Tutorial and training materials
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
Rotunno Melissa et al., Parity-related molecular signatures and breast cancer subtypes by estrogen receptor status. Breast Cancer Research (2014) doi:10.1186/bcr3689
Tang Jing et al., Proteomic profiling of the phosphoproteins in the rat thalamus, hippocampus and frontal lobe after propofol anesthesia General pharmacology and pharmacokinetics. BMC Anesthesiology (2014) doi:10.1186/1471-2253-14-3
Sun Zhen et al., Differential analysis of N-glycoproteome between hepatocellular carcinoma and normal human liver tissues by combination of multiple protease digestion and solid phase based labeling. Clinical Proteomics (2014) doi:10.1186/1559-0275-11-26
Dogan V Meeshanthini et al., The effect of smoking on DNA methylation of peripheral blood mononuclear cells from African American women Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-151
Yoshizaki Hisayoshi et al., Elucidation of the evolutionary expansion of phosphorylation signaling networks using comparative phosphomotif analysis Comparative and evolutionary genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-546