MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates

Hwang, Sohyun; Kim, Hyojin; Shim, Hongseok; Kang, Byung Ha; Yang, Sunmo; Shim, Jae Ho; Shin, Seung Yeon; Marcotte, Edward M.; Lee, Insuk

doi:10.1093/nar/gkv1155

Cited by 37 publications

(31 citation statements)

References 33 publications

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“…The Monarch Initiative (monarchinitiative.org; Mungall et al 2017) integrates genotype to phenotype data across multiple species to support biomedical research. MouseNet2 (http://www.inetbio.org/mousenet/; Kim et al 2016) integrates gene network data, particularly from microarray experiments, for the discovery of novel disease genes and disease pathways.…”

Section: Discussionmentioning

confidence: 99%

Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species

Knowlton

Smith

2017

Mamm Genome

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The widespread use of CRISPR/Cas and other targeted endonuclease technologies in many species has led to an explosion in the generation of new mutations and alleles. The ability to generate many different mutations from the same target sequence either by homology-directed repair with a donor sequence or non-homologous end joining-induced insertions and deletions necessitates a means for representing these mutations in literature and databases. Standardized nomenclature can be used to generate unambiguous, concise, and specific symbols to represent mutations and alleles. The research communities of a variety of species using CRISPR/Cas and other endonuclease-mediated mutation technologies have developed different approaches to naming and identifying such alleles and mutations. While some organism-specific research communities have developed allele nomenclature that incorporates the method of generation within the official allele or mutant symbol, others use metadata tags that include method of generation or mutagen. Organism-specific research community databases together with organism-specific nomenclature committees are leading the way in providing standardized nomenclature and metadata to facilitate the integration of data from alleles and mutations generated using CRISPR/Cas and other targeted endonucleases.

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Section: Discussionmentioning

confidence: 99%

Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species

Knowlton

Smith

2017

Mamm Genome

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“…Recently, an improved MouseNet v2 database was released, which incorporates large-scale experimental data from mouse models and also eight other vertebrate models. 6 The data collection enables a cross-species functional network analysis to build new hypothesis on the origin of a disease and infer disease associations.…”

Section: Direct Method: Animal Modelsmentioning

confidence: 99%

How to Map the Genetic Basis for Conditions that are Comorbid with Male Infertility

2017

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Studying conditions that are comorbid with infertility can provide a picture of the overall health of a patient population that is younger than the typical cases of age-related diseases that preoccupy our health care system. If strong predictive relationships could be established between infertility and life-threatening disease, interventions can be established early in life for at-risk individuals. Here, we discuss how genomic tools can be used to identify diseases and traits that are likely to be comorbid with male infertility. We divide these approaches broadly into two categories: direct and indirect. Direct approaches require knowledge of the specific genetic variants associated with male infertility, while indirect approaches can work with only gene lists, or even no a priori knowledge of disease–gene architecture. Using existing data from human and mouse studies, we demonstrate that one indirect approach based on gene networks provides support for the recent epidemiological findings that infertility is a risk factor for cancer and cardiovascular disease. Finding comorbidities of male infertility is an important goal for the reproductive medicine community. We outline existing resources that will play a valuable role in this quest, and describe new resources that must be developed for maximum progress.

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“…With a few clicks, researchers can input their gene or genes of interest, and look for co-expression relationships that may be conserved across large phylogenetic distances. While co-expression is a key component of other web servers and databases such as COXPRESdb (18), ATTED-II (19), GeneFriends (20), PlaNet (21), MouseNet (22) and GeneMANIA (23), few provide data beyond the standard model organisms (human, mouse, fly, roundworm, yeast, and Arabidopsis). Those that do, lack the ability to make cross-species comparisons.…”

Section: Introductionmentioning

confidence: 99%

CoCoCoNet: Conserved and Comparative Co-expression Across a Diverse Set of Species

Lee

Shah

Ballouz

et al. 2020

Preprint

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ABSTRACTCo-expression analysis has provided insight into gene function in organisms from Arabidopsis to Zebrafish. Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties, or by finding alternative model systems where their co-expression is conserved. Here, we present CoCoCoNet as a tool for identifying conserved gene modules and comparing co-expression networks. CoCoCoNet is a resource for both data and methods, providing gold-standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species. We show how CoCoCoNet can be used in two use cases. In the first, we demonstrate deep conservation of a nucleolus gene module across very divergent organisms, and in the second, we show how the heterogeneity of autism mechanisms in humans can be broken down by functional groups, and translated to model organisms. CoCoCoNet is free to use and available to all at https://milton.cshl.edu/CoCoCoNet, with data and R scripts available at ftp://milton.cshl.edu/data.

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MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates

Cited by 37 publications

References 33 publications

Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species

Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species

How to Map the Genetic Basis for Conditions that are Comorbid with Male Infertility

CoCoCoNet: Conserved and Comparative Co-expression Across a Diverse Set of Species

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