• GeneRank

  • Referenced in 17 articles [sw27064]
  • with a network structure derived from gene annotations (gene ontologies) or expression profile correlations. Using...
  • GOstat

  • Referenced in 20 articles [sw10975]
  • necessary to analyze the functional annotations of all genes in this list. The Gene-Ontology ... tool to annotate and analyze the functions of a large number of genes. Here ... analyzed list of genes. This program automatically obtains the GO annotations from a database ... statistics of which annotations are overrepresented in the analyzed list of genes. This results...
  • DAVID

  • Referenced in 66 articles [sw17292]
  • biological terms into organized classes of related genes or biology, called biological modules. This organization ... functional annotation. It is a powerful method to group functionally related genes and terms into...
  • iSS-PseDNC

  • Referenced in 16 articles [sw22438]
  • sites that play important roles in gene structure annotation and even in RNA splicing. Although...
  • ToppGene Suite

  • Referenced in 8 articles [sw30169]
  • functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis ... genes in the interactome. Functional annotation-based disease candidate gene prioritization uses a fuzzy-based ... similarity between any two genes based on semantic annotations. The similarity scores from individual features ... value of each annotation of a test gene is derived by random sampling...
  • Evigan

  • Referenced in 5 articles [sw14331]
  • variable quality of evidence relevant to gene annotation argues for a probabilistic framework that automatically ... models. RESULTS: Evigan is an automated gene annotation program for eukaryotic genomes, employing probabilistic inference ... from the training sets used by individual gene finders), Evigan is particularly attractive for newly ... curated annotation is available. The ability to produce a ranked list of alternative gene models...
  • RegulonDB

  • Referenced in 53 articles [sw25948]
  • gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters ... origin of their effectors and by gene ontology class. We have now computational predictions...
  • PANTHER

  • Referenced in 15 articles [sw22973]
  • used to define HMMs, but gene ontology functional annotations can now be made ... gain and loss of function by ancestral genes during evolution. Finally, PANTHER now includes stable...
  • Gpos-PLoc

  • Referenced in 11 articles [sw26870]
  • entries are without subcellular location annotations. In the gene ontology database, the corresponding percentage ... without subcellular component annotations is even higher. With the avalanche of gene products generated ... database that either have no subcellular location annotation or are annotated with uncertain terms such...
  • CAMERA

  • Referenced in 6 articles [sw30339]
  • test for enrichment of a particular gene annotation category amongst the differential expression results from...
  • OrthoMCL

  • Referenced in 15 articles [sw29602]
  • orthologous groups is useful for genome annotation, studies on gene/protein evolution, comparative genomics ... larger genomes may contain multiple paralogous genes, and sequence information is often incomplete. OrthoMCL provides ... same gene to be merged. Comparison with previously assigned EC annotations suggests a high degree ... incorporating P. falciparum genes identifies numerous enzymes that were incompletely annotated in first-pass annotation...
  • AmiGO

  • Referenced in 8 articles [sw25694]
  • AmiGO: Online access to ontology and annotation data. AmiGO is a web application that allows ... browse and visualize ontologies and related gene product annotation (association) data. AmiGO can be used...
  • ProbCD

  • Referenced in 5 articles [sw20338]
  • efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with ... throughput experimental techniques and (ii) probabilistic gene annotation...
  • GO-TermFinder

  • Referenced in 12 articles [sw10921]
  • visualizing the collective annotation of a list of genes to GO terms ... data, calculating the statistical significance of each annotation. GO::TermFinder can be used...
  • MAPPFinder

  • Referenced in 7 articles [sw23711]
  • biology by integrating the annotations of the Gene Ontology (GO) Project with the free software ... GenMAPP graphical files where gene relationships can be explored, annotated, and files can be freely...
  • mGene

  • Referenced in 4 articles [sw23030]
  • approximately 2200 predicted genes were not contained in the current genome annotation. Testing a subset ... these genes by RT-PCR and sequencing, we confirmed expression ... them. mGene missed 300 annotated genes, out of which 205 were unconfirmed. RT-PCR testing ... species-specific gene inventions. In a quality assessment of several available annotations for these genomes...
  • GOToolBox

  • Referenced in 4 articles [sw13897]
  • retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained...
  • EasyGene

  • Referenced in 7 articles [sw17322]
  • been devised to help in discriminating real genes from the masses of random Open Reading ... genomes have too many short ORFs annotated as genes. Results: In this paper, we present...
  • GOtcha

  • Referenced in 4 articles [sw17189]
  • novel gene product is typically predicted by transitive assignment of annotation from similar sequences ... predicting gene product function by annotation with Gene Ontology (GO) terms. GOtcha predicts GO term ... identification of conflicts or uncertainty in annotation. Results: The GOtcha method was applied...
  • GSEA-P

  • Referenced in 4 articles [sw30024]
  • form of concise gene set annotations called Gene Set Cards. These additions, as well...