GSCA / GSCALite – Gene Set Cancer Analysis

GSCA / GSCALite

:: DESCRIPTION

GSCA is an integrated database for genomic and immunogenomic gene set cancer analysis.

GSCALite is a web-based analysis platform for gene set cancer analysis. The alterations on DNA or RNA of cancer related genes may be contribute to the cancer initiation, progress, diagnosis, prognosis, therapy. As the cancer genomics big data available, it is very useful and urgent to provide a platform for gene set analysis in cancer.

::DEVELOPER

An-Yuan Guo’s Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Liu CJ, Hu FF, Xia MX, Han L, Zhang Q, Guo AY.
GSCALite: a web server for gene set cancer analysis.
Bioinformatics. 2018 Nov 1;34(21):3771-3772. doi: 10.1093/bioinformatics/bty411. PMID: 29790900.

GSCA / cGSCA – Gene Set Control Analysis

GSCA / cGSCA

:: DESCRIPTION

GSCA is a new computational framework for linking gene sets with transcriptional control.

C-GSCA tool performs a hierarchical clustering of over-represented samples found by GSCA.

::DEVELOPER

GSCA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Exp Hematol. 2013 Apr;41(4):354-66.e14. doi: 10.1016/j.exphem.2012.11.008. Epub 2012 Dec 4.
Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data.
Joshi A1, Hannah R, Diamanti E, Göttgens B.

GSCA 2.0 – Gene Set Context Analysis

GSCA 2.0

:: DESCRIPTION

GSCA is an open source software package to transform massive amounts of Publicly available gene Expression Data (PED) into a tool for making new discoveries.

::DEVELOPER

Zhicheng Ji

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 GSCA

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2016 Jan 8;44(1):e8. doi: 10.1093/nar/gkv873. Epub 2015 Sep 8.
Turning publicly available gene expression data into discoveries using gene set context analysis.
Ji Z, Vokes SA, Dang CV, Ji H

GSCA 1.1.1 – Identification of Differentially Co-expressed Gene Sets

GSCA 1.1.1

:: DESCRIPTION

GSCA (Gene Set Co-Expression Analysis) is a sofware to identify differentially co-expressed gene sets. The GSCA approach provides a false discovery rate controlled list of interesting gene sets, does not require that genes be highly correlated in at least one biological condition and is readily applied to data from individual or multiple experiments, as we demonstrate using data from studies of lung cancer and diabetes.

::DEVELOPER

Kendziorski Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package

:: DOWNLOAD

  GSCA

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Nov 1;25(21):2780-6. doi: 10.1093/bioinformatics/btp502. Epub 2009 Aug 18.
Statistical methods for gene set co-expression analysis.
Choi Y, Kendziorski C.