Searching WormBase for Information about <i>Caenorhabditis elegans</i>

Schwarz, Erich M.; Sternberg, Paul W.

doi:10.1002/0471250953.bi0108s14

Cited by 4 publications

(6 citation statements)

References 58 publications

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“…The Osprey platform (20) facilitates the study of protein-protein interaction networks and protein complexes by integrating the interaction information from the Biomolecular Interaction Network Database (21) and the General Repository for Interaction Datasets (22), which includes >50,000 of the interactions.…”

Section: Methodsmentioning

confidence: 99%

Microarray analysis of genes and gene functions in disc degeneration

Tang

Wang

Liu

et al. 2013

Experimental and Therapeutic Medicine

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The aim of the present study was to screen differentially expressed genes (DEGs) in human degenerative intervertebral discs (IVDs), and to perform functional analysis on these DEGs. The gene expression profile was downloaded from the Gene Expression Omnibus database (GSE34095)and included six human IVD samples: three degenerative and three non-degenerative. The DEGs between the normal and disease samples were identified using R packages. The online software WebGestalt was used to perform the functional analysis of the DEGs, followed by Osprey software to search for interactions between the DEGs. The Database for Annotation, Visualization and Integrated Discovery was utilized to annotate the DEGs in the interaction network and then the DEGs were uploaded to the Connectivity Map database to search for small molecules. In addition, the active binding sites for the hub genes in the network were obtained, based on the Universal Protein database. By comparing the gene expression profiles of the non-degenerative and degenerative IVDs, the DEGs between the samples were identified. The DEGs were significantly associated with transforming growth factor β and the extracellular matrix. Matrix metalloproteinase 2 (MMP2) was identified as the hub gene of the interaction network of DEGs. In addition, MMP2 was found to be upregulated in degenerative IVDs. The screened small molecules and the active binding sites of MMP2 may facilitate the development of methods to inhibit overexpression of MMP2.

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Section: Methodsmentioning

confidence: 99%

Microarray analysis of genes and gene functions in disc degeneration

Tang

Wang

Liu

et al. 2013

Experimental and Therapeutic Medicine

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“…UNIT here (Shaw, ) concentrates on the rich collection of resources available through the Mouse Genome Informatics (MGI) Web site, which includes nucleotide and protein sequence data, as well as information on molecular functions, phenotypic variants, mapping data, and expression patterns. UNIT here (Schwartz and Sternberg, ) discusses WormBase, the major biological database for the nematode Caenorhabditis elegans ; in addition to sequence information, WormBase contains information on gene expression patterns and neuronal connectivity. UNIT here (Lamesch et al., ) provides an overview of The Arabidopsis Information Resource (TAIR), a Web resource devoted to all aspects of Arabidopsis biology such as gene expression, mutant phenotypes, germplasms, clones, genetic markers, genetic and physical maps, and biochemical pathways.…”

Section: Overviewmentioning

confidence: 99%

The Importance of Biological Databases in Biological Discovery

Baxevanis¹,

Bateman

2015

CP in Bioinformatics

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Biological databases play a central role in bioinformatics. They offer scientists the opportunity to access a wide variety of biologically relevant data, including the genomic sequences of an increasingly broad range of organisms. This unit provides a brief overview of major sequence databases and portals, such as GenBank, the UCSC Genome Browser, and Ensembl. Model organism databases, including WormBase, The Arabidopsis Information Resource (TAIR), and those made available through the Mouse Genome Informatics (MGI) resource, are also covered. Non‐sequence‐centric databases, such as Online Mendelian Inheritance in Man (OMIM), the Protein Data Bank (PDB), MetaCyc, and the Kyoto Encyclopedia of Genes and Genomes (KEGG), are also discussed. © 2015 by John Wiley & Sons, Inc.

