Aids to create structured controlled vocabularies, arranged in ontologies, that can be applied to plant-based database information. PO brings an integrated approach of adopting common annotation standards and a set of reference ontologies for plants. The project is a collaborative project that depends on coordination with several national and international projects.
Provides aligned, annotated and phylogenetically ordered sequences of the Signal recognition particle (SRP) components. SRPDB is a database that provides alphabetically and phylogenetically ordered lists of SRP RNA and SRP protein sequences. This online resource is also organized for additional proteins that play a role in SRP-mediated protein transport or are related to SRP components. The SRPDB lists 115 sequences from all phylogenetic groups.
Provides experimental data on in vitro selected DNA/RNA oligomers (aptamers) and the applets for recognition of these oligomers. SELEX_DB stores selected affinity-enriched sequences from different combinatorial libraries. The database is supplemented by two databases, SYSTEM and CROSS_TEST, storing both the experimental systems and their cross-validation tests. It includes reference to the literature source with SELEX_BIB database and SELEX_TOOLS, the recognition applet package.
Aims to decipher the gene networks underpinning mouse hematopoiesis. The immune transcriptome compendium has revealed unsuspected cell lineage relations and the network reconstruction has identified novel regulatory factors of hematopoiesis.
Helps to discover cell-lineage–specific genes. Nano-dissection is an iterative computational approach that predicts cell-lineage–specific expression of human genes using high-throughput genomic expression data derived from tissue homogenates. This method uses an iterative machine learning framework that makes robust predictions, even when only limited prior knowledge about cell-lineage–specific markers is available.
Provides an access to the three collections of gene expression signatures for knowledge reuse and exploration. The CREEDS database visualizes all of the signatures in a packed circles layout in which similar signatures are closer to each other. It also includes interactive heatmaps of hierarchically clustered matrices of all signatures. A search engine is available in order to allow users to search by text or by providing lists of up and down DEGs (differentially expressed genes).
A database and online resource for survival data in animals. As well as a substantial increase in data and additions to existing graphical and statistical survival analysis features, SurvCurv now includes extended mathematical mortality modelling functions and survival density plots for more advanced representation of groups of survival cohorts.
Assists users in investigating and optimizing methods for reprogramming and differentiation of induced pluripotent stem cells (iPSC). PCBC is a publicly available online collaborative research platform that provides data annotation, documentation, and file provenance. This resource also includes metadata, in vitro and in vivo differentiation, qPCR, RNA-seq, miRNA-seq, copy number variation, and DNA methylation data.
Gathers information related to gene and protein sequences from complete prokaryotic genomes. BAGET is repository that provides for each record a graphical representation of a chromosome centered on the gene of interest and its corresponding DNA sequence. Searches can be made by gene name or by browsing a list including groups of hundred genes, displayed by chromosomal position. The queried data can be downloaded in RTF format.
Identifies and catalogues genetic vulnerabilities across hundreds of genomically characterized cancer cell lines. Achilles is a project to facilitates the discovery of context-specific dependencies, genes that when suppressed only have an effect on the viability of the particular cell lines. These data set can be exploited to discover pathways to which specific tumor subtypes are preferentially dependent.
Assists researchers in performing genome wide comparative analyses for a series of model organisms. MorphDB provides access to MORPH’s predictions for six important model organisms: Arabidopsis thaliana, Medicago truncatula, Populus trichocarpa, Solanum lycopersicum, Solanum tuberosum, Catharanthus roseus, Oryza sativa and Zostera marina. It integrates the MORPH candidate gene predictions across species using orthogroup data.
Studies the genome of the Pacific oyster, Crassostrea gigas. GigaTON provides a web browser that allows a convenient view of the target contig counterparts in numerous other databases at a single glance. It offers a high versatility tool both in terms of request criteria and retrieved attributes that can be easily downloaded. The tool includes user-friendly ‘search, browse and retrieve’ online tools.
Allows easy access to historical data on Gene Ontology (GO) / Gene Ontology annotation (GOA). GOTrack contains historical information on GO for human and major model organisms. This resource enables quick exploration of GO and GO annotations over time, and evaluation of how changes impact interpretation of analyses derived from GOA. It also permits inspection of the effects of changes over time on enrichment result stability.
Gathers information about transcribed pseudogenes (TPGs) and explores the relationships between TPG and its cognate gene with miRNA decoyed mechanisms and TPG-derived eSTIs. PseudoMap furnishes an expression profile for TPGs and their associated cognates as well as miRNA regulators of TPGs and their parental genes. Moreover, it permits TPG-derived esiRNAs detection and allows to build their interactions as well as their interacting gene targets in the human genome.
Provides a portal to healthspan-associated pathways. Healthspan Pathways allows users to access to network graphs of health-associated genes and their interactions. This data source enables to export the different graphs and permits users to display human genetic association and caloric restriction, graphs on caenorhabditis elegans and human/caenorhabditis elegans pathway overlap.
