Tutorial

I. Search variants and their regulatory features
Users can search regulatory variants by variants, target genes and related regulatory elements.

1. Search by variants

Please paste your variants in the input region of "Quick search" or of "Search->Variant search", and then select options appropriate to your analysis aim (for "Variant search"), and then click "Search".
Input format
Variant could be submitted one per line with either its dbSNP/dbVar ID or its chromosomal location(hg19). The maximum of variant number for one job is 500 (suggested). The maximum length for a single variant is 1 M.
1) dbSNP/dbVar ID
    rs268
    nsv222
2) Chromosomal location
    chr14:100705101-100705201
    chr12:21305101-21305465
    chrX:55041617-55042101
If a single nucleotide variant(SNV) was submitted with chromosomal location, enter it as 0-based coordinates.
    chr14:100705101-100705102
    chr12:21305101-21305101
    chrX:55041617-55041618
Demo Data
Nine novel non-coding SNVs associated to tumor, identified by Nils et al. (3) at 2014, were used as demo data for example.
    chr5:1295169-1295170
    chr5:1295228-1295229
    chr5:1295243-1295244
    chr5:1295242-1295243
    chr5:1295250-1295251
    chr5:1295253-1295254
    chr5:1295326-1295327
    chr5:1295524-1295525
    chr5:1295916-1295917
Option

2. Search by genes
Input format: Gene official symbol (one per line)

Option

3. Search by elements
Variants in experimentally supported binding regions or predicted TFBSs, variants in mature miRNA/predicted miRNA binding sites, and variants in lncRNAs may be queried by entering the element name and the target gene name.
Input format: Name of TF/miRNA/lncRNA and official symbol of target genes.

II. Search result
rVarBase provides a result summary page for each job, from which detailed variant feature report page can be linked. All analysis results can be downloaded. This page shows: 1) Input and analysis parameters and 2) Result summary for all queried variants. Variant locations are linkable to the detail report pages for each variant.

III. Variant feature report
This page reports results of regulatory analysis and optional supplemental analysis. The regulatory analysis results report target genes that potentially regulated by input variants, possible regulatory manner, and involved regulatory elements. The supplemental results include extended variants (LD proxies and CNVs covered input variant) and associated phenotypes (diseases and gene expression abundance) for input variants. For matched TFBS inside TF binding region, its information (matched TF, location, source and binding matrix) is shown in separating window which could be linked from the "Variant report" page.


IV. Download
All analysis results can be downloaded on "Search result" page. A FTP link (ftp://rv.psych.ac.cn/pub/rv/ ) is provided for whole-data download.



V. Reference
1. Fredriksson, N.J., Ny, L., Nilsson, J.A. and Larsson, E. (2014) Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types. Nature genetics, 46, 1258-1263.

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