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Column Descriptions

SNP Details

gene symbol: HGNC gene symbol (e.g. AGT)

hg18 coordinates: overlapped rsids extracted from papers with UCSC genome browser table 'SNPS (130)', corresponding to the dbSNP build 130 (most recent hg18 build from Apr 30 2009).

hg19 coordinates: overlapped rsids extracted from papers with UCSC genome browser table 'SNPS (135)', corresponding to the dbSNP build 135 (most recent hg19 build from Oct 12 2011).

genomic regions: used UCSC genes (vs RefSeq genes) track to determine genomic region. The genomic region corresponds to the gene that contains or is closest to the SNP. In instances where the gene studied in the corresponding paper is not the closest gene to the SNP, the genomic region displayed corresponds to the closest gene to the SNP and this gene is displayed with the genomic region (e.g. exon BCL10), and not to the gene studied in the paper. In the majority of instances in which the closest gene is the same as the gene studied, only the region is listed (e.g. exon).

distance from TSS: distance from transcription start site of the studied gene. The sign +/- is with respect to the orientation of the gene (and not the 5' to 3' of the chromosome)

mutation: Base pair mutations are given as A/C.  Amino acid mutations are given as E27Q.  Risk alleles are in red.  Uniprot  was used to determine most recent name for amino acid mutations. Older builds, which papers often use and are more commonly known, are in parentheses.

chromosome: the chromosome in which the SNP is located

rsID: rsID of SNP

p-value/q-value: the p-values associated with the SNP and the significance after correction, if any. NS indicates "not significant" and red indicates a p-value of <=0.05

Article and Study Details

journal and article information: journal name, first author and last author, year, PubMed ID

type of study: candidate gene approach, genome-wide association study, etc.

ethnicity/race: list classifications given by article as well as more broad inferred ones (e.g. "Caucasian")

sample type: maternal vs. fetal, collected from cord blood, serum, etc.

number of women: counts are always presented post-filtering and reflect the actual number of women (offspring, men, etc) used in the study.

primigravidae: percentage of women pregnant/giving birth for the first time (if all, then 100%)

maternal/fetal measurements: weight, height, bmi, etc., where all values are the mean (std in parentheses) unless otherwise specified

Details Page Descriptions

inclusion criteria: can include disease, e.g. preeclamptic women within hypertension population, or criteria such as "required to have severe preeclampsia or HELLP syndrome" and includes the study's definition of the diseases (whether definition of "preeclamptic" requires hypertension and proteinuria and gives thresholds for proteinuria, systolic blood pressure, diastolic blood pressure, with severe preeclampsia values in parentheses). All details of inclusion criteria with numerical constraints included. Essentially a summary of other columns in the "details" page such as "hypertension" or "systolic BP".

PE exclusion criteria: lists diseases the study filtered for for exclusion in preeclamptic women, e.g. CHT (chronic hypertension)

controls Inclusion/Exclusion Criteria: lists the criteria for selection of controls for the study

systolic and diastolic blood pressure: the blood pressure threshold required for a patient to be diagnosed as preeclamptic

additional PE criteria: include further criteria for classification as "preeclamptic"

Explanations

genomic regions: used UCSC genes (vs RefSeq genes) track to determine genomic region. The genomic region corresponds to the gene that contains or is closest to the SNP. In instances where the gene studied in the corresponding paper is not the closest gene to the SNP, the genomic region displayed corresponds to the closest gene to the SNP and this gene is displayed with the genomic region (e.g. exon BCL10), and not to the gene studied in the paper. In the majority of instances in which the closest gene is the same as the gene studied, only the region is listed (e.g. exon).

mutation: Base pair mutations are given as A/C.  Amino acid mutations are given as E27Q.  Risk alleles are in red.  Uniprot  was used to determine most recent name for amino acid mutations. Older builds, which papers often use and are more commonly known, are in parentheses.

Total 'records satisfying filters': The number of 'records satisfy filters' total of our PESNPdb resource is greater than the total number of entries we provide in the exported .csv file of PESNPdb because the PESNPdb table lists uncurated articles that will be batch curated in the future, whereas the exported file does not include uncurated articles. The purpose of listing uncurated articles in our resource is to allow users to know that we are actively curating and are aware of these articles. If you have an article that is not in the resource and is also not listed as an uncurated article, please consider submitting it here.

How to Filter

  • Numeric Filter
    • Use symbols to filter data numerically
    • Symbols: <, >, <=, >=, ==, !=
      • e.g. >=2010 (any value greater than or equal to 2010)
      • e.g. !=3 (any value excluding 3)
    • Without symbols for exact query
      • e.g. 3 (equal to exactly 3) * Note: ==3 will also have the same effect
  • String Filter
    • Matches all results containing the query.
      • e.g. blood sample (any result containing the term 'blood sample' such as 'maternal blood sample')
    • Use "|" to indicate OR
      • e.g. Caucasian|Australian|Asian (any result containing terms Caucasian OR Australian OR Asian)
    • Use "quotes" to match a exact term
      • e.g. "VEGFA" (with quotations, returns only result exactly matching the term "VEFGA")

Curation

  • A link to all articles curated is available at the bottom of the PESNPdb homepage
  • All articles studied SNPs in association with pre-eclampsia. 
  • Articles with both significant (p<=.05) and non-significant SNP associations were curated.

Cite Us

  • PESNPdb : A comprehensive database for SNPs studied in association with pre-eclampsia. Geetu Tuteja, Emily Cheng, Hrysoula Papadakis, Gill Bejerano. Placenta, 33 (12) (2012), pp. 1055-1057.

About Us

Useful links

Database for Preterm Birth

A technical note to improve the reporting of studies of the human placenta.

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