Asterias – Applications for the Analysis of Gene Expression and aCGH data

Asterias

:: DESCRIPTION

Asterias is an integrated collection of freely-accessible web tools for the analysis of gene expression and aCGH data. Asterias includes applications for the analysis of genomic (and, to a lesser extent, proteomic) data that cover from data normalization to development of prediction models for survival data. Most of our applications use parallelization (via MPI) and run on a server with 60 CPUs for computation. And most of our applications allow the user to obtain additional information about the genes (chromosomal location, PubMed ids, Gene Ontology terms, etc) by using clickable links in tables and/or figures, thus allowing for enhanced interpretability of the results.

The tools include: normalization of expression and aCGH data (DNMAD); converting between different types of gene/clone and protein identifiers (IDconverter/IDClight); filtering and imputation (preP); finding differentially expressed genes related to patient class and survival data (Pomelo II); searching for models of class prediction (Tnasas); using random forests to search for minimal models for class prediction or for large subsets of genes with predictive capacity (GeneSrF); searching for molecular signatures and predictive genes with survival data (SignS); detecting regions of genomic DNA gain or loss (ADaCGH).

::DEVELOPER

 Bioinfo Unit@CNIO

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  Asterias

:: MORE INFORMATION

Citation

Cancer Inform. 2007 Feb 3;3:1-9.
Asterias: a parallelized web-based suite for the analysis of expression and aCGH data.
Alibés A, Morrissey ER, Ca?ada A, Rueda OM, Casado D, Yankilevich P, Díaz-Uriarte R.

PLA – Piecewise-constant and Low-rank Approximation for Multi-sample aCGH Data Analysis

PLA

:: DESCRIPTION

PLA – Piecewise-constant and Low-rank Approximation for Multi-sample aCGH Data Analysis

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 PLA

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Mar 31. [Epub ahead of print]
Piecewise-constant and low-rank approximation for identification of recurrent copy number variations.
Zhou X1, Liu J, Wan X, Yu W.

Stepgram 2.12 – Application for Aberration Calling in aCGH data

Stepgram 2.12

:: DESCRIPTION

The Stepgram application is used to detect aberrations in DNA copy number data from aCGH (array-based comparative genomic hybridization) experiments.

::DEVELOPER

Doron Lipson

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Stepgram

:: MORE INFORMATION

Citation

Doron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial and Zohar Yakhini,
Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis“.
Journal of Computational Biology, 13(2):215-228, 2006

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