miReduce – Correlate the logarithm of Expression Fold Changes

miReduce

:: DESCRIPTION

miReduce correlates the logarithm of expression fold changes of a set of genes with the motif content of the regulatory sequences of these genes. In particular, it correlates the genome wide mRNA log fold changes in experiments involving the knockout/knockdown/overexpression of one or more miRNAs with the motif content of the 3’UTRs. The model is based on linear regression, and is intended for genome-wide studies.

::DEVELOPER

N. Rajewsky Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 miReduce

:: MORE INFORMATION

Citation

Pranidhi Sood, Azra Krek, Mihaela Zavolan, Giuseppe Macino, and Nikolaus Rajewsky
Cell-type-specific signatures of microRNAs on target mRNA expression“,
Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2746-51. Epub 2006 Feb 13.

Correlate 1.03 – Integrative Analysis of 2 Genomic Data Sets

Correlate 1.03

:: DESCRIPTION

Correlate is an Excel plug-in for performing an integrative analysis of two genomic data sets.

If two sets of assays (e.g. gene expression and DNA copy number) have been performed on the same set of patient samples then sparse CCA can be used to find a set of variables in assay 1 that is maximally correlated with a set of variables in assay 2.

::DEVELOPER

Sam Gross / Balasubramanian Narasimhan / Robert Tibshirani /Daniela Witten

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Correlate

:: MORE INFORMATION

paper: Witten DM, Tibshirani R, and T Hastie (2009) A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 10(3): 515-534