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Found 18 result(s)

Stanford Microarray Database

SMD

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>>>!!!<<< SMD has been retired. After approximately fifteen years of microarray-centric research service, the Stanford Microarray Database has been retired. We apologize for any inconvenience; please read below for possible resolutions to your queries. If you are looking for any raw data that was directly linked to SMD from a manuscript, please search one of the public repositories. NCBI Gene Expression Omnibus EBI ArrayExpress All published data were previously communicated to one (or both) of the public repositories. Alternatively, data for publications between 1997 and 2004 were likely migrated to the Princeton University MicroArray Database, and are accessible there. If you are looking for a manuscript supplement (i.e. from a domain other than smd.stanford.edu), perhaps try searching the Internet Archive: Wayback Machine https://archive.org/web/ . >>>!!!<<< The Stanford Microarray Database (SMD) is a DNA microarray research database that provides a large amount of data for public use.

The Cell Map

TheCellMap

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TheCellMap.org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae. In particular, TheCellMap.org allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize subnetworks, using data-driven network layouts in an intuitive and interactive manner.

Organelle Genome Megasequencing Program

OGMP

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The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.

STRING

Known and Predicted Protein-Protein Interactions

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STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: - Genomic Context - High-throughput Experiments - (Conserved) Coexpression - Previous Knowledge STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.

BeetleBase

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<<<!!!<<< This database doesn't exist anymore. 2017-09-05 >>>!!!>>>

Allen Brain Map

Data Portal

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The Allen Brain Atlas provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search and viewing tools for the adult and developing brain in mouse, human and non-human primate

GOBASE

The Organelle Genome Database

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!!! >>> the repository is offline >>> !!! GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE is currently expanding to include information on representative bacteria that are thought to be specifically related to the bacterial ancestors of mitochondria and chloroplasts

OrtholugeDB

The Ortholog Database

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OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. It is also a resource for reciprocal best BLAST-based ortholog predictions, in-paralog predictions (recently duplicated genes) and ortholog groups in Bacteria and Archaea. The Ortholuge method improves the specificity of high-throughput orthology prediction.

ErythronDB

Erythron Database

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<<<!!!<<< The original ErythronDB site is now retired! Code for generating the web site is available here https://github.com/ErythronDB/erythrondb-docker. >>>!!!>>>

SILVA

A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data.

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SILVA is a comprehensive, quality-controlled web resource for up-to-date aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains alongside supplementary online services. In addition to data products, SILVA provides various online tools such as alignment and classification, phylogenetic tree calculation and viewer, probe/primer matching, and an amplicon analysis pipeline. With every full release a curated guide tree is provided that contains the latest taxonomy and nomenclature based on multiple references. SILVA is an ELIXIR Core Data Resource.

The MaxQuant DataBase

MaxQB

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MaxQB stores and displays collections of large proteomics projects and allows joint analysis and comparison. As a first dataset is contains proteome data of 11 different human cell lines. The 11 cell line proteomes together identify proteins expressed from more than half of all human genes. For each protein of interest, expression levels estimated by label-free quantification can be visualized across the cell lines. Similarly, the expression rank order and estimated amount of each protein within each proteome are plotted.

The Plastics-Active Enzymes Database

PAZy

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Plastics are widely used in our economy and each year, at least 350-400 million tons are being produced at a global level. Due to poor recycling and low circular use, tens of millions of tons accumulate annually in marine and terrestrial environments. While it has become obvious that micro and macroplastics contaminate our environments recent research has identified few bacteria and fungi actively degrading plastics by enzymatic reactions. In general these are promiscuous enzymes (hydrolases) acting on low crystaline and mostly low density polymers of PET, ester-based PUR and oligomers of PA. Notably today, no enzymes have been characterized on a biochemical level for polymeric and crystaline PE, ether-based PUR, PS, PVC, PP. While many publications report on plastic degradation often, no convincing biochemical data have been published. Therefore the PAZy database lists exclusively biochemically characterized plastic-active enzymes. Predicted and putative enzymes that were not characterized on a biochemical, functional or structural level are not included in the PAZy database. The entries are manually curated.

