CaSNP – Collection of Copy Number Alteration (CNA) from SNP Arrays

CaSNP

:: DESCRIPTION

CaSNP is a comprehensive collection of copy number alteration (CNA) from SNP arrays.It collects 11,485 Affymetrix SNP arrays of 34 different cancer types in 105 studies to profile the genome-wide CNA and SNP in each.

::DEVELOPER

CaSNP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data.
Cao Q, Zhou M, Wang X, Meyer CA, Zhang Y, Chen Z, Li C, Liu XS.
Nucleic Acids Res. 2011 Jan;39(Database issue):D968-74. doi: 10.1093/nar/gkq997.

TAGCNA 1.0 – Identify Significant Consensus Events from Copy Number Alterations in Cancer Genome

TAGCNA 1.0

:: DESCRIPTION

TAGCNA is designed to identify significant consensus events from copy number alterations in cancer genome.

::DEVELOPER

Xiguo Yuan: xiguoyuan/at/mail.xidian.edu.cn

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • R package
:: DOWNLOAD

 TAGCNA

:: MORE INFORMATION

Citation

PLoS One. 2012;7(7):e41082. doi: 10.1371/journal.pone.0041082. Epub 2012 Jul 18.
TAGCNA: a method to identify significant consensus events of copy number alterations in cancer.
Yuan X, Zhang J, Yang L, Zhang S, Chen B, Geng Y, Wang Y.

OncodriveCIS 1.1.0 – Assesses the Influence of Copy Number Alterations (CNA) in the Gene Expression

OncodriveCIS 1.1.0

:: DESCRIPTION

OncodriveCIS  is a method to identify genes that accumulate copy number alterations important for tumour development. This is done by computing the functional impact of CNAs by measuring their effect on the expression of the genes affected.

::DEVELOPER

 The Biomedical Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 OncodriveCIS

:: MORE INFORMATION

Citation

Tamborero D, Lopez-Bigas N and Gonzalez-Perez A.
Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression.
PLoS ONE 8(2): e55489. doi:10.1371/journal.pone.0055489