GoMiner: a resource for biological interpretation of genomic and proteomic data

By B. Zeeberg, Weimin Feng, Geoffrey Wang, May D. Wang, A. Fojo, M. Sunshine, Sudarshan Narasimhan, David W. Kane, W. Reinhold, S. Lababidi and 4 more. Genome Biology, 2003

1,268 citations recorded by the source corpus.

We have developed GoMiner, a program package that organizes lists of 'interesting' genes (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. GoMiner provides quantitative and statistical output files and two useful visualizations. The first is a tree-like structure analogous to that in the AmiGO browser and the second is a compact, dynamically interactive 'directed acyclic graph'. Genes displayed in GoMiner are linked to major public bioinformatics resources.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/31c5beeafccb48877530db023610e8604b1136ea

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Citations in the corpus

Analyzing gene expression data in terms of gene sets: methodological issues (2007, neutral): “Contact: j.j.goeman@lumc.nl”
GENOMIC DATA ANALYSIS (2004, methodology): “For the case of clearly defined subsets of genes, many authors have employed Fisher's exact test or variants thereof (Zeeberg et al., 2003; Draghici et al., 2003; Beissbarth and Speed, 2004).”
Pathways to the analysis of microarray data. (2005, methodology): “Gominer Fisher Exact test, Relative enrichment Re GO Install (java) http://discover.nci.nih.gov/ gominer/ [ 45 ]”
Aging of blood can be tracked by DNA methylation changes at just three CpG sites (2014, methodology): “Gene Ontology classification of genes associated with AR-CpGs was performed with GoMiner software [57] in relation to all CpGs on the BeadChip (Fisher’s exact test).”
Differential gene expression after total replacement of dietary fish meal and fish oil by plant products in rainbow trout (Oncorhynchus mykiss) liver (2009, neutral): “gov/gominer/ ) (Zeeberg et al., 2003).”
Gene Expression Signature of Cigarette Smoking and Its Role in Lung Adenocarcinoma Development and Survival (2008, methodology): “The GoMiner results (Appendix S2D) confirmed that the mitosis genes (12 altered genes among the 127 mitotic genes on the HGU133A chip, p,0.001), and more generally those involved in cell cycle were the most commonly altered in the tumor tissue (Table 2).”
Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support (2008, neutral): “Some fifty tools have been developed to date for the characterization of gene sets, exploiting Gene Ontology annotations [141] and other resources (e.g., Onto-Express [142] and GoMiner [143]).”
BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks (2005, neutral): “Several tools exist that analyze GO term enrichment in a given gene set (Berriz et al., 2003; Hosack et al., 2003; Zeeberg et al., 2003; Al-Shahrour et al., 2004; Beißbarth and Speed, 2004; Boyle et al., 2004; Masseroli et al., * To whom correspondence should be addressed.”
Microarray data analysis: from disarray to consolidation and consensus (2006, background): “This is inappropriate for several reasons, including the fact that it assumes that transcripts are expressed independentl”
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges (2012, neutral): “gov/gominer) [72,73]”
GATHER: a systems approach to interpreting genomic signatures (2006, methodology): “Methodologically, it builds upon previous methods that annotate genes with functional descriptors from Gene Ontology (GO) (Zeeberg et al., 2003; Al-Shahrour et al., 2004) or other sources (Zhang et al., 2005).”
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists (2009, neutral): “A large repertoire of tools for enrichment analysis has been developed in recent years, including GoMiner [3], FatiGO [4], BiNGO [5], GOAT [6], DAVID [7] and others.”
Enrichment or depletion of a GO category within a class of genes: which test? (2007, background): “Notations (see Table 2): the total number of genes is denoted by n, the total number of genes belonging to the GO category of interest by n + 1 , the number of DE genes by n 1 + : n, n + 1 and n 1 + are hence ﬁxed by the experiment.”
Integration of biological networks and gene expression data using Cytoscape (2007, methodology): “Commonly used expression analysis methods identify active biological processes from expression profiles by finding enriched gene annotation terms in the lists of differentially expressed gene”
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (2006, background): “Figure 2E shows a Gene Ontology (GO) (Zeeberg et al., 2003) analysis of the in vivo phosphoproteome.”