Physical mapping data at Canada's Michael Smith Genome Sciences Centre - Data

Physical Mapping Data Access

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FPC Mapping data files from species that have been fingerprinted at Canada's Michael Smith Genome Sciences Centre (BCGSC).

PANDIT

Protein and Associated Nucleotide Domains with Inferred Trees

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<<<!!!<<< Efforts to obtain renewed funding after 2008 were unfortunately not successful. PANDIT has therefore been frozen since November 2008, and its data are not updated since September 2005 when version 17.0 was released (corresponding to Pfam 17.0). The existing data and website remain available from these pages, and should remain stable and, we hope, useful. >>>!!!>>> PANDIT is a collection of multiple sequence alignments and phylogenetic trees. It contains corresponding amino acid and nucleotide sequence alignments, with trees inferred from each alignment. PANDIT is based on the Pfam database (Protein families database of alignments and HMMs), and includes the seed amino acid alignments of most families in the Pfam-A database. DNA sequences for as many members of each family as possible are extracted from the EMBL Nucleotide Sequence Database and aligned according to the amino acid alignment. PANDIT also contains a further copy of the amino acid alignments, restricted to the sequences for which DNA sequences were found.

SuperTarget

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<<<!!!<<< This repository is no longer available. >>>!!!>>>

DNAmod

DNA modification database

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Covalent DNA modifications have been found in numerous organisms and more are continually being discovered and characterized, as detection methods improve. Many of these modifications can affect the conformation of the DNA double helix, often resulting in downstream effects upon transcription factor binding. Some of these modifications have been demonstrated to be stable, while others are viewed as merely transient. DNAmod catalogues information on known DNA modifications, of which the well-known 5-methylcytosine is only one. It aims to profile modifications' properties, building upon data contained within the Chemical Entities of Biological Interest (ChEBI) database. It also provides literature citations and includes curated annotations on mapping techniques and natural occurrence information.

The Neuro C-BIG Repository Data Portal (Beta)

C-BIG Repository Data Portal - Beta Version

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An Open Science resource that promotes scientific research and discovery in neurological diseases and accelerates the development of new treatments. It includes a growing collection of biospecimens, longitudinal clinical and neuropsychiatric information, imaging and genetic data from patients with neurological disease as well as healthy controls.

THEMIS

Acceleration, Reconnection, Turbulence and Electrodynamics of the Moon’s Interaction with the Sun

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The THEMIS mission is a five-satellite Explorer mission whose primary objective is to understand the onset and macroscale evolution of magnetospheric substorms. The five small satellites were launched together on a Delta II rocket and they carry identical sets of instruments including an electric field instrument (EFI), a flux gate magnetometer (FGM), a search coil magnetometer (SCM), a electro-static analyzer, and solid state telescopes (SST). The mission consists of several phases. In the first phase, the spacecraft will all orbit as a tight cluster in the same orbital plane with apogee at 15.4 Earth radii (RE). In the second phase, also called the Dawn Phase, the satellites will be placed in their orbits and during this time their apogees will be on the dawn side of the magnetosphere. During the third phase (also known as the Tail Science Phase) the apogees will be in the magnetotail. The fourth phase is called the Dusk Phase or Radiation Belt Science Phase, with all apogees on the dusk side. In the fifth and final phase, the apogees will shift to the sunward side (Dayside Science Phase). The satellite data will be combined with observations of the aurora from a network of 20 ground observatories across the North American continent. The THEMIS-B (THEMIS-P1) and THEMIS-C (THEMIS-P2) were repurposed to study the lunar environment in 2009. The spacecraft were renamed ARTEMIS (Acceleration, Reconnection, Turbulence and Electrodynamics of the Moon’s Interaction with the Sun), with the P1 and P2 designations maintained.