Learn how to use GoMiner, a set of publicly available tools that can enable you to ascribe biological significance to large lists of genes by annotating them with their corresponding Gene Ontology, or GO, categories. GoMiner extracts these annotated terms associated with each gene to provide a synopsis of the biology for you. It is available in both web-based and downloadable versions and it not only annotates gene lists with GO descriptions, but it also clusters them into groups and provides detailed statistics. Once you learn what types of biological categories your genes of interest are enriched in you can quickly understand some of the underlying biology and learn where to focus your future studies. Links to additional information from sources such as Entrez's structural database, MMDB, BioCarta, Reactome, and more are also provided. Furthermore, there are several additional tools to help convert gene lists into any format you wish, manipulate and export your data in many ways and generate fantastic visuals to display your results.
You will learn:
This tutorial is a part of the tutorial group Text-related tools. You might find the other tutorials in the group interesting:
PubMatrix: PubMatrix, an on-line tool for multiplex literature mining of the PubMed database.
iHOP: Information Hyperlinked Over Proteins text mining resource
STRING: known and predicted protein-protein interactions
Textpresso: Text-mining the biological literature
Gene Ontology: Gene Ontology controlled vocabularies in biology
XplorMed: eXploring Medline abstracts
Controlled Vocabularies: Standardized term lists that can enhance interactions with biological databases
DAVID: A tool that analyzes large lists of genes to provide biological meaning
Entrez Overview: Overview of NCBI's Entrez Search Resource
PubMed: PubMed access to biomedical research literature
Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.
Tip of the Week: Update to NCBI's Cn3D Viewer: As I say in the tip movie, I like to visit NCBI's homepage & just roam around over there to get an idea of what's new. They develop so many bioscience tools, algorithms & other resources that there's ...
Tip of the Week: Translating Gene IDs with MatchMiner: As we were creating a tutorial on the GoMiner resource from the Genomics and Bioinformatics group at the National Cancer Institute (NCI), we found another handy NCI tool named the MatchMiner. MatchMin...
Recent BioMed Central research articles citing this resource
Yoshizaki Hisayoshi et al., Large-scale analysis of the evolutionary histories of phosphorylation motifs in the human genome. GigaScience (2015) doi:10.1186/s13742-015-0057-6
Fortino Vittorio et al., BACA: bubble chArt to compare annotations Transcriptome analysis. BMC Bioinformatics (2015) doi:10.1186/s12859-015-0477-4
Hebert Olivier Francois et al., Identification of candidate mimicry proteins involved in parasite-driven phenotypic changes. Parasites Vectors (2015) doi:10.1186/s13071-015-0834-1
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Lee Jamie et al., Male and female mice show significant differences in hepatic transcriptomic response to 2,3,7,8-tetrachlorodibenzo- p -dioxin Human and rodent genomics. BMC Genomics (2015) doi:10.1186/s12864-015-1840-6