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Citations per year

Number of citations per year for the bioinformatics software tool PLATA

Tool usage distribution map

This map represents all the scientific publications referring to PLATA per scientific context
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PLATA specifications


Unique identifier OMICS_23179
Alternative name Probe Level Alternative Transcript Analysis
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.0
Stability Stable
Numpy, Scipy, Pyrex, Pytables, Pyx, MAT
Maintained Yes


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus




No version available


  • person_outline Chris Burge
  • person_outline Rickard Sandberg
  • person_outline Philip Sharp

Publication for Probe Level Alternative Transcript Analysis

PLATA citations


A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays

BMC Bioinformatics
PMCID: 5445373
PMID: 28545391
DOI: 10.1186/s12859-017-1687-8

[…] a linear model to the observed data aiming to identify non-zero interaction terms between the sample groups and the exons. However, it has been argued that the ANOSVA method performed poorly []. The Probe Level Alternative Transcript Analysis (PLATA) method is based on the normalization of probe level intensities: first the probe-wise intensities, using gene level summarized values, are computed; […]


3′UTR shortening identifies high risk cancers with targeted dysregulation of the ceRNA network

Sci Rep
PMCID: 4066258
PMID: 24953077
DOI: 10.1038/srep05406

[…] ted their roles in tumorigenesis, and several studies have successfully analyzed tandem 3′UTR shortening with exon array data. The exon array probes were first mapped to hg19 using methods similar to PLATA and Rmodel (). Instead of applying a modified t-test to individual samples in a manner similar to those used in previous studies, we adopted a multivariate Bayesian approach such that for each t […]


Probe level estimation improves the detection of differential splicing in Affymetrix exon array studies

Genome Biol
PMCID: 2728531
PMID: 19607685
DOI: 10.1186/gb-2009-10-7-r77

[…] ying non-zero interaction terms between sample groups and exons [], but this approach did not show favourable performance in the evaluations carried out by Affymetrix []. Recently, a procedure called PLATA (Probe-Level Alternative Transcript Analysis) was introduced, which normalizes the expression intensities first probe-wise using the gene-level summary values and then compares the group means o […]

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PLATA institution(s)
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
PLATA funding source(s)
Supported by the Knut and Alice Wallenberg Foundation; the Cancer Research Institute; the Gina De Felice and Robert M. Lefkowitz (1975) Fund; United States Public Health Service grants RO1-GM34277 from the National Institutes of Health, PO1-CA42063 and U19 AI056900 from the National Cancer Institute to PAS and partially by Cancer Center Support (core) grant P30-CA14051 from the National Cancer Institute; and by R01- HG002439 from the NHGRI.

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