overview

ClickGene website: An Overview

In genetics, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an examination of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. GWASs typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major human diseases, but can equally be applied to any other organism.

The aim of this ClickGWAS is to make it possible for you to do GWAS by only mouse-clicking. As long as you know how to Google, you can use these web-based analysis tools provided by us by yourself. Therefore, your precious time can be saved for other more meaningful research. Until now, all data was downloaded from the “Legacy GDC portal” which was updated before 10/05/2016. New updated data is coming! All non-primary samples are removed before any preprocessing and analyzing by us. Gene expression is the level 3 data preprocessed by TCGA which was measured by the platform Illumina HiSeq 2000 RNA Sequencing Version 2. The level 3 CNV (Copy Number Variation) data was measured by Affymetrix Genome-Wide Human SNP Array 6.0. The annotation file of hg19 was used as a reference for the locations of genes (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/). The CNV value of a gene was defined as the average value of all of the segments' CNV values corresponding to the gene. More category data GWAS analyzing methods are coming! Please go to Legacy GDC portal for more details of these data. Data analysis was restricted to autosomes.

  • Open-Access: we won't charge anything for using the analysis tools we provided. But if you use the results or plots created or obtained by the tools provided with this website, please be sure that you mention our website in the Material and Methods section in your articles, presentations, reports and other documents.
  • Data visualization: To make the exploration of data as easy as possible, different kinds of plots are provided to visualizing almost all kinds of genomic alterations including mRNA expression, copy number variation and so on.
  • Downloading and Installation free: No necessary to download any data or install any software or apps. Therefore, it's totally green for your computer.
  • Figure DIY: Modify marker shapes, colors and other details of the figures to make them your own style.
  • Flexible: Different file type and size for figure downloading.
  • Handy: For your convinence, the sample ID and other necessary details of each individual sample will show up as long as you put your mouse on the corresponding marker in the plots.
  • Downloadable: The corresponding data for visualizing or data-mining are all downloadable for your further research.

For more information about available methods and options, please go to ClickGene Website.

ClickGene is accessible using a web browser such as Safari, Chrome, Internet Explorer, Firefox and so on at the following URL: http://www.clickgenome.org

The welcome page displays an overview of main available provided analyses methods:

It will automatically skip to the HOME page after a few seconds. You also can click the “Skip Now” button at the right bottom of this page to skip into the HOME page if you do not want to wait at all.

  • overview.txt
  • Last modified: 2019/07/05 16:10
  • by tongyifan