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Found 16 result(s)

Human protein-protein interaction network database search

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<<<!!!<<< This repository is no longer available. >>>!!!>>> A human interactome map. The sequencing of the human genome has provided a surprisingly small number of genes, indicating that the complex organization of life is not reflected in the gene number but, rather, in the gene products – that is, in the proteins. These macromolecules regulate the vast majority of cellular processes by their ability to communicate with each other and to assemble into larger functional units. Therefore, the systematic analysis of protein-protein interactions is fundamental for the understanding of protein function, cellular processes and, ultimately, the complexity of life. Moreover, interactome maps are particularly needed to link new proteins to disease pathways and the identification of novel drug targets.

NONCODE

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NONCODE is an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs). Now, there are 16 species in NONCODE(human, mouse, cow, rat, chicken, fruitfly, zebrafish, celegans, yeast, Arabidopsis, chimpanzee, gorilla, orangutan, rhesus macaque, opossum and platypus).The source of NONCODE includes literature and other public databases. We searched PubMed using key words ‘ncrna’, ‘noncoding’, ‘non-coding’,‘no code’, ‘non-code’, ‘lncrna’ or ‘lincrna. We retrieved the new identified lncRNAs and their annotation from the Supplementary Material or web site of these articles. Together with the newest data from Ensembl , RefSeq, lncRNAdb and GENCODE were processed through a standard pipeline for each species.

FlyReactome

a curated knowledgebase of drosophila melanogaster pathways

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<<<!!!<<< This repository is no longer available. This record is out dated >>>!!!>>>- eir fields, maintained by the FlyReactome staff.

Pombase

The scientific resource for fission yeast

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PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets.

Human Genetic Variation Repository

HGVD

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The Human Genetic Variation Database (HGVD) aims to provide a central resource to archive and display Japanese genetic variation and association between the variation and transcription level of genes. The database currently contains genetic variations determined by exome sequencing of 1,208 individuals and genotyping data of common variations obtained from a cohort of 3,248 individuals.

CorrDB

Animal Trait Correlation Database

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CorrDB has data of cattle, relating to meat production, milk production, growth, health, and others. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.

Fungal Mitochondrial Genome Project

FMGP

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The goals of FMGP are to: (i) sequence complete mitochondrial genomes from all major fungal lineages, (ii) infer a robust fungal phylogeny, (iii) define the origin of the fungi, their protistan ancestors, and their specific phylogenetic link to the animals, (iv) investigate mitochondrial gene expression, introns, RNAse P RNA structures, mobile elements.

NITRC

Neuroimaging Informatics Tools and Resources Clearinghouse

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Neuroimaging Tools and Resources Collaboratory (NITRC) is currently a free one-stop-shop environment for science researchers that need resources such as neuroimaging analysis software, publicly available data sets, and computing power. Since its debut in 2007, NITRC has helped the neuroscience community to use software and data produced from research that, before NITRC, was routinely lost or disregarded, to make further discoveries. NITRC provides free access to data and enables pay-per-use cloud-based access to unlimited computing power, enabling worldwide scientific collaboration with minimal startup and cost. With NITRC and its components—the Resources Registry (NITRC-R), Image Repository (NITRC-IR), and Computational Environment (NITRC-CE)—a researcher can obtain pilot or proof-of-concept data to validate a hypothesis for a few dollars.

Mammalian Transcriptomic Database

MTD

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MTD is focused on mammalian transcriptomes with a current version that contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts, and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features.

International HapMap Project

国际人类基因组单体型图计划

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<<<!!!<<< OFFLINE >>>!!!>>> A recent computer security audit has revealed security flaws in the legacy HapMap site that require NCBI to take it down immediately. We regret the inconvenience, but we are required to do this. That said, NCBI was planning to decommission this site in the near future anyway (although not quite so suddenly), as the 1,000 genomes (1KG) project has established itself as a research standard for population genetics and genomics. NCBI has observed a decline in usage of the HapMap dataset and website with its available resources over the past five years and it has come to the end of its useful life. The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. The Project is a collaboration among scientists and funding agencies from Japan, the United Kingdom, Canada, China, Nigeria, and the United States. All of the information generated by the Project will be released into the public domain. The goal of the International HapMap Project is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. By making this information freely available, the Project will help biomedical researchers find genes involved in disease and responses to therapeutic drugs. In the initial phase of the Project, genetic data are being gathered from four populations with African, Asian, and European ancestry. Ongoing interactions with members of these populations are addressing potential ethical issues and providing valuable experience in conducting research with identified populations. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. The Project officially started with a meeting in October 2002 (https://www.genome.gov/10005336/) and is expected to take about three years.

BioVel

Biodiversity Virtual e-Laboratory

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<<<!!!<<< This repository is no longer available. >>>!!!>>> BioVeL is a virtual e-laboratory that supports research on biodiversity issues using large amounts of data from cross-disciplinary sources. BioVeL supports the development and use of workflows to process data. It offers the possibility to either use already made workflows or create own. BioVeL workflows are stored in MyExperiment - Biovel Group http://www.myexperiment.org/groups/643/content. They are underpinned by a range of analytical and data processing functions (generally provided as Web Services or R scripts) to support common biodiversity analysis tasks. You can find the Web Services catalogued in the BiodiversityCatalogue.

Birdbase

A database of avian genes & genomes

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<<<!!!<<< This repository is no longer available. >>>!!!>>> The sequencing of several bird genomes and the anticipated sequencing of many more provided the impetus to develop a model organism database devoted to the taxonomic class: Aves. Birds provide model organisms important to the study of neurobiology, immunology, genetics, development, oncology, virology, cardiovascular biology, evolution and a variety of other life sciences. Many bird species are also important to agriculture, providing an enormous worldwide food source worldwide. Genomic approaches are proving invaluable to studying traits that affect meat yield, disease resistance, behavior, and bone development along with many other factors affecting productivity. In this context, BirdBase will serve both biomedical and agricultural researchers.

Human Intermediate Filament Database

HIFD

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The Intermediate Filament Database will function as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants. Suggestions on ways to improve the database are also welcome.

Cancer Cell Line Encyclopedia

CCLE

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The Cancer Cell Line Encyclopedia project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.

Pathway Commons

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Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely available under the license terms of each contributing database.

Swiss HIV Cohort Study & Swiss Mother and Child HIV Cohort Study

SHCS & MoCHIV

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The Swiss HIV Cohort Study (SHCS), established in 1988, is a systematic longitudinal study enrolling HIV-infected individuals in Switzerland. It is a collaboration of all Swiss University Hospital infectious disease outpatient clinics, two large cantonal hospitals, all with affiliated laboratories, and with affiliated smaller hospitals and private physicians carrying for HIV patients. The Swiss Mother and Child HIV Cohort Study (MoCHiV) is integrated into the SHCS. It aims at preventing mother to child transmission and enrolls HIV-infected pregnant women and their children. The SHCS involves practically all researchers being active in patient-oriented HIV research in Switzerland. The clinics can delegate recruitment of participants and follow-up visits to other outpatient clinics or to specialized private physicians, provided that the requirements of the protocol can be entirely fulfilled and controlled. The laboratories can contract other laboratories for some of the analyses.