Provides a resource for adult neurogenesis. SVZ Cell Atlas is an online database that previews the regulation of subventricular zone (SVZ) neurogenesis by LRP2, an endocytic receptor required for SVZ maintenance. It also includes proof of principle demonstrating the power of the single RNA-cell in identifying neural cell type specific functions in function loss models.
Provides a repository for spatial transcriptomics of C. elegans males and hermaphrodites. C. elegans Tomo-Seq gathers gene expression profiles per individual section and per aggregated anatomic region. Users can explore gene expression maps by filling in a gene name to obtain: expression in the aggregated maps, expression in the individual male and hermaphrodite expression maps and spatially co-expressed genes based on similarity in expression patterns at a user defined correlation threshold.
Aids users the use single-cell datasets. DropViz confronts cell types to one another, finds cell populations that express genes of interest and computes many kinds of analyses. It implements an analysis strategy based on independent components analysis (ICA). This method reduces large datasets to a smaller number of dimensions in which entities have score distributions that are maximally structured and statistically independent.
Tracks and stores projects, screens, assays, cell lines and library information. HTS-DB provides full data tracking, interactive data visualization and analysis and comparison of screening results both within projects and between different projects. It also provides a repository for additional measurements obtained from screens that were not the focus of the project, such as cell viability, and groups these data so that it can provide a gene-centric summary across several different cell lines and conditions.
Provides access to sexual reproduction associated genes. MCRiceRepGP is a database that gathers the results of genome-wide discovery of sexual reproduction associated genes in rice. More than 2,000 protein coding and 700 long intergenic non-coding RNAs (lincRNA) genes were predicted to be involved in sexual reproduction.
Provides genomics and proteomics products and services for academic and governmental research institutes, pharmaceutical and biotechnology industry. Genecopoeia, Inc. is a US-based manufacturer that released into market the largest number of human full length protein coding open reading frame (ORF) cDNA clones in multiple sets of vector systems with various features which make these clones suitable for a variety of functional assays, protein expression and easy purification in many cell types as well as cell free transcription and translation coupling systems, and large scale functional genomics and proteomics studies.
Allows users to search for similar diseases of a selecting disease. DisSim is a resource providing a way to query similarity score of pair-wise diseases. Users can choose between five methods for calculating similarity of pair-wise: SemFunSim, Resnik, Wang, PSB or Lin. This database is part of DincRNA, a bioinformatics resource for disease similarity calculation and non-coding RNA functional analysis.
Gathers more than 43000 human genes about 320000 transcripts. CHESS is a repository which proposes five downloadable files displaying: (i) a set for gene annotation aligned according human genome release GRCh38.p8; (ii) a gene list of the complete database with additional features; (iii) a FASTA file including the sequences of the censused proteins; (iv) a modified annotation file limited to reference chromosomes and mitochondrion; and (v) a set of annotation enriched by data from RefSeq.
Assists researchers in selecting region of interest to induce exon skipping. Skip-e is an online resource that contains an interactive genome viewer. It was developed to design antisense oligonucleotide (AON) and allele-specific oligonucleotide (ASO), data that have been used in post-genome era. This database can also be used to restore a functional protein or silence a gene.
Provides information about antisense oligonucleotides (ODNs). AOBase is developed for both ODNs selection and ODNs design. The database can be used to select effective ODNs for gene expression modulation. It can also contribute to mining rules and is useful for researchers to develop algorithms for rational ODNs design.
Assists users in analyzing messenger RNA (mRNA) expression data. ChEA permits researchers to submit lists of mammalian gene symbols for which the program computes over-representation of transcription factor targets from the ChIP-X database. This database permits the reconstruction of an initial network of transcription factors connected, based on shared overlapping targets and binding site proximity.
Aims to collect all ribozyme and aptamer sequences and their detailed and correct annotation. RiboaptDB provides users with a web interface with flexibility to select either ribozyme or aptamer sequences and to browse the corresponding information. It allows online sequence submission to the database. This repository can be useful for identifying available aptamers and artificial ribozymes, for acquiring information about in vitro selection experiment, and for better understanding the distribution of functional nucleic acids in the given sequence space.
Offers general functional annotation information in both single- and batch-search mode. NMC Annotation Tool enables users to query the GeneTools database by singe gene search or by batch search after submission of a gene reporter list for a microarray experiment. These annotations are from several types of database such as: UniGene, Entrez Gene, SwissProt and GeneOntology.
Provides structured and detailed information about the experimental conditions under which aptamers were selected and their binding affinity quantified. Aptamer Base is an open collaborative database with a unique resource that can be updated and curated in a decentralized manner, thereby accommodating the ever evolving filed of aptamer research. Aptamer Base describes the pH, temperature, salt concentrations and the buffering agent for all systematic evolution of ligands by exponential enrichment (SELEX) experiments.
1 - 3 of 3