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on page 1 showing 20 out of 1,558 results from 1 sources

Cite this (1000 Genomes: A Deep Catalog of Human Genetic Variation, RRID:SCR_006828)

URL: http://www.1000genomes.org/

Resource Type: Resource, organization portal, database, consortium, data set, portal, data or information resource

International collaboration producing an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts, in an effort to provide a foundation for investigating the relationship between genotype and phenotype. The genomes of about 2500 unidentified people from about 25 populations around the world were sequenced using next-generation sequencing technologies. Redundant sequencing on various platforms and by different groups of scientists of the same samples can be compared. The results of the study are freely and publicly accessible to researchers worldwide. The consortium identified the following populations whose DNA will be sequenced: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States. The goal Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. Sequencing is still too expensive to deeply sequence the many samples being studied for this project. However, any particular region of the genome generally contains a limited number of haplotypes. Data can be combined across many samples to allow efficient detection of most of the variants in a region. The Project currently plans to sequence each sample to about 4X coverage; at this depth sequencing cannot provide the complete genotype of each sample, but should allow the detection of most variants with frequencies as low as 1%. Combining the data from 2500 samples should allow highly accurate estimation (imputation) of the variants and genotypes for each sample that were not seen directly by the light sequencing. All samples from the 1000 genomes are available as lymphoblastoid cell lines (LCLs) and LCL derived DNA from the Coriell Cell Repository as part of the NHGRI Catalog. The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via their mirrored ftp sites. ftp://ftp.1000genomes.ebi.ac.uk ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes

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Cite this (1000 Genomes Project and AWS, RRID:SCR_008801)

URL: http://aws.amazon.com/1000genomes/

Resource Type: Resource, data set, data or information resource

A dataset containing the full genomic sequence of 1,700 individuals, freely available for research use. The 1000 Genomes Project is an international research effort coordinated by a consortium of 75 companies and organizations to establish the most detailed catalogue of human genetic variation. The project has grown to 200 terabytes of genomic data including DNA sequenced from more than 1,700 individuals that researchers can now access on AWS for use in disease research free of charge. The dataset containing the full genomic sequence of 1,700 individuals is now available to all via Amazon S3. The data can be found at: http://s3.amazonaws.com/1000genomes The 1000 Genomes Project aims to include the genomes of more than 2,662 individuals from 26 populations around the world, and the NIH will continue to add the remaining genome samples to the data collection this year. Public Data Sets on AWS provide a centralized repository of public data hosted on Amazon Simple Storage Service (Amazon S3). The data can be seamlessly accessed from AWS services such Amazon Elastic Compute Cloud (Amazon EC2) and Amazon Elastic MapReduce (Amazon EMR), which provide organizations with the highly scalable compute resources needed to take advantage of these large data collections. AWS is storing the public data sets at no charge to the community. Researchers pay only for the additional AWS resources they need for further processing or analysis of the data. All 200 TB of the latest 1000 Genomes Project data is available in a publicly available Amazon S3 bucket. You can access the data via simple HTTP requests, or take advantage of the AWS SDKs in languages such as Ruby, Java, Python, .NET and PHP. Researchers can use the Amazon EC2 utility computing service to dive into this data without the usual capital investment required to work with data at this scale. AWS also provides a number of orchestration and automation services to help teams make their research available to others to remix and reuse. Making the data available via a bucket in Amazon S3 also means that customers can crunch the information using Hadoop via Amazon Elastic MapReduce, and take advantage of the growing collection of tools for running bioinformatics job flows, such as CloudBurst and Crossbow.

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    2DMAP

Cite this (2DMAP, RRID:SCR_009036)

URL: http://www.genlink.wustl.edu/software

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for constructing 2-d crossover-based map.

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    2LD

Cite this (2LD, RRID:SCR_000826)

URL: https://github.com/gaow/genetic-analysis-software/blob/master/pages/2LD.md

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software program for calculating linkage disequilibrium (LD) measures between two polymorphic markers.

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    2SNP

Cite this (2SNP, RRID:SCR_009038)

URL: https://github.com/gaow/genetic-analysis-software/blob/master/pages/2SNP.md

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. An algorithm resource for scalable phasing method for trios and unrelated individuals.

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Cite this (5 prime end Serial Analysis of Gene Expression Database, RRID:SCR_001680)

URL: http://5sage.gi.k.u-tokyo.ac.jp/

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 30, 2012. A database that displays the observed frequencies of individual 5' end SAGE tags and previously unknown transcription start sites in the promoter regions, introns and intergenic regions of known genes. 5'SAGE will be useful for analyzing promoter regions and start site variation in different tissues, and is freely available.

