• RegulonDB

  • Referenced in 51 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...
  • TRANSFAC

  • Referenced in 74 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...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • models of the cell that incorporate gene regulation, metabolism and signaling have not been established ... building such integrative models based on gene sets, and running simulations to conduct experiments ... protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular...
  • BGX

  • Referenced in 15 articles [sw06935]
  • analyse the results, such as ranking genes by expression level as well as statistically based ... amount of up and down regulated genes between two conditions...
  • Ginsim

  • Referenced in 29 articles [sw09090]
  • focus on the cross-regulations between five genes (within and between two cells), which implements...
  • TIGRESS

  • Referenced in 9 articles [sw23826]
  • TIGRESS: Trustful Inference of Gene REgulation using Stability Selection. BACKGROUND: Inferring the structure of gene ... call TIGRESS (for Trustful Inference of Gene REgulation with Stability Selection), was ranked among ... inference methods in the DREAM5 gene network inference challenge. In particular, TIGRESS was evaluated...
  • BSmooth

  • Referenced in 11 articles [sw23483]
  • important epigenetic modification involved in gene regulation, which can now be measured using whole-genome...
  • GOTM

  • Referenced in 9 articles [sw13869]
  • analysis and data visualization for sets of genes called GOTree Machine (GOTM). This tool ... intended to analyze sets of co-regulated genes identified from microarray analysis but is adaptable...
  • BioOptimizer

  • Referenced in 6 articles [sw17421]
  • gene transcription start sites, to regulate gene expression. The experimental determination of TFs binding sites ... application to sets of co-regulated genes in bacteria. In addition, this scoring function formulation...
  • iMiRNA-PseDPC

  • Referenced in 10 articles [sw22425]
  • functioning in transcriptional and post-transcriptional regulation of gene expression. The human genome may encode ... characterized, miRNAs are widely deemed as important regulators of biological processes. Aberrant expression of miRNAs...
  • RankProd

  • Referenced in 6 articles [sw07961]
  • Rank Product method for identifying differentially expressed genes with application in meta-analysis. Non-parametric ... identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false...
  • VarMixt

  • Referenced in 5 articles [sw21100]
  • gene expression data. MOTIVATION: Identifying differentially regulated genes in experiments comparing two experimental conditions...
  • Matrix eQTL

  • Referenced in 5 articles [sw20450]
  • aims to determine genomic regions that regulate gene transcription. Expression QTL is used to study...
  • Hy3S

  • Referenced in 5 articles [sw23355]
  • devices, especially ones that rely on regulated gene expression to produce useful behavior. By combining...
  • SIRENE

  • Referenced in 7 articles [sw17419]
  • programs that involve the regulated transcription of thousands of genes. The elucidation of transcriptional regulatory ... proposed to infer gene regulatory networks from gene expression data, a recent comparison ... only predict a limited number of known regulations at a reasonable precision level. Results ... method for the inference of gene regulatory networks from a compendium of expression data...
  • VirtualLeaf

  • Referenced in 4 articles [sw28766]
  • multilevel cross talk between gene regulation, patterned cell division and cell expansion, and tissue mechanics ... methodologies implicitly assume a direct relation between genes and traits at the level ... products in regulatory networks, the conditions of gene expression, etc. This interplay is impossible ... provide biologically intuitive in silico objects (“cells”, “regulation networks”) required for setting up a simulation...
  • PLMLA

  • Referenced in 4 articles [sw36907]
  • various biological processes, especially in gene regulation. Identification of protein methylation and acetylation sites would...
  • MethylSig

  • Referenced in 4 articles [sw23506]
  • methylation plays critical roles in gene regulation and cellular specification without altering DNA sequences...
  • HPAM

  • Referenced in 3 articles [sw10931]
  • systems and integrating them into genetic networks. Gene expression is determined by protein-protein interactions ... promoter regions of those regulated genes. Therefore, identifying these protein-DNA interactions, by means ... becomes crucial for determining which genes participate in a regulation process, how they behave...
  • miRecords

  • Referenced in 6 articles [sw29356]
  • small noncoding RNAs capable of regulating other genes’ expression. Much progress has been made...