共查询到20条相似文献,搜索用时 15 毫秒
1.
Luna A Sunshine ML van Iersel MP Aladjem MI Kohn KW 《Bioinformatics (Oxford, England)》2011,27(15):2165-2166
MOTIVATION: A plugin for the Java-based PathVisio pathway editor has been developed to help users draw diagrams of bioregulatory networks according to the Molecular Interaction Map (MIM) notation. Together with the core PathVisio application, this plugin presents a simple to use and cross-platform application for the construction of complex MIM diagrams with the ability to annotate diagram elements with comments, literature references and links to external databases. This tool extends the capabilities of the PathVisio pathway editor by providing both MIM-specific glyphs and support for a MIM-specific markup language file format for exchange with other MIM-compatible tools and diagram validation. AVAILABILITY: The PathVisio-MIM plugin is freely available and works with versions of PathVisio 2.0.11 and later on Windows, Mac OS X and Linux. Information about MIM notation and the MIMML format is available at http://discover.nci.nih.gov/mim. The plugin, along with diagram examples, instructions and Java source code, may be downloaded at http://discover.nci.nih.gov/mim/mim_pathvisio.html. 相似文献
2.
《Nucleosides, nucleotides & nucleic acids》2013,32(5-7):1029-1032
The online service PROSIT (Pseudo-Rotational Online Service and Interactive Tool) is a free service available at http://cactus.nci.nih.gov/prosit/ that performs pseudorotational analysis of nucleosides(tides). PROSIT reads the 3D coordinates of nucleosides and returns the pseudorotational phase angle P, puckering amplitude νmax, and other related information. As examples, the sugar conformations in a parallel-stranded guanine tetraplex and a four-way Holliday junction are presented here. 相似文献
3.
A random variance model for detection of differential gene expression in small microarray experiments 总被引:9,自引:0,他引:9
MOTIVATION: Microarray techniques provide a valuable way of characterizing the molecular nature of disease. Unfortunately expense and limited specimen availability often lead to studies with small sample sizes. This makes accurate estimation of variability difficult, since variance estimates made on a gene by gene basis will have few degrees of freedom, and the assumption that all genes share equal variance is unlikely to be true. RESULTS: We propose a model by which the within gene variances are drawn from an inverse gamma distribution, whose parameters are estimated across all genes. This results in a test statistic that is a minor variation of those used in standard linear models. We demonstrate that the model assumptions are valid on experimental data, and that the model has more power than standard tests to pick up large changes in expression, while not increasing the rate of false positives. AVAILABILITY: This method is incorporated into BRB-ArrayTools version 3.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html). SUPPLEMENTARY MATERIAL: ftp://linus.nci.nih.gov/pub/techreport/RVM_supplement.pdf 相似文献
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Gene Set Expression Comparison kit for BRB-ArrayTools 总被引:1,自引:0,他引:1
6.
caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid
Saltz J Oster S Hastings S Langella S Kurc T Sanchez W Kher M Manisundaram A Shanbhag K Covitz P 《Bioinformatics (Oxford, England)》2006,22(15):1910-1916
MOTIVATION: The complexity of cancer is prompting researchers to find new ways to synthesize information from diverse data sources and to carry out coordinated research efforts that span multiple institutions. There is a need for standard applications, common data models, and software infrastructure to enable more efficient access to and sharing of distributed computational resources in cancer research. To address this need the National Cancer Institute (NCI) has initiated a national-scale effort, called the cancer Biomedical Informatics Grid (caBIGtrade mark), to develop a federation of interoperable research information systems. RESULTS: At the heart of the caBIG approach to federated interoperability effort is a Grid middleware infrastructure, called caGrid. In this paper we describe the caGrid framework and its current implementation, caGrid version 0.5. caGrid is a model-driven and service-oriented architecture that synthesizes and extends a number of technologies to provide a standardized framework for the advertising, discovery, and invocation of data and analytical resources. We expect caGrid to greatly facilitate the launch and ongoing management of coordinated cancer research studies involving multiple institutions, to provide the ability to manage and securely share information and analytic resources, and to spur a new generation of research applications that empower researchers to take a more integrative, trans-domain approach to data mining and analysis. AVAILABILITY: The caGrid version 0.5 release can be downloaded from https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/. The operational test bed Grid can be accessed through the client included in the release, or through the caGrid-browser web application http://cagrid-browser.nci.nih.gov. 相似文献
7.
