MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data

By Scott Doniger, N. Salomonis, Kam D. Dahlquist, K. Vranizan, Steven C. Lawlor, Bruce R. Conklin. Genome Biology, 2003

929 citations recorded by the source corpus.

MAPPFinder is a tool that creates a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP http://www.GenMAPP.org. The results are displayed in a searchable browser, allowing the user to rapidly identify GO terms with over-represented numbers of gene-expression changes. Clicking on GO terms generates GenMAPP graphical files where gene relationships can be explored, annotated, and files can be freely exchanged.

Subfields: Aerospace Engineering

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Citations in the corpus

Pathway-based personalized analysis of cancer (2013, methodology): “The third method we tested was the MAPPFinder module of GenMAPP (6), which we adapted to provide a score for every pathway in each sample (this algorithm was also designed to yield a single score per pathway for an entire cohort).”
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists (2007, background): “A number of publicly available bioinformatics tools have addressed the first three points above, including, but not limited to, GoMiner, DAVID, EASE, GOstat, Onto-express, GoToolBox, FatiGO, GOSSIP, GFINDer, GOBar, and so on [1-25].”
Pathway level analysis of gene expression using singular value decomposition (2005, background): “One approach along these lines identifies similarities, such as shared pathways or GO annotations [5], between genes previously identified in an individual gene analysis [ 6 ,7].”
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges (2012, methodology): “ORA uses one or more variations of the following strategy [4–11]”
WebGestalt: an integrated system for exploring gene sets in various biological contexts (2005, methodology): “In addition to organizing gene sets within the context of GO, MAPPFinder (11), DAVID (12) and GFINDer (13) provide the option of organizing and visualizing gene sets within the context of KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.”
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists (2008, positive): “Thus, more and more recent tools, such as Onto-Express (62), DAVID (61), POSOC (83), BayGO (52), FatiGO+ (56), MAPPFinder (7), FuncCluster (43) and FunNet, have started to integrate BioCarta, KEGG, or other pathway visualizations in order to more eﬃciently examine the user’s genes in a network conte”
GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies (2004, methodology): “GoMiner[10], MAPPFinder[11] and GoSurfer[12] are standalone software packages while FatiGO[7] and Onto-Express[8,9] are web-based software.”
A systems biology approach for pathway level analysis. (2007, methodology): “The factor ⌬E (g) represents the signed normalized measured expression change of the gene g determined using one of the available methods (Quackenbush 2001; Churchill 2002; Draghici 2002; Yang and Speed 2002).”