Methylation

Methylation

The Methylation tab contains information on methylation positions for a Spanish population.

The samples belong to individuals who may or may not be within the CSVS. We collect statistical information (mean, standard deviation). and we annotate with CSVS frequencies.

Filters

Similar to Search CSVS, the tool provided search filters (left column).

1. Position:

   This filter is required and have two possibilities:

   • Chromosomal Location: Region where narrow your search. Chromosome:Start-End. Ex.: 1:10004570-10046460.
   • Gene: Visualize a particular gene. If you want see more than one gene, separate them with commas. Ex.: BRCA2,PPL. The maximum number of genes you accept is 3.

   You must indicate a search region y/or a gene to Search.

2. Subpopulations:

   Use ICD-10 (10th revision of the International Statistical Classification of Diseases and Related Health Problems), and other projects groups: MGP (Medical Genome Proyect) or IBIS (107 Spanish individuals from 1000 Genomes Project).

   • IBS (107 Spanish individuals from 1000genomes)
   • Healthy controls
   • I Certain infectious and parasitic diseases
   • II Neoplasms
   • III Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism
   • IV Endocrine, nutritional and metabolic diseases
   • V Mental and behavioural disorders
   • VI Diseases of the nervous system
   • VII Diseases of the eye and adnexa
   • VIII Diseases of the ear and mastoid process
   • IX Diseases of the circulatory system
   • X Diseases of the respiratory system
   • XI Diseases of the digestive system
   • XII Diseases of the skin and subcutaneous tissue
   • XIII Diseases of the musculoskeletal system and connective tissue
   • XIV Diseases of the genitourinary system
   • XV Pregnancy, childbirth and the puerperium
   • XVI Certain conditions originating in the perinatal period
   • XVII Congenital malformations, deformations and chromosomal abnormalities
   • XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified
   • XIX Injury, poisoning and certain other consequences of external causes
   • XX External causes of morbidity and mortality
   • XXI Factors influencing health status and contact with health services
   • XXII Codes for special purposes
   • MGP (267 healthy controls)
   • MGP (healthy controls, Solid 4)

   In addition, new groups have been added and these correspond to parents of people in that group, but NOTE: they do not seem like this disease, nevertheless you can not discard they are carrier for pathogenic variants in the case of recessive diseases.

   • I Certain infectious and parasitic diseases (controls)
   • II Neoplasms (controls)
   • III Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism (controls)
   • IV Endocrine, nutritional and metabolic diseases (controls)
   • V Mental and behavioural disorders (controls):
   • VI Diseases of the nervous system (controls)
   • VII Diseases of the eye and adnexa (controls)
   • VIII Diseases of the ear and mastoid process (controls)
   • IX Diseases of the circulatory system (controls)
   • X Diseases of the respiratory system (controls)
   • XI Diseases of the digestive system (controls)
   • XII Diseases of the skin and subcutaneous tissue (controls)
   • XIII Diseases of the musculoskeletal system and connective tissue (controls)
   • XIV Diseases of the genitourinary system (controls)
   • XV Pregnancy, childbirth and the puerperium (controls)
   • XVI Certain conditions originating in the perinatal period (controls)
   • XVII Congenital malformations, deformations and chromosomal abnormalities (controls)
   • XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified (controls)
   • XIX Injury, poisoning and certain other consequences of external causes (controls)
   • XX External causes of morbidity and mortality (controls)
   • XXI Factors influencing health status and contact with health services (controls)
   • XXII Codes for special purposes (controls)

   The subpopulation is displayed if there is data.

   If you do not select any subpopulation in the search, this filter will not be used, so all the subpopulation will be used. This is important at the moment to show the information about CSVS frequency (view more detail in section Results)

3. Methylation Array: there are data from different sequencing technologies:

   • 450K
   • 850K-EPICv1
   • EPICv2
   • Unknown

   If you do not select any technology in the search, this filter will not be used, so all the technologies will be used.

4. Tissues:

   • Blood
   • Fibroblasts
   • Unknown

   If you do not select any tissue in the search, this filter will not be used, so all the tissues will be used.

5. Genders:

   • Female
   • Male
   • Unknown

   If you do not select any gender in the search, this filter will not be used, so all the genders will be used.

6. Sampling age: range between birth and date obtain the sample. The values are inclusive.

   • Min
   • Max

   If you do not select any age in the search, this filter will not be used, so all the age will be used.

Results

When the user selects the desired filters, he must press to search to perform the search.The search result will be displayed in a data table. The table shows the methylation positions enriched with other annotations from num variants of the CSVS database in this position. In addition, it filters by subpopulation the frequency about CSVS.

Fields

The information shown would be the following:

• Chr: Chromosome position.

• Position: Methylation position.

• Gene: Gene or genes in which the variant is located.

• Methylation:

  • Samples: Number of samples that meet the filters
  • Avg: Average
  • stdDesv: Standard deviation

• CSVS: annotations about CSVS

  • Alleles: variants that exist in this chromosome-position in CSVS

  • Samples/All:

    • samples: Number of samples in CSVS that meet the filters (subpopulation) in this position.
    • all: Number of all samples in CSVS that exists variants in this position (without filters). IMPORTANT: There may be subpopulation in CSVS that no exists in the filter methylation subpopulation. You must deselect all population filter to display all frequencies without restrictions. Por example, in CSVS may be controls that no exists in methylation position.

  • 0 Freq: allele frequency for reference (filtered by selected subpopulations)

  • 1 Freq: allele frequency for alternative (filtered by selected subpopulations)

  • MAF: Minor Allele Frequency, the lowest value between 0 Freq and 1 Freq (filtered by selected subpopulations)

Extra information

If you click on one of the displayed methylation position, you will see additional information in the bottom part.

Genomic variants

The first tab that we find at the bottom part is "Genomic variants". This tab only shows if there is a variant in this position and that it meets the selected filters (subpopulations).
In this tab, you can see the summary of the variants and their annotations. If you want more info about the variants, go to the "Search" tab.

Methylation

In this section you can see the graph of all the samples that have this methylation position. Additionally, there are some statistical information, as min, max, mean or quartiles that help us to understand the distribution.

There are two groups:

• Subpopulations: All selected subpopulations.

  NOTES:

  • If you selected "Healthy Controls", this option was included.
  • This also happens when you do not select any subpopulations.
  • This information takes into account the rest of the selected filters.

• Healthy controls: Only "Healthy controls" group.

  NOTE:

  • This information takes into account the rest of the selected filters.

The graph shows the red line that corresponds to the average Healthy Control.

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