Welcome to ncVAR_db!

Repo for the ncVAR database You can download this database using

git clone https://github.com/Gardner-BinfLab/ncVarDB

Motivation

Variants within the non-coding genome are frequently associated with phenotypes in genome-wide association studies. These regions may be involved in the regulation of gene expression, encode functional non coding RNAs, splicing, or other cellular functions. We have curated a list of well characterised non-coding human genome variants based on published evidence for causing functional consequences. In order to minimise possible annotation errors, two curators have independently verified the supporting evidence for pathogenicity of each non-coding variant from published literature. ##Add paper link

Project structure

Contained in this project are the final datasets, scripts, and additional raw data used in generating the ncVar database.

Data:

The final datasets, and the raw data used in the generation of the figures and benign dataset. Some files were too big for github but can be found on our Zenodo repository

Scripts:

A collection of scripts and (some) intermediate data files used to generate results

FATHHM-XF:

Files produced by FATHHM-XF data analysis.

CADD:

Scripts and files necessary for CADD data analysis.

DANN:

Scripts and files necessary for DADD data analysis.

Features

The ncVar database contains curated pathogenic variants, with a supplied benign control dataset.

The information contained in this database is as follows:

ID: An ID for this database

Genome: The genome that the variant was found in

Chr: The chromosome the variant is in

Pos: The starting position of the variant (referring to the first affected nucleotide)

Ref: The reference genome sequence

Alt: The variant sequence

Mutation_type: the type of mutation of the variant (single, insertion, deletion)

Mutation_position: The genomic position of the variant (intronic, 5utr, 3utr, ncRNA)

MAF: The frequency of the minor allele (Alt)

X_ref: Any ID’s from other databases e.g. dbSNP [REF] ClinVar [REF], OMIM [REF], Literature

The pathogenic dataset has an extra two columns:

Pubmed_ID: A pubmed identifier that relates to literature that confirms the pathogenicity of the variant

Phenotype: The phenotype associated with the variant (sourced from XXXX)