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Cite this (5S Ribosomal RNA Database, RRID:SCR_007545)

URL: http://biobases.ibch.poznan.pl/5SData/

Resource Type: Resource, data or information resource, database

A database on nucleotide sequences of 5S rRNAs and their genes. The database contains 1985 primary structures of 5S rRNA and 5S rDNA, and was last updated in 2002, according to the website. They include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. The nucleotide sequences of the 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of the source organisms. The sequences for particular organisms can be retrieved as single files using a taxonomic browser or in multiple sequence structural alignments. The multiple sequence alignments of 5S ribosomal RNAs can be downloaded in TAB-delimited and FASTA formats.

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Cite this (AASK Clinical Trial and Cohort Study, RRID:SCR_006985)

URL: http://archives.niddk.nih.gov/patient/aask/aask.aspx

Resource Type: Resource, disease-related portal, topical portal, research forum portal, portal, clinical trial, data or information resource

Clinical trial investigating whether a specific class of antihypertensive drugs (beta-adrenergic blockers, calcium channel blockers, or angiotensin converting enzyme inhibitors) and/or the level of blood pressure would influence progression of hypertensive kidney disease in African Americans. The initiative consisting of 21 clinical centers and a data-coordinating center is followed by a Continuation of AASK Cohort Study to investigate the environmental, socio-economic, genetic, physiologic, and other co-morbid factors that influence progression of kidney disease in a well-characterized cohort of African Americans with hypertensive kidney disease. Only patients who were previously in the randomized trial are eligible for the cohort study. A significant discovery was made in the treatment strategy for slowing kidney disease caused by hypertension. Angiotensin-converting enzyme (ACE) inhibitors, compared with calcium channel blockers, were found to slow kidney disease progression by 36 percent, and they drastically reduced the risk of kidney failure by 48 percent in patients who had at least one gram of protein in the urine, a sign of kidney failure. ACE inhibitors have been the preferred treatment for hypertension caused by diabetes since 1994; however, calcium channel blockers have been particularly effective in controlling blood pressure in African Americans. The AASK study now recommends ACE inhibitors to protect the kidneys from the damaging effects of hypertension. The Continuation of AASK Cohort Study will be followed at the clinical centers. The patients will be provided with the usual clinical care given to all such patients at the respective centers. Baseline demographic information, selected laboratory tests, and other studies are being obtained at the initiation of the Continuation Study. The patients will be seen quarterly at the centers, and some selected studies done at these visits. Samples will be obtained and stored for additional studies and analyses at a later date.

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    Abgent

Cite this (Abgent, RRID:SCR_008393)

URL: http://abgent.com

Resource Type: Resource, antibody supplier, core facility, service resource, access service resource, reagent supplier, material resource

An antibody supplier and core facility.

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Cite this (ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters, RRID:SCR_002276)

URL: http://genome.imim.es/datasets/abs2005/index.html

Resource Type: Resource, data or information resource, database

Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available.

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    AceView

Cite this (AceView, RRID:SCR_002277)

URL: http://www.ncbi.nlm.nih.gov/ieb/research/acembly/

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER SUPPORTED, documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions.

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    ACT

Cite this (ACT, RRID:SCR_009033)

URL: http://www.epigenetic.org/Linkage/act.html,

Resource Type: Resource, software resource, software application

Software application that contains the following modules: ibd, calculates the proportion of gene shared identical by decent for a nuclear family; ibdn, (modified program of ERPA), which implements a method for assessing increased-allele sharing between all pairs of affected relatives within a pedigree; multic, multivariate analysis for complex traits; ml, estimation of variance components using maximum likelihood; ql, estimation of variance components using quasi likelihood; relcov, generates first degree relationship coefficients for extended families; sim2s, the simulation program that was used to test ACT; cage, Cohort Analysis for Genetic Epidemiology; gh: GeneHunter, heavily modified to assist multipoint calculation using multic; TDT: TDT programs written in SAS; gcc and f77 compilers are necessary. Executable programs are included for compatible operating systems, i.e., Solaris2.6. (entry from Genetic Analysis Software)

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Cite this (ADA GENNID Study, RRID:SCR_000527)

URL: http://ccr.coriell.org/Sections/Collections/ADA/?SsId=12

Resource Type: Resource, data set, biomaterial supply resource, data or information resource, material resource, cell repository

