GO::TermFinder-open source software for accessing gene ontology terms associated with a list of genes. Summary: GO::TermFinder comprises a set of object-oriented Perl modules for accessing Gene Ontology (GO) information and evaluating and visualizing the collective annotation of a list of genes to GO terms. It can be used to draw conclusions from microarray and other biological data, calculating the statistical significance of each annotation. GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script. Availability: The full source code and documentation for GO::TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/

References in zbMATH (referenced in 12 articles )

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  1. Rubert, Diego P.; Araujo, Eloi; Stefanes, Marco A.; Stoye, Jens; Martinez, Fábio V.: Searching and inferring colorful topological motifs in vertex-colored graphs (2020)
  2. Wang, Rongquan; Wang, Caixia; Liu, Guixia: A novel graph clustering method with a greedy heuristic search algorithm for mining protein complexes from dynamic and static PPI networks (2020)
  3. How, Javier J.; Navlakha, Saket: Evidence of Rentian scaling of functional modules in diverse biological networks (2018)
  4. Chang, Chang; Tang, Chao: Community detection for networks with unipartite and bipartite structure (2014)
  5. Airoldi, Edoardo M.; Wang, Xiaopei; Lin, Xiaodong: Multi-way blockmodels for analyzing coordinated high-dimensional responses (2013)
  6. Faure, Andre J.; Seoighe, Cathal; Mulder, Nicola J.: Investigating the effect of paralogs on microarray gene-set analysis (2011) ioport
  7. Yu, Liang; Gao, Lin; Li, Kui; Zhao, Yi; Chiu, David K. Y.: A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification (2011) ioport
  8. Eden, Eran; Navon, Roy; Steinfeld, Israel; Lipson, Doron; Yakhini, Zohar: \textitgorilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists (2009) ioport
  9. Niida, Atsushi; Smith, Andrew D.; Imoto, Seiya; Aburatani, Hiroyuki; Zhang, Michael Q.; Akiyama, Tetsu: Gene set-based module discovery in the breast cancer transcriptome (2009) ioport
  10. Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru: Network-based predictions and simulations by biological state space models: search for drug mode of action (2009) ioport
  11. Marco, Antonio; Marin, Ignacio: A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification (2007) ioport
  12. Zhao, Hongya; Yan, Hong: Houghfeature, a novel method for assessing drug effects in three-color cdna microarray experiments (2007) ioport