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SMD / Stanford Microarray Database
A research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. The primary mission of SMD is to be a research tool that supports researchers from the point of data generation to data publication and dissemination, but it also provides unrestricted access to analysis tools and public data from 300 publications. In addition to supporting ongoing research, SMD makes its source code fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD.
LCB-DWH / Linnaeus Centre for Bioinformatics Data Warehouse
A web-based infrastructure for reliable and secure microarray gene expression data management and analysis that provides an online service for the scientific community. The LCB-DWH is an effort towards a complete system for storage (using the BASE system), analysis and publication of microarray data. Important features of the system include: access to established methods within R/Bioconductor for data analysis, built-in connection to the Gene Ontology database and a scripting facility for automatic recording and re-play of all the steps of the analysis.
RAD / RNA Abundance Database
Provides a comprehensive MIAME-supportive infrastructure for gene expression data management and makes extensive use of ontologies. Specific details on protocols, biomaterials, study designs, etc. are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format (e.g. ArrayExpress). This infrastructure enables a large variety of queries that incorporate visualization and analysis tools and have been tailored to serve the specific needs of projects focusing on particular organisms or biological systems.
HCSGD / Human Cellular Senescence Gene Database
Assists users on human cellular senescence. HCSGD combines multiple online published data sources into a senescence gene annotation platform. Genes are annotated with gene ontology (GO) annotation and microRNA/drug/compound target information. This software provides features like visualization of cellular senescence gene networks, browsing annotated functional information and the recovering senescence-associated genes with a web interface.
M3db
Helps user to extract the information on the pathway meta-analysis of metastatic melanoma for the two stages, Cutaneous Metastasis and Lymph Node. M3db contains 642 microarray samples meta-analysed which were used to generate melanoma reconstructed networks representing four different stages of melanoma progression to extract genes with altered molecular circuitry wiring as compared to a normal cellular state. It shows how anti-melanoma drug target efficacy decreases once the melanoma cells program itself for metastasis.
Genopolis
Provides a resource that allows different groups performing microarray experiments related to a common subject to create a common coherent knowledge base and to analyse it. The Genopolis database has been implemented as a dedicated system for the scientific community studying dendritic and macrophage cells functions and host-parasite interactions. The Genopolis Database system allows the community to build an object based MIAME compliant annotation of their experiments and to store images, raw and processed data from the Affymetrix GeneChip® platform.
ScreenMill
Hosts two web applications and one engine. ScreenMill is available online and allows users to obtain quantitative data from high-throughput growth experiments, streamlines the statistical analysis, and offers a novel web-based application to review and visualize data. The three tools are as follows: Colony Measurement Engine (CM Engine) to quantitate colony growth data from plate images; a web-based Data Review Engine (DR Engine) to validate and analyze quantitative screen data, and a web-based Statistics Visualization Engine (SV Engine) to visualize screen data.
CancerMA
An integrated bioinformatic analytical pipeline to automate the identification of novel candidate cancer markers/targets by means of analysing the expression of user-supplied gene lists across a manually curated database of 80 publicly available cancer microarray datasets and 13 cancer types. Such a meta-analysis enhances reliability and generalizability of the analysis results and leads to a more precise estimate of gene expression. Furthermore, the pipeline facilitates automated, homogeneous and reproducible analysis across a large number of datasets, and establishing a simple-to-use online web interface to access the pipeline puts specialist meta-analyses in the hands of biologists.
DNA Microarray Database
Gathers differential expression profiles of genes expressed in neonatal brains and adult spleen and liver of 129X1/SvJ and C57BL/6J strains of mice. DNA Microarray Database can assist researchers in determining whether a differentially expressed gene is influenced by alterations induced by mutation of the target gene itself or by the genetic background of parent 129X1/SvJ and C57BL/6J mice. The database can also help in predicting the crosses needed to produce a specific gene-targeted mouse.
HNdb / Head and Neck database
Aims to provide a unified and comprehensive resource of information on genes and proteins involved in head and neck (HN) squamous cell carcinoma, covering data on genomics, transcriptomics, proteomics, literature citations and also cross-references of external databases. Different literature searches of MEDLINE abstracts were performed using specific Medical Subject Headings (MeSH terms) for oral, oropharyngeal, hypopharyngeal and laryngeal squamous cell carcinomas. A curated gene-to-publication assignment yielded a total of 1370 genes related to HN cancer. The diversity of results allowed identifying novel and mostly unexplored gene associations, revealing, for example, that processes linked to response to steroid hormone stimulus are significantly enriched in genes related to HN carcinomas. Thus, our database expands the possibilities for gene networks investigation, providing potential hypothesis to be tested.
PEPR / Public Expression Profiling Resource
Obsolete
Provides centralized Affymetrix expression profiling data to the public research community, typically before publication in primary research papers. Data released through PEPR are generated within a single centralized research group (Children’s National Medical Center, Microarray Center), with projects originating internally and referred from external institutions. The web interface enables users to export many forms of data associated with any particular profile, including raw image files (.dat), processed image files (.cel) and interpretation files (.txt). It allows researchers to perform on‐line queries of expression profiles by any number of experimental variables (tissue, species, chip type, etc.).
MUSC DNA Microarray Database / Medical University of South Carolina DNA Microarray Database
Obsolete
A web-accessible archive of DNA microarray data. The database was developed using the DNA microarray project /data management system, µArrayDB. Annotations for each DNA microarray project and associated cRNA target information are stored in a MySQL relational database and linked to array hybridization data (raw and normalized). At the discretion of investigators, data are placed into the public domain where they can be interrogated and downloaded through a web browser.
MicroGen
Obsolete
Facilitates workflow management of spotted microarray experiment production, provides an efficient way to gather complete experimental information, and supports collaborative work. In fact, thanks to its well-defined core database architecture, MicroGen facilitates collection and storage of all experimental information according to the MIAME standard. Ordered availability of such information allows subsequent efficient and effective analyses of experimental results. MicroGen also facilitates experimental data comparison. In fact, it allows saving quantitative results also in a standard text format. This increases portability and compatibility of results. Identification of results from experiment with similar characteristic is also facilitated thanks to the complete experimental information orderly stored within the system. MicroGen graphic user interface is very simple and intuitive, providing an easy method for a biologist or a biotechnology technician to read or collect information about performed microarray experiments.
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