• KEGG

  • Referenced in 239 articles [sw13866]
  • KEGG: Kyoto Encyclopedia of Genes and Genomes. KEGG is a database resource for understanding high ... system, consisting of molecular building blocks of genes and proteins (genomic information) and chemical substances...
  • NEURON

  • Referenced in 171 articles [sw03059]
  • speed cache. On the EPFL IBM Blue Gene, almost linear speedup was obtained...
  • impute

  • Referenced in 91 articles [sw14376]
  • Missing value estimation for DNA microarrays. Motivation: Gene expression microarray experiments can generate data sets ... missing expression values. Unfortunately, many algorithms for gene expression analysis require a complete matrix ... gene array values as input. For example, methods such as hierarchical clustering and K-means ... estimation of missing values in gene microarray data. We implemented and evaluated three methods...
  • GeneSrF

  • Referenced in 62 articles [sw08254]
  • GeneSrF: gene selection with random forests (v. 20070524). GeneSrF is a web tool for gene ... that uses random forest. Two approaches for gene selection are used: one is targeted towards ... identifying small, non-redundant sets of genes that have good predictive performance. The second ... used to identify large sets of genes (including redundant genes) related to the outcome...
  • DAVID

  • Referenced in 57 articles [sw17292]
  • DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large ... gene lists. The DAVID Gene Functional Classification Tool http://david.abcc.ncifcrf.gov uses a novel agglomeration algorithm ... condense a list of genes or associated biological terms into organized classes of related genes ... powerful method to group functionally related genes and terms into a manageable number of biological...
  • 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 59 articles [sw09080]
  • 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...
  • RegulonDB

  • Referenced in 48 articles [sw25948]
  • RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental ... origin of their effectors and by gene ontology class. We have now computational predictions ... accessed through overviews of correlations about gene regulation. RegulonDB associated original literature, together with more...
  • GSA

  • Referenced in 37 articles [sw18747]
  • testing the significance of sets of genes. This paper discusses the problem of identifying differentially ... expressed groups of genes from a microarray experiment. The groups of genes are externally defined ... example, sets of gene pathways derived from biological databases. Our starting point is the interesting ... Gene Set Enrichment Analysis (GSEA) procedure of {it A. Subramanian} et al. [Proc. Natl. Acad...
  • edgeR

  • Referenced in 44 articles [sw06936]
  • package for 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 ... fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence...
  • ML-KNN

  • Referenced in 52 articles [sw12923]
  • world multi-label learning problems, i.e. Yeast gene functional analysis, natural scene classification and automatic...
  • BioProspector

  • Referenced in 27 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 ... sampling strategy, examines the upstream region of genes in the same gene expression pattern group...
  • DEseq

  • Referenced in 47 articles [sw10344]
  • DESeq: Differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence...
  • OSCAR

  • Referenced in 44 articles [sw03026]
  • predictors with possibly high correlations, such as gene expression data. In this article...
  • COSA

  • Referenced in 44 articles [sw22936]
  • discussed. Applications in different domains, including gene expression arrays, are presented...
  • BioGRID

  • Referenced in 43 articles [sw17422]
  • formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed with...
  • ARACNE

  • Referenced in 30 articles [sw17200]
  • ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context ... Background: Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic...
  • SparseLOGREG

  • Referenced in 24 articles [sw11449]
  • Simple and Efficient Algorithm for Gene Selection using Sparse Logistic Regression. Motivation: This paper gives ... real-world problems like identifying marker genes and building a classifier in the context ... cancer diagnosis using microarray data. Results: The gene selection method suggested in this paper...
  • E-CELL

  • Referenced in 20 articles [sw07917]
  • further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular ... integrative models of the cell that incorporate gene regulation, metabolism and signaling have not been ... building such integrative models based on gene sets, and running simulations to conduct experiments ... protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism...
  • Ginsim

  • Referenced in 27 articles [sw09090]
  • focus on the cross-regulations between five genes (within and between two cells), which implements ... loss-of-function mutations or ectopically induced gene expression...