Tag: Microarray Data

Diurnal 2.0 – Mining and Viewing Diurnal and Circadian Microarray data for Arabidopsis thaliana, poplar, and rice

Diurnal 2.0

:: DESCRIPTION

Diurnal is a web-based tool for accessing the diurnal and circadian genome-wide expression results of genes from several array experiments conducted on common model plants. The expression patterns of particular loci or array probes can be looked up under a variety of different conditions. For each condition, every expression pattern has been modeled using a periodic pattern, which has then been used to estimate the phase of peak expression.

::DEVELOPER

Mockler Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.
Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay SA, Chory J.
Cold Spring Harb Symp Quant Biol. 2007;72:353-63. doi: 10.1101/sqb.2007.72.006.

MADIBA – MicroArray Data Interface for Biological Annotation

MADIBA

:: DESCRIPTION

MADIBA is a web interface for functional analysis of cluster of genes with same profile of expression for Plasmodium falciparum, Oryza Sativa (rice), Arabidopsis thaliana and Pectobacterium atrosepticum

::DEVELOPER

the Bioinformatics and Computational Biology Unit at the University of Pretoria

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Law PJ, Claudel-Renard C, Joubert F, Louw AI and Berger DK (2008)
MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters
BMC Genomics 9:105

MicroarrayRUS 1.0 – Analysis of Microarray data

MicroarrayRUS 1.0

:: DESCRIPTION

MicroarrayRUS (Microarray Я US) is an R-based program that seamlessly integrates functions from over a dozen or so most-widely used Bioconductor packages to offer researchers a streamlined workflow to perform routine microarray expression data analysis without the need of learning R language.

::DEVELOPER

Yibu Chen, Yilin Dai, Ling Guo, Meng Li, Jin Wu

:: SCREENSHOTS

MicroarrayRUS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

 MicroarrayRUS

:: MORE INFORMATION

Citation

Yilin Dai, Ling Guo, Meng Li, and Yi-Bu Chen
Microarray R US: a user-friendly graphical interface to bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.
BMC Res Notes. 2012 Jun 8;5(1):282.

WebArray 1.4 – Web platform for analysis of Microarray data

WebArray 1.4

:: DESCRIPTION

WebArray is a web platform for analysis of microarray data. Two-color data and Affymetrix data are supported.

::DEVELOPER

Xiao-Qin Xia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Apache
  • MySQL
  • R language
  • Bioconductor
  • Python
  • Ghostscript

:: DOWNLOAD

 WebArray

:: MORE INFORMATION

Citation

Xia X, McClelland M, Wang Y.
WebArray: an online platform for microarray data analysis.
BMC Bioinformatics. 2005, 6(1): 306.

Decision Forest 2 – Novel Pattern Recognition method for multiclass Classification in Microarray data analysis

Decision Forest 2

:: DESCRIPTION

Decision Forest is a novel pattern-recognition method for analysis of data from microarray experiments, proteomics research, and predictive toxicology

::DEVELOPER

the National Center for Toxicological Research (NCTR).

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

  Decision Forest

:: MORE INFORMATION

Citation

Multiclass Decision Forest–a novel pattern recognition method for multiclass classification in microarray data analysis.
Hong H, Tong W, Perkins R, Fang H, Xie Q, Shi L.
DNA Cell Biol. 2004 Oct;23(10):685-94.

 

MDCS – Microarray Data Classification Server

MDCS

:: DESCRIPTION

The MDCS provides maximal margin Linear Programming method (Antonov et al., 2004) for classification of tumor samples based on microarray data. This procedure detects groups of genes and constructs models (features) that strongly correlate with particular tumor types. The detected features include genes whose functional relations are changed for particular cancer types.

::DEVELOPER

MDCS Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MDCS

:: MORE INFORMATION

Citation:

Antonov, A.V., Tetko, I.V, Prokopenko, V.V., Kosykh,D. & Mewes, H.W.
Web Portal for Classification of Expression Data using Maximal Margin Linear Programming,
Bioinformatics, 2004, 20, 3284-5.

 

geneCBR – Perform Cancer Classification based on Microarray data

geneCBR

:: DESCRIPTION

geneCBR is a model that can perform cancer classification based on microarray data. In order to store the information belonging to each sample, the system uses a fuzzy codification to represent the gene expression levels of each sample. This operation permits the generalization over the whole case base in order to tackle intra-experimental and inter-experimental variations in the data. Based on the fuzzy discretization of real gene expression data into a small number of fuzzy membership functions, the system is capable of constructing a set of prototypes that are able to represent the main characteristics of previously ascertained classes.

::DEVELOPER

GENECBR Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 geneCBR

:: MORE INFORMATION

Citation

D. Glez-Peña; F. Díaz; J.M. Hernández; J.M. Corchado; F. Fdez-Riverola (2009)
geneCBR: a translational tool for multiple-microarray analysis and integrative information retrieval for aiding diagnosis in cancer research.
BMC Bioinformatics. 10:187. ISSN: 1471-2105

 

TFInfer 1.0 – Inference of Transcription Factor Activities from Microarray data

TFInfer 1.0

:: DESCRIPTION

 TFInfer is an open source software for the inference of transcription factor activities from microarray data.

::DEVELOPER

Shahzad Asif (shahzad.asif@ed.ac.uk)  , Guido Sanguinetti (gsanguin@staffmail.ed.ac.uk)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • .Net

:: DOWNLOAD

 TFInfer

:: MORE INFORMATION

Citation:

TFInfer: a tool for probabilistic inference of transcription factor activities.
Asif HM, Rolfe MD, Green J, Lawrence ND, Rattray M, Sanguinetti G.
Bioinformatics. 2010 Oct 15;26(20):2635-6. Epub 2010 Aug 24.

Knorm 1.0 – Microarray Data From Multiple Biologically Interrelated Experiments

Knorm 1.0

:: DESCRIPTION

Knorm provides Knorm correlations between genes (or probes) from microarray data obtained across multiple biologically interrelated experiments. The Knorm correlation adjusts for experiment dependencies (correlations) and reduces to the Pearson coefficient when experiment dependencies are absent. The Knorm estimation approach can be generally applicable to obtain between-row correlations from data matrices with two-way dependencies.

::DEVELOPER

Siew Leng Teng <slteng at stat.berkeley.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Knorm

:: MORE INFORMATION

MSCLtoolbox 200902 – Statistical Analysis of Microarray data

MSCLtoolbox 200902

:: DESCRIPTION

MSCLtoolbox (The MSCL Analyst’s Toolbox) includes a set of scripts accessible as either a customized menu item (Windows) or as stand alone scripts (Mac) for the analysis of Affymetrix gene chip data. The scripts are run in the JMP statistical package, see below. Also available in the toolbox are GCOS database access scripts specific for Affymetrix.

::DEVELOPER

Mathematical and Statistical Computing Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • JMP

:: DOWNLOAD

 MSCLtoolbox

:: MORE INFORMATION

 

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