FNTM: a server for predicting functional networks of tissues in mouse

Abstract

Functional Networks of Tissues in Mouse (FNTM) provides biomedical researchers with tissue-specific predictions of functional relationships between proteins in the most widely used model organism for human disease, the laboratory mouse. Users can explore FNTM-predicted functional relationships for their tissues and genes of interest or examine gene function and interaction predictions across multiple tissues, all through an interactive, multi-tissue network browser. FNTM makes predictions based on integration of a variety of functional genomic data, including over 13 000 gene expression experiments, and prior knowledge of gene function. FNTM is an ideal starting point for clinical and translational researchers considering a mouse model for their disease of interest, researchers already working with mouse models who are interested in discovering new genes related to their pathways or phenotypes of interest, and biologists working with other organisms to explore the functional relationships of their genes of interest in specific mouse tissue contexts. FNTM predicts tissue-specific functional relationships in 200 tissues, does not require any registration or installation and is freely available for use at http://fntm.princeton.edu.

MicroRNA dysregulation and esophageal cancer development depend on the extent of zinc dietary deficiency

“…Functional Networks of Tissues in Mouse (FMTN) [ 65 , 66 ] is a prediction tool for tissue-specific protein interactions for the mouse that is based on the integration of a variety of genomic data and prior knowledge of gene function. To explore the esophagus-specific functional relationships for Fbxw7, Stk40 , and Pdcd4 (tumor-suppressor targets of miR-223, -31, -21), we employed FNTM for the rat.…”

Tribe: The collaborative platform for reproducible web-based analysis of gene sets

“…Tribe has a REST API that serves its resources (collections, versions, genes and publications) as JSON objects, which can be consumed by client servers, applications and even command-line tools. Currently, Tribe is integrated into the GIANT [27], ASD [28], FNTM [29] and WISP (in preparation) webservers ( Figure 4). LOKI [30,31], which parses sets of genes annotated to pathways and processes (such as GO terms [32] and KEGG pathways [33]), produces JSON output and can be configured to send this output to Tribe's API using the OAuth 2.0 protocol [34] (Figure 4).…”

“…Collections can be made public, and no authentication is required for access to public collections. LOKI [30,31], GIANT [27], ASD [28], FNTM [29] and WISP (in preparation) currently connect to Tribe via the OAuth 2.0 protocol. We also provide "tribe-client", an open-source application (used by LOKI, GIANT, ASD, FNTM and WISP) to facilitate the connection of outside webservers and analytical tools to Tribe resources.…”

Functional Network Community Detection Can Disaggregate and Filter Multiple Underlying Pathways in Enrichment Analyses

“…Functional networks are a type of network where genes are connected if they have a high probability of working together in the same pathway or process [8][9][10][11] . To address the challenge posed by multi-pathway gene sets, we developed an approach that incorporates information from functional networks to first partition gene sets into subsets, or communities, which are then analyzed for overrepresented pathways.…”