The mouse Gene Expression Database (GXD): 2007 update

Smith, Cyndi M.; Finger, Jacqueline H.; Hayamizu, Terry F.; McCright, Ingeborg J.; Eppig, Janan T.; Kadin, James A.; Richardson, Joel E.; Ringwald, Martin

doi:10.1093/nar/gkl1003

Cited by 80 publications

(76 citation statements)

References 47 publications

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“…PDE3B KO mice, while fertile, have altered regulation of energy homeostasis and display signs of insulin resistance (65). PDE4D KO mice have retarded growth, reduced viability, and low female fertility (177), whereas PDE4B KO mice produce significantly less TNF-␣ in response to lipopolysaccharide stimulation (176), and PDE4A KO mice have a normal phenotype (351). In all cases, the action of the ablated isoenzyme is not compensated by other PDEs, indicating that expression of multiple PDEs in a tissue is key for physiological functions unique to each.…”

Section: A Physiological Implication For Localization and Function Omentioning

confidence: 99%

Mammalian Cyclic Nucleotide Phosphodiesterases: Molecular Mechanisms and Physiological Functions

Francis

Blount

Corbin

2011

Physiological Reviews

560

546

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The superfamily of cyclic nucleotide (cN) phosphodiesterases (PDEs) is comprised of 11 families of enzymes. PDEs break down cAMP and/or cGMP and are major determinants of cellular cN levels and, consequently, the actions of cN-signaling pathways. PDEs exhibit a range of catalytic efficiencies for breakdown of cAMP and/or cGMP and are regulated by myriad processes including phosphorylation, cN binding to allosteric GAF domains, changes in expression levels, interaction with regulatory or anchoring proteins, and reversible translocation among subcellular compartments. Selective PDE inhibitors are currently in clinical use for treatment of erectile dysfunction, pulmonary hypertension, intermittent claudication, and chronic pulmonary obstructive disease; many new inhibitors are being developed for treatment of these and other maladies. Recently reported x-ray crystallographic structures have defined features that provide for specificity for cAMP or cGMP in PDE catalytic sites or their GAF domains, as well as mechanisms involved in catalysis, oligomerization, autoinhibition, and interactions with inhibitors. In addition, major advances have been made in understanding the physiological impact and the biochemical basis for selective localization and/or recruitment of specific PDE isoenzymes to particular subcellular compartments. The many recent advances in understanding PDE structures, functions, and physiological actions are discussed in this review.

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Section: A Physiological Implication For Localization and Function Omentioning

confidence: 99%

Mammalian Cyclic Nucleotide Phosphodiesterases: Molecular Mechanisms and Physiological Functions

Francis

Blount

Corbin

2011

Physiological Reviews

560

546

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“…We have created custom parsers for biological databases including: AraCyc (Mueller, et al, 2003), GO (Ashburner, et al, 2000), GOA (Camon, et al, 2003), UniProt (Apweiler, et al, 2004) and PFAM (Sonnhammer, et al, 1997). Furthermore, parsers have been developed for a number of general-purpose file formats, including FASTA (Pearson, 1990), OBO (Smith, et al, 2007) and the flat files describing the cross references between GO terms and database entries made available from the GOA database.…”

Section: Data Importmentioning

confidence: 99%

Graph-based sequence annotation using a data integration approach

Pesch

Lysenko

Hindle

et al. 2008

Journal of Integrative Bioinformatics

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SummaryThe automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database AraCyc) which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation. The methods and algorithms presented in this publication are an integral part of the ON-DEX system which is freely available from http://ondex.sf.net/.

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“…For example, in model organism specific databases ZFin (Sprague et al, 2003), Wormbase (Rogers et al, 2008), MEPD (Henrich et al, 2005), Geisha (Bell et al, 2004;Darnell et al, 2007), GXD (Ringwald et al, 1997;Smith et al, 2007), BDGP (Tomancak et al, 2007), and Xenbase (Bowes et al, 2008), and across multiple species in VisiGene (Kuhn et al, 2007), 4DX-press (Haudry et al, 2008), and quickImage (Gilchrist et al, 2008). The general areas of bioimage informatics and related topics are covered in a recent review (Peng, 2008).…”

Section: Introductionmentioning

confidence: 99%

Database of queryable gene expression patterns for Xenopus

Gilchrist

Christensen

Bronchain

et al. 2009

Developmental Dynamics

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The precise localization of gene expression within the developing embryo, and how it changes over time, is one of the most important sources of information for elucidating gene function. As a searchable resource, this information has up until now been largely inaccessible to the Xenopus community. Here, we present a new database of Xenopus gene expression patterns, queryable by specific location or region in the embryo. Pattern matching can be driven either from an existing in situ image, or from a user-defined pattern based on development stage schematic diagrams. The data are derived from the work of a group of 21 Xenopus researchers over a period of 4 days. We used a novel, rapid manual annotation tool, XenMARK, which exploits the ability of the human brain to make the necessary distortions in transferring data from the in situ images to the standard schematic geometry.

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The mouse Gene Expression Database (GXD): 2007 update

Cited by 80 publications

References 47 publications

Mammalian Cyclic Nucleotide Phosphodiesterases: Molecular Mechanisms and Physiological Functions

Mammalian Cyclic Nucleotide Phosphodiesterases: Molecular Mechanisms and Physiological Functions

Graph-based sequence annotation using a data integration approach

Database of queryable gene expression patterns for Xenopus

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