• RegulonDB

  • Referenced in 51 articles [sw25948]
  • database offering curated knowledge of the transcriptional regulatory network of Escherichia coli K12, currently ... electronically encoded database of the genetic regulatory network of any free-living organism. This paper ... evidences, now classified as strong or weak. Transcription factors are classified by origin of their ... RegulonDB v.6.0 now expands beyond transcription initiation, including RNA regulatory elements, specifically riboswitches, attenuators...
  • ARACNE

  • Referenced in 34 articles [sw17200]
  • regulatory networks in mammalian cells, yet general enough to address a wider range of network ... reconstructs the network exactly (asymptotically) if the effect of loops in the network topology ... assess ARACNE’s ability to reconstruct transcriptional regulatory networks using both a realistic synthetic dataset ... Relevance Networks and Bayesian Networks. Application to the deconvolution of genetic networks in human...
  • SIRENE

  • Referenced in 7 articles [sw17419]
  • SIRENE: Supervised inference of regulatory networks. Motivation: Living cells are the product of gene expression ... programs that involve the regulated transcription ... thousands of genes. The elucidation of transcriptional regulatory networks is thus needed to understand ... method decomposes the problem of gene regulatory network inference into a large number of local...
  • gNCA

  • Referenced in 4 articles [sw08821]
  • Analysis (NCA) is a network structure-driven framework for deducing regulatory signal dynamics. In contrast ... connectivity structure from transcriptional regulatory networks to restrict the decomposition to a unique solution. However ... information beyond the network topology such as information obtained from regulatory gene knockouts that constrain ... expands the capability of transcription network analysis by incorporating regulatory signal constraints arising from genetic...
  • PlantTFDB

  • Referenced in 4 articles [sw17023]
  • architecture and evolutionary features of plant transcriptional regulatory networks at ATRM (Brief Guide in English...
  • SGN Sim

  • Referenced in 8 articles [sw29325]
  • tool to model gene regulatory networks (GRN) where transcription and translation are modeled as multiple...
  • C-ImmSim

  • Referenced in 5 articles [sw34210]
  • Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based ... this work is to integrate a gene network of the TH differentiation in an agent ... dynamics of gene activation and transcription. The gene regulatory network includes genes-related molecules that...
  • ModuleMaster

  • Referenced in 1 article [sw23009]
  • ModuleMaster: a new tool to decipher transcriptional regulatory networks. In this article we present ModuleMaster ... newly developed method which not only considers transcription factor binding information but also multivariate functional ... generating GraphML- and R-based whole regulatory network visualizations or generating SBML files for subsequent...
  • BGRMI

  • Referenced in 1 article [sw29320]
  • breast cancer research. Reconstructing gene regulatory networks (GRNs) from gene expression data is a challenging ... sources of prior knowledge to reconstruct transcription regulatory networks of proliferating and differentiating breast cancer...
  • Mirsynergy

  • Referenced in 1 article [sw34555]
  • modules (MiRMs) will aid deciphering aberrant transcriptional regulatory network in cancer but is computationally challenging...
  • ChEA2

  • Referenced in 1 article [sw33105]
  • useful for elucidating the experimentally determined transcriptional networks regulating lists of genes of interest using ... gene-set libraries, we constructed regulatory networks of transcription factors and histone modifications to identify...
  • expansion-network

  • Referenced in 1 article [sw34481]
  • networks using explicit regulatory modules. Gene regulatory networks are a popular tool for modelling important ... many transcription factors to distinct regulatory regions. Recent gene regulatory network models use binding measurements ... specify possible regulatory connections in a given Boolean network, based on transcription factor binding evidence ... expands a regular Boolean network model into a “cis-regulatory” Boolean network model. This expanded...
  • psRNATarget

  • Referenced in 1 article [sw34140]
  • role in gene expression regulatory networks (GRNs). For example, many transcription factors and development-related ... have been reported as targets of these regulatory small RNAs. Although a number of miRNA...
  • ComiRNet

  • Referenced in 1 article [sw34289]
  • miRNA target predictions and predicted miRNA regulatory networks. ComiRNet stores approximately 5 million predicted interactions ... human miRNAs and 30,875 gene transcripts (mRNAs) which are exploited in the construction ... overlapping biclusters representing potential miRNA regulatory networks...
  • HPAM

  • Referenced in 3 articles [sw10931]
  • into genetic networks. Gene expression is determined by protein-protein interactions among regulatory proteins ... motifs that characterize the regulatory factors operating in the transcription of a gene, becomes crucial ... they are connected to build genetic networks. We propose a hybrid promoter analysis methodology (HPAM ... transcription factors, which sometimes require multiple functional binding sites even in close located regulatory regions...
  • SINCERITIES

  • Referenced in 1 article [sw29321]
  • inferring gene regulatory networks from time-stamped cross-sectional single cell transcriptional expression profiles...
  • trigger

  • Referenced in 1 article [sw36166]
  • Bioconductor/R package trigger: Transcriptional Regulatory Inference from Genetics of Gene ExpRession. This R package provides ... pair-wise causal gene regulatory probabilities and construct gene regulatory networks; and (5) identify causal...
  • pandaR

  • Referenced in 0 articles [sw19414]
  • gene regulatory network inference method that begins with amodel of transcription factor-target gene interactions ... network models are then compared between groups to explore transcriptional processes that distinguish the groups ... exploratory data analysis on gene regulatory networks...
  • MGraph

  • Referenced in 1 article [sw21099]
  • allows the user to predict genetic regulatory networks by a graphical gaussian model ... contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. This application ... prediction of genetic regulatory networks, as well as in investigations of various experimental conditions that...
  • SignaLink

  • Referenced in 1 article [sw29339]
  • signaling pathway resource with multi-layered regulatory networks. ... Conclusions: With SignaLink 2 as a single ... analyze signaling pathways, scaffold proteins, modifier enzymes, transcription factors and miRNAs that are important...