VERA & SAM 1.0 – Find Significant Expression Differences in DNA Microarray Data

VERA & SAM 1.0

:: DESCRIPTION

VERA & SAM (Variability and ERror Assessment and Significance of Array Measurement) Estimates error model parameters from replicated, preprocessed experiments, and  uses error model to improve the accuracy of the expression ratio and to assign a value ‘lambda’ to each gene, indicating the likelihood that the gene is differentially expressed.

VERA and SAM are a pair of programs that provide a method to determine whether any given gene is expressed at a different level in one cell population than in another according to microarray data.

::DEVELOPER

the Ideker Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

VERA & SAM

:: MORE INFORMATION

Citation

T. Ideker, V. Thorsson, A. F. Siegel, and L. Hood.
Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data
Journal of Computational Biology 7 (6) 805-817 (2000).

Dapple 0.88pre4 – DNA Microarrays Image Analysis

Dapple 0.88pre4

:: DESCRIPTION

Dapple is a program for quantitating spots on a two-color DNA microarray image. Given a pair of images from a comparative hybridization, Dapple finds the individual spots on the image, evaluates their qualities, and quantifies their total fluorescent intensities.

Dapple is designed to work with microarrays on glass. The spot-finding techniques used are robust to uneven spot sizes and positional deviations caused by “wobbling” of the arraying robot, as well as image noise and artifacts. As long as your spots are consistently circular, Dapple has a good chance of finding them accurately.

::DEVELOPER

Jeremy Buhler

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Dapple

:: MORE INFORMATION

Citation:

J. Buhler, T. Ideker, D. Haynor, “Dapple: Improved Techniques for Finding Spots on DNA Microarrays”, University of Washington Department of Computer Science & Engineering Technical Report UW-CSE-2000-08-05, (2000)  Supplement.

Probe Select – Select Oligos for DNA Microarray

Probe Select

:: DESCRIPTION

Probe Select is the probes program to select oligos for DNA microarray.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Probe Select

:: MORE INFORMATION

Citation

Bioinformatics. 2001 Nov;17(11):1067-76.
Selection of optimal DNA oligos for gene expression arrays.
Li F, Stormo GD.
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Cyber-T – Software and Server for Analysis of DNA Microarray data

Cyber-T

:: DESCRIPTION

Cyber-T is a a microarray analysis web interface from UCI’s Institute for Genomics and Bioinformatics. It accommodates both paired (2-dye) data and data in which control and experiment are on separate experiments (e.g. affymetrix based data). It also supports Bayesian statistical approaches and Bonferroni corrections for significance analysis of differentially expressed clones.

::DEVELOPER

Pierre Baldi and Tony Long at Institute for Genomics and Bioinformatics 

:: REQUIREMENTS

:: DOWNLOAD

 Cyber-T

:: MORE INFORMATION

Citation:

Kayala, M.A. and Baldi, P.,
Cyber-T web server: differential analysis of high-throughput data“,
Nucleic Acids Research, 40 (W1): W553-W559, (2012).

P. Baldi and A.D. Long,
A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-Test and Statistical Inferences of Gene Changes“,
Bioinformatics, 17, 6, 509-519, (2001).

OligoWiz 2.3.0 – Design oligonucleotides for DNA microarrays

OligoWiz 2.3.0

:: DESCRIPTION

OligoWiz performs intelligent design of oligonucleotides for DNA microarrays. It is implemented as a client-server solution, which consist of an easy to use Graphical User Interface (written in Java) which delegates the computationally intensive operations to a powerful Multi-CPU server hosted at the Center for Biological Sequence Analysis.