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“…SGD has emerged as a model MOD, and, as such, has served as the basis for the creation of at least three other MODs: DictyBase (Kreppel et al, ), the Candida Genome Database (Arnaud et al, ), and the Aspergillus Genome Database (Arnaud et al, ). Other well‐known MODs include The Arabidopsis Information Resource (TAIR; Rhee, ; Reiser and Rhee, ), Mouse Genome Informatics (MGI; Blake et al, ; Shaw, ), the Rat Genome Database (RGD; Karolchik et al, ; Twigger et al, ), and WormBase (Stein et al, ; Schwarz and Sternberg, ), to name just a few. A more comprehensive listing of online genetic databases is provided at the end of this unit.…”

Section: Overview and Principlesmentioning

confidence: 99%

“…Readers should remember that while many MODs use similar software and database structures, all MODs are unique and provide differing amounts and types of biological information, as well as different visualization and analysis tools. More detailed descriptions and protocols relating to these specific databases and related tools can be found in Current Protocols in Bioinformatics : GBrowse (Donlin, ), MGI (Shaw, ), RGD (Twigger et al, ), TAIR (Reiser and Rhee, ), WormBase (Schwarz and Sternberg, ), and the UCSC Genome Browser (Karolchik et al, ). Readers are encouraged to familiarize themselves with their favorite MODs by perusing their various Web pages, reading the online help documentation provided by the MOD, and contacting the MOD directly via e‐mail with any specific questions.…”

Section: Commentarymentioning

confidence: 99%

Using Model Organism Databases (MODs)

Engel

MacPherson

2009

CP Essential Lab Tech

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Model Organism Databases (MODs) represent the union of database technology and biology, and are essential to modern biological and medical research. Research communities are producing floods of new data, of increasingly different types and complexity. MODs assimilate this information from a wide variety of sources, organize it in a comprehensible manner, and make it freely available to the public via the Internet. MODs permit researchers to sort through massive amounts of data, providing access to key information that they might otherwise have overlooked. The protocols in this unit offer a general introduction to different types of data available in the growing number of MODs, and approaches for accessing, browsing, and querying these data.Keywords: Genome project r genetics r DNA sequence r gene model r protein function OVERVIEW AND PRINCIPLESRecent advances in DNA sequencing technologies over the past two decades have led to an increase in the number of fully sequenced genomes and other types of publicly available DNA sequences, which has in turn allowed a great expansion in the depth and breadth of experimental data available to today's researcher. In order to make the most of this information, it must be collected, vetted, collated, and made available to the relevant scientific community (i.e., it must be curated). This curation occurs within the context of Model Organism Databases (MODs), which are assuming increasing importance in all areas of biology."Model organisms" are nonhuman organisms that are typically used for biological research. The resulting data can be used as a framework for the interpretation and understanding of similar data from humans or other medically or economically important species. Popular model organisms include budding yeast, fruit flies, and laboratory mice, all of which contain genes that encode proteins and other gene products similar to those found in humans. Genetic manipulation of model organisms is generally the most efficient path to understanding the effects of mutations in their human homologs. Model organisms have become especially effective reference species because vast amounts of data have been generated, collected, and made freely available to the public research community. History of Model Organism DatabasesIn order to help researchers sort through these mountains of data, crucial resources called Model Organism Databases (MODs) have been developed. Each MOD provides easy access to the diverse types of knowledge available for a particular model organism. Two of the earliest MODs were FlyBase and the Saccharomyces Genome Database (SGD), both of which were established in the early 1990s. FlyBase was started by Michael Ashburner and colleagues at Cambridge University, Harvard University, and Indiana University in 1992 as an effort to collate information regarding the genes and mutations of the fruit fly Drosophila melanogaster, one of the most intensely studied eukaryotic

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Searching WormBase for Information about Caenorhabditis elegans

Cited by 4 publications

References 58 publications

Microarray analysis of genes and gene functions in disc degeneration

Microarray analysis of genes and gene functions in disc degeneration

The Importance of Biological Databases in Biological Discovery

Using Model Organism Databases (MODs)

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