Genome informatics for data-driven biology

A report on the 12th International Conference on Genome Informatics, Tokyo, Japan, 17-19 December 2001.     

Mining the genome and regulatory networks

A report on the 16th International Conference on Genome Informatics (GIW 2005), Yokohama, Japan, 19-21 December 2005.     

Meeting reports

Meeting report: 48^th meeting of the ASCB Meeting highlight: Genome Informatics (GIW-2008); 19^th International Conference on Genome Informatics Darwin 200 years     

Genome informatics: taming the avalanche of genomic data

A report on the fourth Cold Spring Harbor Laboratory/Wellcome Trust Conference on Genome Informatics, Hinxton, UK, 22-26 September 2004.     

Open-source software accelerates bioinformatics

A report on the Wellcome Trust/Cold Spring Harbor Genome Informatics meeting, Cold Spring Harbor, USA, 7-11 May 2003.     

Multi-genome biology

A report on the Genome Informatics meeting held at Cold Spring Harbor Laboratory, Cold Spring Harbor, USA, 28 October-1 November 2005.     

Opening sequence: computational genomics in the era of high-throughput sequencing

A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Cold Spring Harbor Laboratories, New York, USA, November 2-5, 2011.     

Basic helix-loop-helix transcription factors regulate the neuroendocrine differentiation of fetal mouse pulmonary epithelium

To clarify the mechanisms that regulate neuroendocrine differentiation of fetal lung epithelia, we have studied the expression of the mammalian homologs of achaete-scute complex (Mash1) (Ascl1 - Mouse Genome Informatics); hairy and enhancer of split1 (Hes1); and the expression of Notch/Notch-ligand system in the fetal and adult mouse lungs, and in the lungs of Mash1- or Hes1-deficient mice. Immunohistochemical studies revealed that Mash1-positive cells seemed to belong to pulmonary neuroendocrine cells (PNEC) and their precursors. In mice deficient for Mash1, no PNEC were detected. Hes1-positive cells belong to non-neuroendocrine cells. In the mice deficient in Hes1, in which Mash1 mRNA was upregulated, PNEC appeared precociously, and the number of PNEC was markedly increased. NeuroD (Neurod1 - Mouse Genome Informatics) expression in the lung was detected in the adult, and was enhanced in the fetal lungs of Hes1-null mice. Expression of Notch1, Notch2, Notch3 and Notch4 mRNAs in the mouse lung increased with age, and Notch1 mRNA was expressed in a Hes1-dependent manner. Notch1, Notch2 and Notch3 were immunohistochemically detected in non-neuroendocrine cells. Moreover, analyses of the lungs from the gene-targeted mice suggested that expression of Delta-like 1 (Dll1 - Mouse Genome Informatics) mRNA depends on Mash1. Thus, the neuroendocrine differentiation depends on basic helix-loop-helix factors, and Notch/Notch-ligand pathways may be involved in determining the cell differentiation fate in fetal airway epithelium.     

GXD: a gene expression database for the laboratory mouse. The Gene Expression Database Group.

The Gene Expression Database (GXD) is a community resource that stores and integrates expression information for the laboratory mouse, with a particular emphasis on mouse development, and makes these data freely available in formats appropriate for comprehensive analysis. GXD is implemented as a relational database and integrated with the Mouse Genome Database (MGD) to enable global analysis of genotype, expression and phenotype information. Interconnections with sequence databases and with databases from other species further extend GXD's utility for the analysis of gene expression data. GXD is available through the Mouse Genome Informatics Web Site at http://www.informatics.jax.org/     

MouseCyc: a curated biochemical pathways database for the laboratory mouse

Linking biochemical genetic data to the reference genome for the laboratory mouse is important for comparative physiology and for developing mouse models of human biology and disease. We describe here a new database of curated metabolic pathways for the laboratory mouse called MouseCyc . MouseCyc has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human.     

Expression of Zash-1a in the postembryonic zebrafish brain allows comparison to mouse Mash1 domains

Four areas in the late embryonic murine forebrain, i.e. the subpallium (striatum), the preoptic region, the ventral thalamus, and the hypothalamus, have been described to express the basic helix-loop-helix (bHLH) gene mammalian achaete-scute homolog Mash1 (Ascl1, Mouse Genome Informatics) in a complementary fashion to another bHLH gene, neurogenin1 (ngn1) (Neurod3, Mouse Genome Informatics), which is expressed in directly adjacent forebrain regions. We report here that the four regions previously identified as subpallium, preoptic region, ventral thalamus and hypothalamus (i.e. ventral inferior lobe) in the postembryonic zebrafish brain show Zash-1a expression at 3 days postfertilization (dpf), whereas none of those areas express the bHLH gene neuroD (nrd) between 2 and 5 dpf. This indicates that two well established alternative genetic pathways involved in neurogenesis in the amniote (mammalian) brain are present in homologous phenotypic locations in the anamniote (zebrafish) brain as well and that these pathways possibly act similarly in the generation of different neuronal phenotypes (e.g. subpallial GABAergic interneurons versus pallial glutamatergic projection neurons, or dopaminergic neurons versus other neurotransmitter phenotypes). Furthermore, previous initial identification of early postembryonic brain subdivisions in the zebrafish is strongly corroborated by these expression patterns.     