caCORE: a common infrastructure for cancer informatics 总被引:4,自引:0,他引:4
Covitz PA Hartel F Schaefer C De Coronado S Fragoso G Sahni H Gustafson S Buetow KH 《Bioinformatics (Oxford, England)》2003,19(18):2404-2412
MOTIVATION:Sites with substantive bioinformatics operations are challenged to build data processing and delivery infrastructure that provides reliable access and enables data integration. Locally generated data must be processed and stored such that relationships to external data sources can be presented. Consistency and comparability across data sets requires annotation with controlled vocabularies and, further, metadata standards for data representation. Programmatic access to the processed data should be supported to ensure the maximum possible value is extracted. Confronted with these challenges at the National Cancer Institute Center for Bioinformatics, we decided to develop a robust infrastructure for data management and integration that supports advanced biomedical applications. RESULTS: We have developed an interconnected set of software and services called caCORE. Enterprise Vocabulary Services (EVS) provide controlled vocabulary, dictionary and thesaurus services. The Cancer Data Standards Repository (caDSR) provides a metadata registry for common data elements. Cancer Bioinformatics Infrastructure Objects (caBIO) implements an object-oriented model of the biomedical domain and provides Java, Simple Object Access Protocol and HTTP-XML application programming interfaces. caCORE has been used to develop scientific applications that bring together data from distinct genomic and clinical science sources. AVAILABILITY: caCORE downloads and web interfaces can be accessed from links on the caCORE web site (http://ncicb.nci.nih.gov/core). caBIO software is distributed under an open source license that permits unrestricted academic and commercial use. Vocabulary and metadata content in the EVS and caDSR, respectively, is similarly unrestricted, and is available through web applications and FTP downloads. SUPPLEMENTARY INFORMATION: http://ncicb.nci.nih.gov/core/publications contains links to the caBIO 1.0 class diagram and the caCORE 1.0 Technical Guide, which provide detailed information on the present caCORE architecture, data sources and APIs. Updated information appears on a regular basis on the caCORE web site (http://ncicb.nci.nih.gov/core). 相似文献
8.
Edmonson MN Zhang J Yan C Finney RP Meerzaman DM Buetow KH 《Bioinformatics (Oxford, England)》2011,27(6):865-866
SUMMARY: Bambino is a variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. The variant detector takes advantage of SAM-specific annotations, and produces detailed output suitable for genotyping and identification of somatic mutations. The assembly viewer can display reads in the context of either a user-provided or automatically generated reference sequence, retrieve genome annotation features from a UCSC genome annotation database, display histograms of non-reference allele frequencies, and predict protein-coding changes caused by SNPs. AVAILABILITY: Bambino is written in platform-independent Java and available from https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html, along with documentation and example data. Bambino may be launched online via Java Web Start or downloaded and run locally. 相似文献
9.
Boyd LB Hunicke-Smith SP Stafford GA Freund ET Ehlman M Chandran U Dennis R Fernandez AT Goldstein S Steffen D Tycko B Klemm JD 《Bioinformatics (Oxford, England)》2011,27(10):1429-1435
MOTIVATION: Business Architecture Models (BAMs) describe what a business does, who performs the activities, where and when activities are performed, how activities are accomplished and which data are present. The purpose of a BAM is to provide a common resource for understanding business functions and requirements and to guide software development. The cancer Biomedical Informatics Grid (caBIG?) Life Science BAM (LS BAM) provides a shared understanding of the vocabulary, goals and processes that are common in the business of LS research. RESULTS: LS BAM 1.1 includes 90 goals and 61 people and groups within Use Case and Activity Unified Modeling Language (UML) Diagrams. Here we report on the model's current release, LS BAM 1.1, its utility and usage, and plans for future use and continuing development for future releases. Availability and Implementation: The LS BAM is freely available as UML, PDF and HTML (https://wiki.nci.nih.gov/x/OFNyAQ). 相似文献
10.