::DEVELOPER

CBS (Center for Biological Sequence Analysis) at Technical University of Denmark

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / UNIX / MacOS X
  • Java

:: DOWNLOAD

OligoWiz Client ; OligoWiz stand-alone

:: MORE INFORMATION

Citation

OligoWiz 2.0 – integrating sequence feature annotation into design of microarray probes
Rasmus Wernersson and Henrik Bjørn Nielsen.
Nucleic Acids Research, 2005, Vol. 33, Web Server issue W611-W615

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays.
Henrik Bjørn Nielsen, Rasmus Wernersson and Steen Knudsen.
Nucleic Acids Research, 2003, Vol. 31, No. 13 3491-3496

ArrayIDer – Structural Re-annotation pipeline for DNA Microarray

ArrayIDer

:: DESCRIPTION

ArrayIDer maps lists of accessions to find equivalent accessions in other public databases. It searches NCBI(including the dbEST or UniGene, EntrezGene, GenBank, RefSeq and GEO databases), UniProtKB, Ensembl, EMBL and DDBJ.

:: DEVELOPER

AgBase, Department of Basic Science,College of Veterinary Medicine, Mississippi State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Jan 23;10:30. doi: 10.1186/1471-2105-10-30.
ArrayIDer: automated structural re-annotation pipeline for DNA microarrays.
van den Berg BH, Konieczka JH, McCarthy FM, Burgess SC.

SSHscreen 2.0.1 – High-throughput screening of SSH cDNA libraries using DNA microarray data

SSHscreen 2.0.1

:: DESCRIPTION

SSHscreen is the R software package for screening forward and reverse cDNA libraries enriched for cowpea drought response genes microarrays,  (i) to normalize the data effectively using spike-in control spot normalization, and (ii) to select clones for sequencing based on the calculation of enrichment ratios with associated statistics.

::DEVELOPER

the Bioinformatics and Computational Biology Unit at the University of Pretoria

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R package

:: DOWNLOAD

 SSHscreen

:: MORE INFORMATION

Citation

Coetzer N, Gazendam I, Oelofse D, Berger DK (2010)
SSHscreen and SSHdb, generic software for microarray based gene discovery: application to the stress response in cowpea.
Plant Methods 6: 10.

Gifi Array Analyzer 1.2 beta – Analysis of DNA Microarray data and Gene Functional Classification data

Gifi Array Analyzer 1.2 beta

:: DESCRIPTION

Gifi Array Analyzer is a Java application for integrated analysis of DNA microarray data and gene functional classification data.Gifi Array Analyzer implements Homals (Homogeneity Analysis by means of Alternating Least Square). Homogeneity analysis is a graphical, multivariate statistical method.

::DEVELOPER

Cui Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux
  • Java

:: DOWNLOAD

  Gifi Array Analyzer

:: MORE INFORMATION

Citation

Yan Cui, Mi Zhou, Wing Hung Wong (2004)
Integrated Analysis of Microarray Data and Gene Function Information.
OMICS A Journal of Integrative Biology, Vol.8, No.2 106-117

GenePublisher 1.03 – Analysis of DNA Microarray Data

GenePublisher 1.03

:: DESCRIPTION

GenePublisher performs automated data analysis from gene expression experiments on a number of different platforms. This server accepts gene tables or Affymetrix CEL files as input, performs numerical and statistical analysis, links the results to various databases, and returns a report of the results. The input data is deleted immediately upon completion of the analysis unless you select the database option below.

::DEVELOPER

CBS (Center for Biological Sequence Analysis) at Technical University of Denmark

:: SCREENSHOTS

:: REQUIREMENTS

  • web browser

:: MORE INFORMATION

Input restrictions:

  • The input CEL files must be compressed with gzip (available from www.gzip.org) and cannot be more than 30 Mbytes in total size. That corresponds to 12 HuGeneFL chips, 10 HG_U95A chips, 22 Focus chips, 8 HG-U133A chips, and so on. The maximum number of chips accepted on this web server is currently 12. There is another server without input restrictions.
  • Avoid using characters _, &, %, # in the input as they may interfere with analysis.

For publication of results, please cite:

GenePublisher: Automated Analysis of DNA Microarray Data.
Knudsen, S., Workman, C., Sicheritz-Ponten, T., and Friis, C.
Nucleic Acids Research. Vol. 31, No. 13 3471-3476.