Resources for genetic management and genomics research on non-human primates at the National Primate Research Centers (NPRCs)

Abstract The National Primate Research Centers (NPRCs) established Working Groups (WGs) for developing resources and mechanisms to facilitate collaborations among non-human primate (NHP) researchers. Here we report the progress of the Genome Banking and the Genetics and Genomics WGs in developing resources to advance the exchange, analysis and comparison of NHP genetic and genomic data across the NPRCs.
The Genome Banking WG has established a National NHP DNA bank comprising 1250 DNA samples from unrelated animals and family trios from the 10 NHP species housed within the NPRC system. The Genetics and Genomics WG is developing SNP arrays that will provide a uniform, highly informative, efficient and low-cost method for rhesus and long-tailed macaque genotyping across the eight NPRCs. This WG is also establishing a Biomedical Informatics Research Network-based portal for shared bioinformatics resources including vital statistics, genotype and population data and information on the National NHP DNA bank.     

The Mouse Gene Expression Database (GXD)

The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling valuable insights into the molecular networks that underlie normal development and disease. GXD is integrated with the Mouse Genome Database (MGD). Extensive interconnections with sequence databases and with databases from other species, and the development and use of shared controlled vocabularies extend GXD's utility for the analysis of gene expression information. GXD is accessible through the Mouse Genome Informatics web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu. shtml.     

Mouse tumor biology database (MTB): enhancements and current status

The Mouse Tumor Biology Database (MTB) is a Web-based resource that provides access to information on tumor frequency and latency, genetics and pathology in genetically defined mice (transgenics, targeted mutations and inbred strains). MTB is designed to serve as an information resource for cancer genetics researchers who use the laboratory mouse as a model system for understanding human disease processes. Data in MTB are obtained from the primary scientific literature and direct submissions by the research community. MTB is accessible from the Mouse Genome Informatics Web site (http://www. informatics.jax.org). User support is available for MTB via Email at mgi-help@informatics.jax.org     

HCOP: a searchable database of human orthology predictions

The HUGO Gene Nomenclature Committee (HGNC) Comparison of Orthology Predictions (HCOP) search tool combines the human, mouse, rat and chicken orthology assertions made by PhIGs, HomoloGene, Ensembl, Inparanoid, Mouse Genome Informatics (MGI) and HGNC, enabling users to identify predicted ortholog pairs for a specified gene or genes. The HCOP resource provides a useful method to integrate, compare and access a variety of disparate sources of human orthology data. The HCOP search tool, data and documentation are available at http://www.gene.ucl.ac.uk/hcop.     

Human genome research enters a new phase

A report on HGM2005, the tenth annual Human Genome Meeting, Kyoto, Japan, 18-21 April 2005.     

Human genome research enters a new phase

A report on HGM2005, the tenth annual Human Genome Meeting, Kyoto, Japan, 18-21 April 2005.     

Database for exchangeable gene trap clones: Pathway and gene ontology analysis of exchangeable gene trap clone mouse lines

Gene trapping in embryonic stem (ES) cells is a proven method for large‐scale random insertional mutagenesis in the mouse genome. We have established an exchangeable gene trap system, in which a reporter gene can be exchanged for any other DNA of interest through Cre/mutant lox‐mediated recombination. We isolated trap clones, analyzed trapped genes, and constructed the database for Exchangeable Gene Trap Clones (EGTC) [ http://egtc.jp ]. The number of registered ES cell lines was 1162 on 31 August 2013. We also established 454 mouse lines from trap ES clones and deposited them in the mouse embryo bank at the Center for Animal Resources and Development, Kumamoto University, Japan. The EGTC database is the most extensive academic resource for gene‐trap mouse lines. Because we used a promoter‐trap strategy, all trapped genes were expressed in ES cells. To understand the general characteristics of the trapped genes in the EGTC library, we used Kyoto Encyclopedia of Genes and Genomes (KEGG) for pathway analysis and found that the EGTC ES clones covered a broad range of pathways. We also used Gene Ontology (GO) classification data provided by Mouse Genome Informatics (MGI) to compare the functional distribution of genes in each GO term between trapped genes in the EGTC mouse lines and total genes annotated in MGI. We found the functional distributions for the trapped genes in the EGTC mouse lines and for the RefSeq genes for the whole mouse genome were similar, indicating that the EGTC mouse lines had trapped a wide range of mouse genes.