Chang JH Hwang KB Oh SJ Zhang BT 《Journal of bioinformatics and computational biology》2005,3(1):61-77
Combined analysis of the microarray and drug-activity datasets has the potential of revealing valuable knowledge about various relations among gene expressions and drug activities in the malignant cell. In this paper, we apply Bayesian networks, a tool for compact representation of the joint probability distribution, to such analysis. For the alleviation of data dimensionality problem, the huge datasets were condensed using a feature abstraction technique. The proposed analysis method was applied to the NCI60 dataset (http://discover.nci.nih.gov) consisting of gene expression profiles and drug activity patterns on human cancer cell lines. The Bayesian networks, learned from the condensed dataset, identified most of the salient pairwise correlations and some known relationships among several features in the original dataset, confirming the effectiveness of the proposed feature abstraction method. Also, a survey of the recent literature confirms the several relationships appearing in the learned Bayesian network to be biologically meaningful. 相似文献
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The Comparative Mouse Genomics Centers Consortium (CMGCC) is a branch of the Environmental Genome Project sponsored by the National Institute of Environmental Health Sciences (NIEHS) focusing upon the identification of human single nucleotide polymorphisms (SNPs) that may confer disease susceptibility within the human population. The goal of the CMGCC (http://www.niehs.nih.gov/cmgcc/) is to make genetic mouse models for human SNPs within cell cycle control, DNA replication and DNA repair genes that may be associated with human pathologies. In order to facilitate information sharing and analysis within the consortium a set of informatics resources have been generated to support the mouse model development efforts. The primary entry point for information about the mouse models developed by the consortium is through the CMGCC Genotype Database (http://mrages.niehs.nih.gov/genotype/), which maintains both a consortium specific and public access display of the available and developing mouse models. 相似文献
13.
Validation of clinical biomarkers and response to therapy is a challenging topic in cancer research. An important source of information for virtual validation is the datasets generated from multi-center cancer research projects such as The Cancer Genome Atlas project (TCGA). These data enable investigation of genetic and epigenetic changes responsible for cancer onset and progression, response to cancer therapies, and discovery of the molecular profiles of various cancers. However, these analyses often require bulk download of data and substantial bioinformatics expertise, which can be intimidating for investigators. Here, we report on the development of a new resource available to scientists: a data base called Glioblastoma Bio Discovery Portal (GBM-BioDP). GBM-BioDP is a free web-accessible resource that hosts a subset of the glioblastoma TCGA data and enables an intuitive query and interactive display of the resultant data. This resource provides visualization tools for the exploration of gene, miRNA, and protein expression, differential expression within the subtypes of GBM, and potential associations with clinical outcome, which are useful for virtual biological validation. The tool may also enable generation of hypotheses on how therapies impact GBM molecular profiles, which can help in personalization of treatment for optimal outcome. The resource can be accessed freely at http://gbm-biodp.nci.nih.gov (a tutorial is included). 相似文献
14.
Wang J Li H Zhu Y Yousef M Nebozhyn M Showe M Showe L Xuan J Clarke R Wang Y 《Bioinformatics (Oxford, England)》2007,23(15):2024-2027
SUMMARY: VISDA (Visual Statistical Data Analyzer) is a caBIG analytical tool for cluster modeling, visualization and discovery that has met silver-level compatibility under the caBIG initiative. Being statistically principled and visually interfaced, VISDA exploits both hierarchical statistics modeling and human gift for pattern recognition to allow a progressive yet interactive discovery of hidden clusters within high dimensional and complex biomedical datasets. The distinctive features of VISDA are particularly useful for users across the cancer research and broader research communities to analyze complex biological data. AVAILABILITY: http://gforge.nci.nih.gov/projects/visda/ 相似文献
15.
MOTIVATION: Single nucleotide polymorphisms (SNPs) are the most common form of genetic variant in humans. SNPs causing amino acid substitutions are of particular interest as candidates for loci affecting susceptibility to complex diseases, such as diabetes and hypertension. To efficiently screen SNPs for disease association, it is important to distinguish neutral variants from deleterious ones. RESULTS: We describe the use of Pfam protein motif models and the HMMER program to predict whether amino acid changes in conserved domains are likely to affect protein function. We find that the magnitude of the change in the HMMER E-value caused by an amino acid substitution is a good predictor of whether it is deleterious. We provide internet-accessible display tools for a genomewide collection of SNPs, including 7391 distinct non-synonymous coding region SNPs in 2683 genes. AVAILABILITY: http://lpgws.nci.nih.gov/cgi-bin/GeneViewer.cgi 相似文献
16.
In the Cancer Genome Atlas (TCGA) project, gene expression of the same set of samples is measured multiple times on different microarray platforms. There are two main advantages to combining these measurements. First, we have the opportunity to obtain a more precise and accurate estimate of expression levels than using the individual platforms alone. Second, the combined measure simplifies downstream analysis by eliminating the need to work with three sets of expression measures and to consolidate results from the three platforms.We propose to use factor analysis (FA) to obtain a unified gene expression measure (UE) from multiple platforms. The UE is a weighted average of the three platforms, and is shown to perform well in terms of accuracy and precision. In addition, the FA model produces parameter estimates that allow the assessment of the model fit.The R code is provided in File S2. Gene-level FA measurements for the TCGA data sets are available from http://tcga-data.nci.nih.gov/docs/publications/unified_expression/. 相似文献
17.
