• RankGene

  • Referenced in 14 articles [sw12319]
  • data. Summary: RankGene is a program for analyzing gene expression data and computing diagnostic genes ... distinguishing between different types of samples. The program integrates into one system a variety ... makes RankGene a useful tool in gene expression analysis and feature selection. Availability: http://genomics10.bu.edu...
  • BioProspector

  • Referenced in 29 articles [sw09375]
  • high throughput genome sequencing and gene expression techniques gives rise to the demand for data ... mining tools. BioProspector, a C program using a Gibbs sampling strategy, examines the upstream ... region of genes in the same gene expression pattern group and looks for regulatory sequence ... modifications greatly improve the performance of the program. Besides showing preliminary success in finding...
  • SIRENE

  • Referenced in 7 articles [sw17419]
  • Living cells are the product of gene expression programs that involve the regulated transcription ... been proposed to infer gene regulatory networks from gene expression data, a recent comparison ... compendium of expression data. The method decomposes the problem of gene regulatory network inference into ... classification problems, that focus on separating target genes from non-targets for each transcription factor...
  • SPINE

  • Referenced in 6 articles [sw29309]
  • effect experiments. Motivation: The complex program of gene expression allows the cell to cope with ... result multiple genes change their expression levels. To this end, an integrated network of protein ... signaling pathways connecting the causal gene to the affected genes are searched for in this ... knockout effects observed. We provide an integer programming formulation for the latter problem and solve...
  • PermutMatrix

  • Referenced in 13 articles [sw22075]
  • arrange gene expression profiles in optimal linear order. PermutMatrix is a program to perform graphical ... hierarchical clustering for gene expression data...
  • GEPCLASS

  • Referenced in 1 article [sw08756]
  • Classification Rule Discovery Tool Using Gene Expression Programming. This work describes ... recently proposed technique – gene expression programming – for knowledge discovery in the data mining task...
  • GenMAPP

  • Referenced in 8 articles [sw12317]
  • expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated ... with GenMAPP are programs to perform a global analysis of gene expression or genomic data...
  • PCP

  • Referenced in 3 articles [sw30033]
  • program for supervised classification of gene expression profiles. Summary: PCP (Pattern Classification Program ... open-source machine learning program for supervised classification of patterns (vectors of measurements). The principal ... diagnostic tests based on measurements of gene expression. PCP implements leading pattern classification and gene ... classifier performance. Importantly, the implementation integrates gene selection and class prediction stages, which is vital...
  • STOCKS

  • Referenced in 13 articles [sw10438]
  • simulation of biochemical processes is presented. The program uses a rigorously derived Gillespie algorithm that ... applicable to the study of prokaryotic gene expression. Features dedicated to the study of cellular ... expression of Escherichia coli beta-galactosidase as an example, it is shown that the program...
  • EDGE

  • Referenced in 9 articles [sw13105]
  • Differential Gene Expression) is an open source, point-and-click software program for the significance...
  • STEM

  • Referenced in 5 articles [sw30034]
  • Java program for clustering, comparing, and visualizing short time series gene expression data from microarray...
  • FSDB

  • Referenced in 1 article [sw02615]
  • signal between overlapping genes. Programmed frameshifting is involved in the expression of many genes ... viruses and bacteria. The mechanism of programmed frameshifting is not fully understood despite many studies ... frameshift signals and the genes using programmed frameshifting for their expression. It also allows...
  • GEDI

  • Referenced in 2 articles [sw21927]
  • toolbox for analysis of large-scale gene expression data. Background: Several mathematical and statistical methods ... software implementations that require advanced computer programming skills. Researchers from other areas may experience difficulties ... scale gene expression analysis to be carried out by biomedical researchers with limited programming skills ... introduce an user-friendly toolbox called GEDI (Gene Expression Data Interpreter), an extensible, open-source...
  • REVEAL

  • Referenced in 28 articles [sw36999]
  • Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between ... input elements controlling each element or gene in the network. This process is unequivocal ... REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable...
  • MAANOVA

  • Referenced in 4 articles [sw08357]
  • functions for statistical analysis of gene expression data from two-color cDNA microarray experiments ... available in both the Matlab and R programming environments ... quality, apply data transformations, estimate relative gene expression from designed experiments with ANOVA models, evaluate...
  • ErmineJ

  • Referenced in 4 articles [sw30047]
  • gene scores or correlation of gene expression profiles. In addition to a graphical user interface ... command line interface and an application programming interface that can be used to automate analyses ... gene sets, visualizing the Gene Ontology as a table or tree, and visualizing gene expression...
  • UpGene

  • Referenced in 3 articles [sw17355]
  • vaccine is the low-level expression of HIV genes in mammalian cells, which ... primer design program to redesign specific coding sequences for maximal gene expression. Using this algorithm...
  • RSIR

  • Referenced in 16 articles [sw26716]
  • information contained in both gene expression measurements and genes’ promoter sequences. Compared with existing methods ... data and cell cycle data. AVAILABILITY: Matlab programs are available upon request from the authors...
  • GEOquery

  • Referenced in 10 articles [sw17285]
  • repository of nearly 140 000 gene expression experiments. The BioConductor project (Gentleman ... software project built in the R statistical programming environment (R Development core Team...
  • miRecords

  • Referenced in 6 articles [sw29356]
  • noncoding RNAs capable of regulating other genesexpression. Much progress has been made in computational ... years. More than 10 miRNA target prediction programs have been established, yet, the prediction ... interactions between 301 miRNAs and 902 target genes in seven animal species. The Predicted Targets...