• GeneRank

  • Referenced in 16 articles [sw27064]
  • network structure derived from gene annotations (gene ontologies) or expression profile correlations. Using both simulated...
  • 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...
  • GOstat

  • Referenced in 18 articles [sw10975]
  • find statistically overrepresented Gene Ontologies within a group of genes. Summary: Modern experimental techniques ... result usually produce a long list of genes, which are potentially interesting in the analyzed ... functional annotations of all genes in this list. The Gene-Ontology (GO) database provides ... functions of a large number of genes. Here, we introduce a tool that utilizes this...
  • GOASVM

  • Referenced in 6 articles [sw22445]
  • selected GO terms in the Gene Ontology annotation (GOA) database as a means to construct...
  • Gpos-PLoc

  • Referenced in 8 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...
  • GOLEM

  • Referenced in 4 articles [sw20340]
  • expandable graph-based view of the gene ontology hierarchy. Furthermore, most existing tools ... above limitations, we have developed GOLEM (Gene Ontology Local Exploration Map), a visualization and analysis ... user either to utilize local gene ontology and annotations files in the absence ... most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global...
  • AmiGO

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

  • Referenced in 6 articles [sw23711]
  • MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray ... biology by integrating the annotations of the Gene Ontology (GO) Project with the free software ... gene-expression changes. Clicking on GO terms generates GenMAPP graphical files where gene relationships ... explored, annotated, and files can be freely exchanged...
  • BiGGEsTS

  • Referenced in 2 articles [sw23417]
  • relevant biological terms annotated with the dataset genes in the Gene Ontology for specific organisms ... biclusters. Biclusters may be analyzed with Gene Ontology annotations to find out which contain statistically...
  • GoFigure

  • Referenced in 2 articles [sw35755]
  • GoFigure: Automated Gene Ontologyannotation. Summary: We have developed a web tool to predict Gene ... BLAST to identify homologous sequences in GO annotated databases. A graph is returned...
  • GOtcha

  • Referenced in 4 articles [sw17189]
  • 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...
  • I-TASSER

  • Referenced in 17 articles [sw17207]
  • functional annotations on ligand-binding sites, Enzyme Commission numbers and Gene Ontology terms. An estimate...
  • GO-TermFinder

  • Referenced in 9 articles [sw10921]
  • accessing Gene Ontology (GO) information and evaluating and visualizing the collective annotation of a list...
  • OrthoDB

  • Referenced in 4 articles [sw22979]
  • annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures ... with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy...
  • Biomine

  • Referenced in 2 articles [sw28409]
  • protein interactions, gene-disease associations and gene ontology annotations. Edges are weighted based on their ... formulate protein interaction prediction and disease gene prioritization tasks as instances of link prediction...
  • R3P-Loc

  • Referenced in 2 articles [sw22444]
  • based on knowledge databases (such as gene ontology annotation (GOA) database) are known...
  • GOSemSim

  • Referenced in 3 articles [sw16934]
  • Summary: The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities...
  • Transcriptator

  • Referenced in 1 article [sw22343]
  • TRANSCRIPTATOR is a computational pipeline to functionally annotate differentially expressed transcripts and carry ... statistical analysis of functional and gene ontology annotation enrichment; identification of enriched biological themes, particularly ... annotation; tabular report for functional and gene ontology annotation for each and every transcripts submitted...
  • Virus-ploc

  • Referenced in 11 articles [sw22421]
  • annotated for their subcellular locations in this regard. As for the gene ontology database ... development of high throughput tools for timely annotating the localization of viral proteins within host...
  • FUNC

  • Referenced in 2 articles [sw16930]
  • detecting significant associations between gene sets and ontological annotations. Background: Genome-wide expression, sequence ... association studies typically yield large sets of gene candidates, which must then be further analysed ... Information about these genes is increasingly being captured and organized in ontologies, such ... identify significant associations between gene sets and ontological annotations. Implemented are several tests in particular...