The purpose of the American Diabetes Association (ADA), GENNID Study (Genetics of non-insulin dependent diabetes mellitus, NIDDM) is to establish a national database and cell repository consisting of information and genetic material from families with well-documented NIDDM. The GENNID Study will provide investigators with the information and samples necessary to conduct genetic linkage studies and locate the genes for NIDDM. Non-Hispanic white, Hispanic, African-American, and Japanese-American multiplex NIDDM families, with a minimum of one affected sib-pair, are being collected by the eight Harold Rifkin Family Acquisition Centers. Detailed family and medical histories are obtained from all participants. Family members with diabetes have fasting blood samples drawn, while nondiabetic family members have an oral glucose tolerance test and, when possible, insulin sensitivity and insulin secretion measurements by frequently sampled intravenous glucose tolerance testing or euglycemic insulin clamp. Lymphoblastoid cell lines are established for all participants. DNA samples and extensive phenotypic data are available from the American Diabetes Association's GENNID study (Genetics of NIDDM). GENNID has collected detailed family histories and a broad array of data on 170 large pedigrees, all of which contain at least one affected sib pair, with a total of 650 affected individuals and approximately 1,200 total subjects. Included are approximately 65 Caucasian, 60 Hispanic, 25 African American, and 20 Japanese American pedigrees. In addition, GENNID also contains DNA and data on 1,000 additional affected sib pairs in each of three groups, African American, Caucasian, and Hispanic. DNA and phenotypic data, including race, gender and age, are available for all members of the pedigrees. The data set includes multiple metabolic factors, including carbohydrate metabolism, lipid metabolism, and body size measures, as well as lifestyle variables obtained by questionnaire (e.g., employment, exercise, etc.). The GENNID resource is ideally suited for genetic linkage and association studies as well as SNP discovery and typing. Investigators interested in obtaining the DNA samples and/or data will need to submit a proposal to the Association that addresses the genetics of type 2 diabetes.

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    ADEGENET

Cite this (ADEGENET, RRID:SCR_000825)

URL: https://cran.r-project.org/web/packages/adegenet/index.html

Resource Type: Resource, software resource, software application

Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

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    ADGO

Cite this (ADGO, RRID:SCR_006343)

URL: http://www.btool.org/ADGO2

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets.

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    ADMIXMAP

Cite this (ADMIXMAP, RRID:SCR_009035)

URL: http://www.homepages.ed.ac.uk/pmckeigu/admixmap/index.html

Resource Type: Resource, software resource, software application

General-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus. (entry from Genetic Analysis Software)

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Cite this (AgedBrainSYSBIO, RRID:SCR_003825)

URL: http://www.agedbrainsysbio.eu/

Resource Type: Resource, organization portal, portal, consortium, data or information resource

Consortium focused on identifying the foundational pathways responsible for the aging of the brain, with a focus on Late Onset Alzheimer's disease. They aim to identify the interactions through which the aging phenotype develops in normal and in disease conditions; modeling novel pathways and their evolutionary properties to design experiments that identify druggable targets. As early steps of neurodegenerative disorders are expected to impact synapse function the project will focus in particular on pre- or postsynaptic protein networks. The concept is to identify subsets of pathways with two unique druggable hallmarks, the validation of interactions occurring locally in subregions of neurons and a human and/or primate accelerated evolutionary signature. The consortium will do this through six approaches: * identification of interacting protein networks from recent Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) data, * experimental validation of interconnected networks working in subregion of a neuron (such as dendrites and dendritic spines), * inclusion of these experimentally validated networks in larger networks obtained from available databases to extend possible protein interactions, * identification of human and/or primate positive selection either in coding or in regulatory gene sequences, * manipulation of these human and/or primate accelerated evolutionary interacting proteins in human neurons derived from induced Pluripotent Stem Cells (iPSCs) * modeling predictions in drosophila and novel mouse transgenic models * validation of new druggable targets and markers as a proof-of-concept towards the prevention and cure of aging cognitive defects. The scientists will share results and know-how on Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) gene discovery, comparative functional genomics in mouse and drosophila models, in mouse transgenic approaches, research on human induced pluripotent stem cells (hiPSC) and their differentiation in vitro and modeling pathways with emphasis on comparative and evolutionary aspects. The four European small to medium size enterprises (SMEs) involved will bring their complementary expertise and will ensure translation of project results to clinical application.

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    AGEINF

Cite this (AGEINF, RRID:SCR_009039)

URL: https://github.com/gaow/genetic-analysis-software/blob/master/pages/AGEINF.md

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application used to infer the age of a rare, selectively-neutral mutation.

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    aGEM

Cite this (aGEM, RRID:SCR_013349)

URL: http://agem.cnb.csic.es/VisualOmics/aGEM/

Resource Type: Resource, data or information resource, database

Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement many functional genomics studies. The platform allows the integration of gene expression data with spatial-temporal anatomic data by means of an intuitive and user friendly display.

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    AgingDB

Cite this (AgingDB, RRID:SCR_010226)

URL: http://link.springer.com/article/10.1007%2Fs11357-003-0002-y

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

A database that stores information on the biomolecules which are modulated during aging and by caloric restriction (CR). To enhance its usefulness, data collected from studies of CR''''s anti-oxidative action on gene expression, oxidative stress, and many chronic age-related diseases are included. AgingDB is organized into two sections A) apoptosis and the various mitochondrial biomolecules that play a role in aging; B) nuclear transcription factors known to be_sensitive to oxidative environment. AgingDB features an imagemap of biomolecular signal pathways and visualized information that includes protein-protein interactions of biomolecules. Authorized users can submit a new biomolecule or edit an existing biomolecule to reflect latest developments.

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