• impute

  • Referenced in 93 articles [sw14376]
  • value estimation for DNA microarrays. Motivation: Gene expression microarray experiments can generate data sets with ... expression values. Unfortunately, many algorithms for gene expression analysis require a complete matrix of gene...
  • edgeR

  • Referenced in 46 articles [sw06936]
  • differential expression analysis of digital gene expression data. t is expected that emerging digital gene ... expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics ... fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence...
  • TRANSFAC

  • Referenced in 73 articles [sw17201]
  • TRANSFAC: an integrated system for gene expression regulation. TRANSFAC is a database on transcription factors ... mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features of scaffold/matrix...
  • Cytoscape

  • Referenced in 66 articles [sw09080]
  • network; to visually integrate the network with expression profiles, phenotypes, and other molecular states ... interaction pathways correlating with changes in gene expression, a study of protein complexes involved ... Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models...
  • DEseq

  • Referenced in 48 articles [sw10344]
  • DESeq: Differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence...
  • BioProspector

  • Referenced in 28 articles [sw09375]
  • upstream regulatory regions of co-expressed genes. The development of high throughput genome sequencing ... gene expression techniques gives rise to the demand for data-mining tools. BioProspector ... region of genes in the same gene expression pattern group and looks for regulatory sequence...
  • COSA

  • Referenced in 45 articles [sw22936]
  • discussed. Applications in different domains, including gene expression arrays, are presented...
  • OSCAR

  • Referenced in 44 articles [sw03026]
  • with possibly high correlations, such as gene expression data. In this article, a new method...
  • SAM

  • Referenced in 20 articles [sw08356]
  • False Discovery Rates for Detecting Differential Gene Expression in DNA Microarrays. SAM is a computer ... package for correlating gene expression with an outcome parameter such as treatment, survival time ... general approach to detecting differential gene expression in DNA microarrays. Some recently developed methodology...
  • EBarrays

  • Referenced in 31 articles [sw08355]
  • developed an empirical Bayes methodology for gene expression data to account for replicate arrays, multiple...
  • SSS

  • Referenced in 29 articles [sw07794]
  • computers. We discuss an example from gene expression cancer genomics, comparisons with MCMC and other...
  • Ginsim

  • Referenced in 28 articles [sw09090]
  • function mutations or ectopically induced gene expression...
  • GeneRank

  • Referenced in 16 articles [sw27064]
  • based on the fold-change of gene expression between a reference and a ”treated” sample ... results usually combines lists of differentially expressed genes with previous knowledge about their biological function ... mathematical properties. It combines gene expression information with a network structure derived from gene annotations ... gene ontologies) or expression profile correlations. Using both simulated and real data we find that...
  • RankGene

  • Referenced in 14 articles [sw12319]
  • RankGene: identification of diagnostic genes based on expression data. Summary ... RankGene is a program for analyzing gene expression data and computing diagnostic genes based ... makes RankGene a useful tool in gene expression analysis and feature selection. Availability: http://genomics10.bu.edu...
  • GSA

  • Referenced in 37 articles [sw18747]
  • problem of identifying differentially expressed groups of genes from a microarray experiment. The groups...
  • RSIR

  • Referenced in 15 articles [sw26716]
  • understanding of regulatory circuitries controlling the expression of genes. In this paper, we propose ... combine information contained in both gene expression measurements and genes’ promoter sequences. Compared with existing...
  • E-CELL

  • Referenced in 20 articles [sw07917]
  • interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism ... hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis...
  • multtest

  • Referenced in 20 articles [sw08262]
  • directly applicable to identifying differentially expressed genes in DNA microarray experiments...
  • BicAT

  • Referenced in 13 articles [sw12371]
  • interface software for the analysis of gene expression data. It provides five biclustering ... analysis and exploration of the gene expression data, e.g. microarrays...
  • DEGseq

  • Referenced in 11 articles [sw07998]
  • package for identifying differentially expressed genes from RNA-seq data. High-throughput RNA sequencing ... package to identify differentially expressed genes or isoforms for RNA-seq data from different samples ... plot to detect and visualize gene expression difference...