J'Neka S. Claxton Pablo C. Sandoval Gary Liu Chung-Lin Chou Jason D. Hoffert Mark A. Knepper 《PloS one》2013,8(12)
Protein carbamylation is a post-translational modification that can occur in the presence of urea. In solution, urea is in equilibrium with ammonium cyanate, and carbamylation occurs when cyanate ions react with the amino groups of lysines, arginines, protein N-termini, as well as sulfhydryl groups of cysteines. The concentration of urea is elevated in the renal inner medulla compared with other tissues. Due to the high urea concentration, we hypothesized that carbamylation can occur endogenously within the rat inner medulla. Using immunoblotting of rat kidney cortical and medullary homogenates with a carbamyl-lysine specific antibody, we showed that carbamylation is present in a large number of inner medullary proteins. Using protein mass spectrometry (LC-MS/MS) of rat renal inner medulla, we identified 456 unique carbamylated sites in 403 proteins, including many that play important physiological roles in the renal medulla [Data can be accessed at https://helixweb.nih.gov/ESBL/Database/Carbamylation/Carbamylation_peptide_sorted.html]. We conclude that protein carbamylation occurs endogenously in the kidney, modifying many physiologically important proteins. 相似文献
18.
Computation method to identify differential allelic gene expression and novel imprinted genes 总被引:2,自引:0,他引:2
MOTIVATION: Genomic imprinting plays an important role in both normal development and diseases. Abnormal imprinting is strongly associated with several human diseases including cancers. Most of the imprinted genes were discovered in the neighborhood of the known imprinted genes. This approach is difficult to extend to analyze the whole genome. We have decided to take a computational approach to systematically search the whole genome for the presence of mono-allelic expressed genes and imprinted genes in human genome. RESULTS: A computational method was developed to identify novel imprinted or mono-allelic genes. Individuals represented in human cDNA libraries were genotyped using Bayesian statistics, and differential expression of polymorphic alleles was identified. A significant reduction in the number of libraries that expressed both alleles, measured by Z-statistics, is a strong indicator for an imprinted or a mono-allelic gene. AVAILABILITY: The data sets are available at http://leelab.nci.nih.gov/leelab/jsp/IGDM/IGDM.html 相似文献
19.
MOTIVATION: The T-cell receptor, a major histocompatibility complex (MHC) molecule, and a bound antigenic peptide, play major roles in the process of antigen-specific T-cell activation. T-cell recognition was long considered exquisitely specific. Recent data also indicate that it is highly flexible, and one receptor may recognize thousands of different peptides. Deciphering the patterns of peptides that elicit a MHC restricted T-cell response is critical for vaccine development. RESULTS: For the first time we develop a support vector machine (SVM) for T-cell epitope prediction with an MHC type I restricted T-cell clone. Using cross-validation, we demonstrate that SVMs can be trained on relatively small data sets to provide prediction more accurate than those based on previously published methods or on MHC binding. SUPPLEMENTARY INFORMATION: Data for 203 synthesized peptides is available at http://linus.nci.nih.gov/Data/LAU203_Peptide.pdf 相似文献
20.
Congenital fibrosis of the vertically acting extraocular muscles maps to the <Emphasis Type="Italic">FEOM3</Emphasis> locus 总被引:5,自引:0,他引:5
The diagnosis of congenital fibrosis of the extraocular muscles (CFEOM) encompasses several different inherited strabismus syndromes characterized by congenital restrictive ophthalmoplegia affecting extraocular muscles innervated by the oculomotor and/or trochlear nerves. The OMIM database (http://www.ncbi.nlm.nih.gov/Omim/) currently contains four familial CFEOM phenotypes: CFEOM1-3, which map to the FEOM1-3 loci (MIM 135600, 602078, 604361), respectively, and congenital fibrosis of the vertically acting extraocular muscles (MIM 600638), reported in a single family without a corresponding genotype. We have had the opportunity to study the reported family with this fourth phenotype and now demonstrate that their phenotype can be reclassified as CFEOM3 and that it maps to FEOM3, flanked by D16S498 to 16qter, with a maximum lod score of 6.0. 相似文献