• GOTM

  • Referenced in 9 articles [sw13869]
  • interpreting sets of interesting genes using Gene Ontology hierarchies. Microarray and other high-throughput technologies ... tree-like structure to navigate the Gene Ontology Directed Acyclic Graph for input gene sets ... users to identify the most important Gene Ontology categories for the input gene sets...
  • 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...
  • Virus-ploc

  • Referenced in 14 articles [sw22421]
  • this regard. As for the gene ontology database, the corresponding percentage is 23.8%. Such...
  • MultiLoc2

  • Referenced in 8 articles [sw22456]
  • MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BACKGROUND: Knowledge ... predictor by incorporating phylogenetic profiles and Gene Ontology terms. Two different datasets were used ... system. By incorporating phylogenetic profiles and Gene Ontology terms MultiLoc2 yields higher accuracies compared...
  • Gpos-PLoc

  • Referenced in 11 articles [sw26870]
  • without subcellular location annotations. In the gene ontology database, the corresponding percentage is approximately ... even higher. With the avalanche of gene products generated in the post-genomic...
  • WoLF PSORT

  • Referenced in 11 articles [sw27721]
  • proteins and links to UniProt and Gene Ontology are provided. Taken together, this information allows...
  • ClueGO

  • Referenced in 9 articles [sw22916]
  • several clusters (lists of genes). From the ontology sources used, the terms are selected ... related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO ... updatable with the newest files from Gene Ontology, KEGG, WikiPathways and Reactome. To extend...
  • MAPPFinder

  • Referenced in 7 articles [sw23711]
  • MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray ... integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP ... terms with over-represented numbers of gene-expression changes. Clicking on GO terms generates GenMAPP...
  • GOASVM

  • Referenced in 6 articles [sw22445]
  • location predictor by incorporating term-frequency gene ontology into the general form of Chou ... Recently, several computational methods based on Gene Ontology (GO) have been proposed to tackle this ... selected GO terms in the Gene Ontology annotation (GOA) database as a means to construct...
  • Onto-Tools

  • Referenced in 10 articles [sw10974]
  • pathways. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function ... determined by the extent to which the genes present on the array represent specific pathways...
  • AmiGO

  • Referenced in 8 articles [sw25694]
  • query, browse and visualize ontologies and related gene product annotation (association) data. AmiGO ... used online at the Gene Ontology (GO) website to access the data provided...
  • GOLEM

  • Referenced in 4 articles [sw20340]
  • GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BACKGROUND: The Gene Ontology ... excellent software tools for navigating the gene ontology have been developed. However, no existing system ... 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...
  • GenMAPP

  • Referenced in 8 articles [sw12317]
  • pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build ... with easy to use graphics tools. Color genes on MAPP files based on user-imported...
  • QuickGO

  • Referenced in 5 articles [sw30018]
  • QuickGO: a web-based tool for Gene Ontology searching. Summary: QuickGO is a web-based ... that allows easy browsing of the Gene Ontology (GO) and all associated electronic and manual...
  • WebGestalt

  • Referenced in 7 articles [sw17514]
  • sets in various biological contexts, including Gene Ontology, tissue expression pattern, chromosome distribution, metabolic ... biological areas that are important to a gene set and warrant further investigation. In order...
  • Gpos-mPLoc

  • Referenced in 7 articles [sw25878]
  • proteins by fusing the information of gene ontology, as well as the functional domain information...
  • OBO-Edit

  • Referenced in 6 articles [sw35375]
  • editor developed and maintained by the Gene Ontology Consortium. Implemented in Java, OBO-Edit uses...
  • GOToolBox

  • Referenced in 4 articles [sw13897]
  • gene data sets based on Gene Ontology. We have developed methods and tools based ... Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms ... gene dataset; the clustering of functionally related genes within a set; and the retrieval ... genes sharing annotations with a query gene. GO annotations can also be constrained...
  • ErmineJ

  • Referenced in 4 articles [sw30047]
  • genes such as pathways or Gene Ontology categories. The most common method for such analysis ... look for ”over-representation” of groups among genes selected as being differentially expressed or otherwise ... modifying gene sets, visualizing the Gene Ontology as a table or tree, and visualizing gene...
  • COXPRESdb

  • Referenced in 6 articles [sw41318]
  • cluster analyses with enrichment analyses in Gene Ontology and in cis elements, along with interactive ... analyses of functional and regulatory networks of genes in a variety of animal species...