Tag: Genetic Interaction

E-MAPs 1.1 – Imputing Quantitative Genetic Interactions

E-MAPs 1.1

:: DESCRIPTION

E-MAPs (Epistatic miniarray profiles) are a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. The datasets resulting from E-MAP experiments typically take the form of a symmetric pairwise matrix of interaction scores. These datasets have a significant number of missing values – up to 35% – that can reduce the effectiveness of some data analysis techniques and prevent the use of others.

::DEVELOPER

the Machine Learning Group (MLG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /Mac OsX
  • Python

:: DOWNLOAD

 E-MAPs

:: MORE INFORMATION

Citation

Missing value imputation for epistatic MAPs
Colm Ryan , Derek Greene , Gerard Cagney and Pádraig Cunningham
BMC Bioinformatics 2010, 11:197 doi:10.1186/1471-2105-11-197

Zodiac – Depiction of Genetic Interactions in Cancer by integrating TCGA data

Zodiac

:: DESCRIPTION

Zodiac is a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data. It is an evolution of existing knowledge by treating it as a prior graph, integrating it with a likelihood model derived by Bayesian graphical model based on TCGA data, and producing a posterior graph as updated and data-enhanced knowledge. In short, Zodiac realizes “Prior interaction map + TCGA data → Posterior interaction map.”

::DEVELOPER

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Zhu Y, Xu Y, Helseth DL Jr, Gulukota K, Yang S, Pesce LL, Mitra R, Müller P, Sengupta S, Guo W, Silverstein JC, Foster I, Parsad N, White KP, Ji Y.
Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data.
J Natl Cancer Inst. 2015 May 8;107(8):djv129. doi: 10.1093/jnci/djv129. PMID: 25956356; PMCID: PMC4554190.