Protein details/Single nucleotide variation: Difference between revisions
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The single nucleotide variation section of the [[Protein details]] page in GlyGen provides a detailed list of somatic and germline nucleotide mutations. | The single nucleotide variation section of the [[Protein details]] page in GlyGen provides a detailed list of somatic and germline nucleotide mutations. | ||
== Single Nucleotide Variation == | ==Single Nucleotide Variation== | ||
Single nucleotide variation is presented in 2 tabs on the [[Protein details]] page in GlyGen. | Single nucleotide variation is presented in 2 tabs on the [[Protein details]] page in GlyGen. | ||
=== Disease associated Mutations === | ===Disease associated Mutations=== | ||
This tab shows a list of mutations in the genetic sequence that are associated with a disease. The following columns are presented in the table: | This tab shows a list of mutations in the genetic sequence that are associated with a disease. The following columns are presented in the table: | ||
* '''Source''' - | *'''Source''' - GlyGen evidence linking to the databases and papers that provided the glycosylation information | ||
* '''Filter''' '''annotations''' - | *'''Filter''' '''annotations''' - Pass/fail filter results from mapping cancer terms to Disease Ontology ID. Eg. Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%) | ||
* '''Genomic locus''' - | *'''Genomic locus''' - The genomic position of the reported mutation. Eg. Chr7:81399287 | ||
* '''Start Pos.''' - | *'''Start Pos.''' - Start position of the site in the amino acid sequence. Eg. 1 | ||
* '''End Pos.''' - | *'''End Pos.''' - End position of the site in the amino acid sequence. Eg. 1 | ||
* '''Sequence''' - | *'''Sequence''' - Reference or wild-type amino acid residue change resulting from variation. Eg. M→ L | ||
* '''Disease''' - | *'''Disease''' - DOID and term corresponding to reported disease. Eg. thyroid gland cancer (DOID:1781) | ||
* '''MAF''' - | *'''MAF''' - The frequency at which the second most common allele occurs in a given population. | ||
=== Non-disease associated Mutations === | ===Non-disease associated Mutations=== | ||
This tab shows a list of mutations in the genetic sequence that are associated with a disease. The following columns are presented in the table: | This tab shows a list of mutations in the genetic sequence that are not associated with a disease. The following columns are presented in the table: | ||
* '''Source''' - | *'''Source''' - GlyGen evidence linking to the databases and papers that provided the glycosylation information | ||
* '''Filter annotations''' - | *'''Filter annotations''' - | ||
* '''Genomic locus''' - | *'''Genomic locus''' - | ||
* '''Start Pos.''' - | *'''Start Pos.''' - | ||
* '''End Pos.''' - | *'''End Pos.''' - | ||
* '''Sequence''' - | *'''Sequence''' - | ||
* '''MAF''' - | *'''MAF''' - | ||
== Source of information == | ==Source of information== | ||
== Data access == | ==Data access== | ||
== Data harmonization == | ==Data harmonization== | ||
== Data filtering == | ==Data filtering== | ||
Revision as of 19:39, 3 December 2021
The single nucleotide variation section of the Protein details page in GlyGen provides a detailed list of somatic and germline nucleotide mutations.
Single Nucleotide Variation
Single nucleotide variation is presented in 2 tabs on the Protein details page in GlyGen.
Disease associated Mutations
This tab shows a list of mutations in the genetic sequence that are associated with a disease. The following columns are presented in the table:
- Source - GlyGen evidence linking to the databases and papers that provided the glycosylation information
- Filter annotations - Pass/fail filter results from mapping cancer terms to Disease Ontology ID. Eg. Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%)
- Genomic locus - The genomic position of the reported mutation. Eg. Chr7:81399287
- Start Pos. - Start position of the site in the amino acid sequence. Eg. 1
- End Pos. - End position of the site in the amino acid sequence. Eg. 1
- Sequence - Reference or wild-type amino acid residue change resulting from variation. Eg. M→ L
- Disease - DOID and term corresponding to reported disease. Eg. thyroid gland cancer (DOID:1781)
- MAF - The frequency at which the second most common allele occurs in a given population.
Non-disease associated Mutations
This tab shows a list of mutations in the genetic sequence that are not associated with a disease. The following columns are presented in the table:
- Source - GlyGen evidence linking to the databases and papers that provided the glycosylation information
- Filter annotations -
- Genomic locus -
- Start Pos. -
- End Pos. -
- Sequence -
- MAF -