The Mouse Genome Database genotypes::Phenotypes

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Nucleic Acids Research (Impact Factor: 9.11). 12/2008; 37(Database issue):D712-9. DOI: 10.1093/nar/gkn886
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The Mouse Genome Database (MGD,, integrates genetic, genomic and phenotypic information about the laboratory mouse, a primary animal model for studying human biology and disease. Information in MGD is obtained from diverse sources, including the scientific literature and external databases, such as EntrezGene, UniProt and GenBank. In addition to its extensive collection of phenotypic allele information for mouse genes that is curated from the published biomedical literature and researcher submission, MGI includes a comprehensive representation of mouse genes including sequence, functional (GO) and comparative information. MGD provides a data mining platform that enables the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. MGI can be accessed by a variety of methods including web-based search forms, a genome sequence browser and downloadable database reports. Programmatic access is available using web services. Recent improvements in MGD described here include the unified mouse gene catalog for NCBI Build 37 of the reference genome assembly, and improved representation of mouse mutants and phenotypes.

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Article: The Mouse Genome Database genotypes::Phenotypes

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    • "For AtT-20 cells, as a pituitary epithelial cell line, there are several terms related to epithelial cell function, including ‘cell–cell junction organization’, ‘cellular response to radiation’, ‘plasma membrane organization’ and particularly ‘regulation of insulin receptor signaling pathway’, indicating the role that the pituitary plays in responding to insulin. The over-represented terms from the Mouse Genome Database genotypes::phenotypes (43) are also indicative of specific STAT3 functions in the four cellular types, including ‘abnormal cytokine secretion’ (macrophages), ‘abnormal adaptive immunity’ (CD4+ T cells), ‘complete embryonic lethality’ (ESCs) and ‘increased body temperature’ (AtT-20 cells, since one of the functions of the pituitary is to regulate body temperature) (Figure 5B). Collectively, the GO analyses of the cell type-specific STAT3-binding events suggest that the functional specificity of STAT3 in each cell type is contained within the cell type-specific lists of STAT3-binding events and not within the shared overlap of peaks common to all four cellular types, which as we have previously shown has diverse cell type-independent functions. "
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    ABSTRACT: Transcription factors (TFs) regulate gene expression by binding to short DNA sequence motifs, yet their binding specificities alone cannot explain how certain TFs drive a diversity of biological processes. In order to investigate the factors that control the functions of the pleiotropic TF STAT3, we studied its genome-wide binding patterns in four different cell types: embryonic stem cells, CD4(+) T cells, macrophages and AtT-20 cells. We describe for the first time two distinct modes of STAT3 binding. First, a small cell type-independent mode represented by a set of 35 evolutionarily conserved STAT3-binding sites that collectively regulate STAT3's own functions and cell growth. We show that STAT3 is recruited to sites with E2F1 already pre-bound before STAT3 activation. Second, a series of different transcriptional regulatory modules (TRMs) assemble around STAT3 to drive distinct transcriptional programs in the four cell types. These modules recognize cell type-specific binding sites and are associated with factors particular to each cell type. Our study illustrates the versatility of STAT3 to regulate both universal- and cell type-specific functions by means of distinct TRMs, a mechanism that might be common to other pleiotropic TFs.
    Nucleic Acids Research 01/2013; 41(4). DOI:10.1093/nar/gks1300 · 9.11 Impact Factor
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    • "The gene list used in the functional enrichment analysis came from genes associated with Gene Ontology terms (Ashburner et al., 2000), KEGG pathways (Kanehisa et al., 2008), MSigDb database (Subramanian et al., 2005) and mammalian phenotypes (Blake et al., 2009). The statistical significance of gene list enrichment was determined based on the False Discovery Rate (fdr) cut-off of 0.1. "
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    ABSTRACT: Embryonic eyelid closure involves forward movement and ultimate fusion of the upper and lower eyelids, an essential step of mammalian ocular surface development. Although its underlying mechanism of action is not fully understood, a functional mitogen-activated protein kinase kinase kinase 1 (MAP3K1) is required for eyelid closure. Here we investigate the molecular signatures of MAP3K1 in eyelid morphogenesis. At mouse gestational day E15.5, the developmental stage immediately prior to eyelid closure, MAP3K1 expression is predominant in the eyelid leading edge (LE) and the inner eyelid (IE) epithelium. We used Laser Capture Microdissection (LCM) to obtain highly enriched LE and IE cells from wild type and MAP3K1-deficient fetuses and analyzed genome-wide expression profiles. The gene expression data led to the identification of three distinct developmental features of MAP3K1. First, MAP3K1 modulated Wnt and Sonic hedgehog signals, actin reorganization, and proliferation only in LE but not in IE epithelium, illustrating the temporal-spatial specificity of MAP3K1 in embryogenesis. Second, MAP3K1 potentiated AP-2α expression and SRF and AP-1 activity, but its target genes were enriched for binding motifs of AP-2α and SRF, and not AP-1, suggesting the existence of novel MAP3K1-AP-2α/SRF modules in gene regulation. Third, MAP3K1 displayed variable effects on expression of lineage specific genes in the LE and IE epithelium, revealing potential roles of MAP3K1 in differentiation and lineage specification. Using LCM and expression array, our studies have uncovered novel molecular signatures of MAP3K1 in embryonic eyelid closure.
    Developmental Biology 11/2012; 374(1). DOI:10.1016/j.ydbio.2012.11.020 · 3.55 Impact Factor
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    • "There are prominent differences in total and large TR amount in different databases. It can be explained with a difference in the methodology of genome sequencing and assembly [80,81]. In the genome assembly process the additional sequence sources (e.g. "
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    ABSTRACT: Functional and morphological studies of tandem DNA repeats, that combine high portion of most genomes, are mostly limited due to the incomplete characterization of these genome elements. We report here a genome wide analysis of the large tandem repeats (TR) found in the mouse genome assemblies. Using a bioinformatics approach, we identified large TR with array size more than 3 kb in two mouse whole genome shotgun (WGS) assemblies. Large TR were classified based on sequence similarity, chromosome position, monomer length, array variability, and GC content; we identified four superfamilies, eight families, and 62 subfamilies - including 60 not previously described. 1) The superfamily of centromeric minor satellite is only found in the unassembled part of the reference genome. 2) The pericentromeric major satellite is the most abundant superfamily and reveals high order repeat structure. 3) Transposable elements related superfamily contains two families. 4) The superfamily of heterogeneous tandem repeats includes four families. One family is found only in the WGS, while two families represent tandem repeats with either single or multi locus location. Despite multi locus location, TRPC-21A-MM is placed into a separated family due to its abundance, strictly pericentromeric location, and resemblance to big human satellites. To confirm our data, we next performed in situ hybridization with three repeats from distinct families. TRPC-21A-MM probe hybridized to chromosomes 3 and 17, multi locus TR-22A-MM probe hybridized to ten chromosomes, and single locus TR-54B-MM probe hybridized with the long loops that emerge from chromosome ends. In addition to in silico predicted several extra-chromosomes were positive for TR by in situ analysis, potentially indicating inaccurate genome assembly of the heterochromatic genome regions. Chromosome-specific TR had been predicted for mouse but no reliable cytogenetic probes were available before. We report new analysis that identified in silico and confirmed in situ 3/17 chromosome-specific probe TRPC-21-MM. Thus, the new classification had proven to be useful tool for continuation of genome study, while annotated TR can be the valuable source of cytogenetic probes for chromosome recognition.
    BMC Genomics 10/2011; 12(1):531. DOI:10.1186/1471-2164-12-531 · 3.99 Impact Factor
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