Dataset Information

GSDS 2.0: an upgraded gene feature visualization server.

ABSTRACT:

Unlabelled

: Visualizing genes' structure and annotated features helps biologists to investigate their function and evolution intuitively. The Gene Structure Display Server (GSDS) has been widely used by more than 60?000 users since its first publication in 2007. Here, we reported the upgraded GSDS 2.0 with a newly designed interface, supports for more types of annotation features and formats, as well as an integrated visual editor for editing the generated figure. Moreover, a user-specified phylogenetic tree can be added to facilitate further evolutionary analysis. The full source code is also available for downloading.

Availability and implementation

Web server and source code are freely available at http://gsds.cbi.pku.edu.cn.

Contact

gaog@mail.cbi.pku.edu.cn or gsds@mail.cbi.pku.edu.cn

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Hu B

PROVIDER: S-EPMC4393523 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature

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Publications

GSDS 2.0: an upgraded gene feature visualization server.

Hu Bo B Jin Jinpu J Guo An-Yuan AY Zhang He H Luo Jingchu J Gao Ge G

Bioinformatics (Oxford, England) 20141210 8

<h4>Unlabelled</h4>: Visualizing genes' structure and annotated features helps biologists to investigate their function and evolution intuitively. The Gene Structure Display Server (GSDS) has been widely used by more than 60 000 users since its first publication in 2007. Here, we reported the upgraded GSDS 2.0 with a newly designed interface, supports for more types of annotation features and formats, as well as an integrated visual editor for editing the generated figure. Moreover, a user-speci ...[more]

PMID: 25504850

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Project description:Cigarette smoking is a major cause of death worldwide resulting in over six million deaths per year. Cigarette smoke contains complex mixtures of chemicals that are harmful to nearly all organs of the human body, especially the lungs. Cigarette smoking is considered the major risk factor for many lung diseases, particularly chronic obstructive pulmonary diseases (COPD) and lung cancer. However, the underlying molecular mechanisms of smoking-induced lung injury associated with these lung diseases still remain largely unknown. Expression microarray techniques have been widely applied to detect the effects of smoking on gene expression in different human cells in the lungs. These projects have provided a lot of useful information for researchers to understand the potential molecular mechanism(s) of smoke-induced pathogenesis. However, a user-friendly web server that would allow scientists to fast query these data sets and compare the smoking effects on gene expression across different cells had not yet been established. For that reason, we have integrated eight public expression microarray data sets from trachea epithelial cells, large airway epithelial cells, small airway epithelial cells, and alveolar macrophage into an online web server called SEGEL (Smoking Effects on Gene Expression of Lung). Users can query gene expression patterns across these cells from smokers and nonsmokers by gene symbols, and find the effects of smoking on the gene expression of lungs from this web server. Sex difference in response to smoking is also shown. The relationship between the gene expression and cigarette smoking consumption were calculated and are shown in the server. The current version of SEGEL web server contains 42,400 annotated gene probe sets represented on the Affymetrix Human Genome U133 Plus 2.0 platform. SEGEL will be an invaluable resource for researchers interested in the effects of smoking on gene expression in the lungs. The server also provides useful information for drug development against smoking-related diseases. The SEGEL web server is available online at http://www.chengfeng.info/smoking_database.html.

Dataset Information

GSDS 2.0: an upgraded gene feature visualization server.

Unlabelled

Availability and implementation

Contact

Supplementary information

Publications

GSDS 2.0: an upgraded gene feature visualization server.

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