closes the pop-up window.

Click here to trigger typical popup.

SNP Pop-ups Clicking on the link on an rs ID shows a pop-up with the following information, if available:

Evidence basis: higher values on a scale of 0-10 are assigned by Opus 23 editors to the evidence basis for a SNP where it is a key polymorphism in published research articles with large numbers of subjects and high statistical significance
Power factor: the value for power factor on a 0-10 scale is determined by Opus 23 editors according to the amount a polymorphism in this SNP is known to affect the overall gene function or have an effect on disease risk
Curation level: the number of times Opus 23 editors have manually added information to the SNP data
Gene: the HGNC symbol of the gene in which the SNP is located. Some SNPs might not be in a coding region of the chromosome, and may be designated as 'intergenic', or display locus information, including chromosome number, arm (p or q) and locus number
GMAF: Global minor allele frequency is a number indicating the minor allele frequency reported by dbSNP for the rs ID in a default global population
Chromosome: The chromosome on which the SNP is located
Position: The position on the chromosome where the SNP is located using the human GRCh38 reference assembly. N.B. 23andMe currently report position data based on GRCh37.
Risk Allele: Shows which allele has been designated the risk by Opus 23 editors. This is usually the minor allele, that is, the nucleotide least frequently found in the general population. Sometimes the risk allele may be the dbSNP ancestral allele, as this has been assessed as being associated with a higher level of disease risk than the minor allele. The currently loaded client’s genotype is listed with red/yellow/green color coding for homozygous positive / heterozygous / homozygous negative
Frequency: if frequency data exists for the SNP it will show as a color-coded graph for various populations
HapMap Revision: shows the International HapMap Project revision number used for assessing the SNP data. The current release is #28
dbSNP Orientation: The direction in which the chromosomal strand is read according to dbSNP. This will be listed as ‘PLUS’, read in the forward direction, or ‘MINUS (converted)’, read in the reverse direction, and showing that Opus 23 has converted the nucleotides to correspond with dbSNP
Naturopathic Agents Known to Influence Expression: These are hand-curated links from published studies showing how a natural agent has an agonist or antagonist effect on gene expression. Sometimes this may be 'unidentified, - this is where the agent is known to influence expression but a curator has not yet associated it as an agonist or antagonist.
Algorithms: If any Opus 23 algorithms use this SNP they will be linked here
Consequences: These are hand-curated notes from editors who have added information about the SNP that may be useful
Additional data: If the SNP contains additional data that Opus 23 can retrieve from any of the public sources, it will display here. This typically includes clinical consequences and relevant PubMed references

Gene Pop-ups

Clicking on the link on a gene symbol shows a pop-up with the following information, if available:

Symbol for the gene: Opus 23 Pro always uses the approved gene symbol for every gene.
Full name of the gene: The officially approved full name of the gene
Gene Description: A description of the gene. This text is typically retrieved from genome.gov.
Algorithms: If any Opus 23 Pro algorithms include this gene they will be linked here
Naturopathic Agents Known to Influence Expression: These are hand-curated links from published studies showing how a natural agent has an agonist or antagonist effect on gene expression. Sometimes this may be 'unidentified, - this is where the agent is known to influence expression but a curator has not yet associated it as an agonist or antagonist
SNP results for the client: A list of SNPs linked to this gene that are in the Opus 23 Pro database. Click on any SNP to bring up its information screen. SNP results are displayed according to a consistent color scheme: Orange-colored boxes indicate SNPs for which the client genotype is homozygous for the risk allele; yellow boxes indicate that the client is heterozygous for the risk allele; grey boxes indicate that the client is homozygous for the non-risk allele; green boxes indicate that the client is homozygous for a SNP associated with some positive benefit
Pie chart with drill-down: If Opus can locate HapMap data for the SNPs in the gene it will display their frequencies as a pie chart with drill-down. The SNPs are displayed in the interior circle and its genotypes with their frequencies of occurrence in the outer circle

It's elemental: In Opus 23 Pro, anything that you can interact with is referred to as an 'element'. An element could be a SNP, gene, drug, herb, algorithm, etc. Generally when the Help Docs refer to an element, it means that whatever it is describing applies to any of these things.

Curating via popups

A symbol next to the gene name will either say "ADD UNCURATED" or "CURATED", depending on whether the gene has been added to the active curation dataset (i.e the set of genes or algorithms that will be sent on to the client report.) Click on the appropriate icon to add or delete the gene or algorithm from the current curation dataset.