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HDTD / High-Dimensional Transposable Data
In multiple-tissue gene expression studies, the rows correspond to genes and the columns to tissues, and genes and tissues might to be correlated with each other. The unique feature of HDTD is the implementation of sound statistical methods that account for and estimate both the tissue- and gene-wise correlation, thus facilitating reliable inference about the form of the mean gene expression levels and the functional relationship among genes and/or tissues.
ATGC transcriptomics
Provides non-expert computer users with accessible biological data management and simple data integration, as it can be used without any prior knowledge of programming, database administration. ATGC transcriptomics presents a more comprehensive interface for ontological storage and browsing as a method to explore information and relationships between transcripts and other features of interest, such as the concept of alternative splicing, and relationships between transcripts and genes (or genomic loci) with functional annotation. ATGC offers the opportunity to expand the database schema by adding other modules that store information from different data sources.
TCDD.Transcriptomics
Provides datasets with standardized data from studies into 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) -mediated responses of the mammalian transcriptomic landscape. TCDD.Transcriptomics gathers data from over 40 studies dealing with human, rat and mouse. Liver, hypothalamus, adipose and kidney tissue types are included along with many doses and time points following exposure. Users can also get normalized RNA abundance data, results from linear modeling and extensive sample annotation.
PAHKB / Pulmonary Arterial Hypertension KnowledgeBase
Obsolete
A comprehensive database committed to establishing a comprehensive resource for pulmonary arterial hypertension. PAHKB extracts genetic data from all available sources, including those from association studies, genetic mutation, gene expression, animal model, supporting literature, various genomic annotations, gene networks, cellular and regulatory pathways, as well as microRNAs. Moreover, PAHKB provides online tools for data browsing and searching, data integration, pathway graphical presentation, and gene ranking.
INsPeCT / INtegrative Platform for Cancer Transcriptomics
Obsolete
Allows to perform comprehensive in-silico analyses of microarray, ChIP-seq, and RNA-seq data. INsPeCT is a web-application which provides an easy-to-use interface to a comprehensive, integrated suite of tools for rapid in silico analysis of microarray, ChIP-seq and RNA-seq data and/or lists of genes. It also provides access to the novel analytical framework (RMaNI regulatory module network inference) and to the widely used WGCNA (weighted gene co-expression network analysis) tool for inference and analysis of transcriptional regulatory networks using microarray data.
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FlyBase
It is the leading website and database of Drosophila genes and genomes. FlyBase curates a variety of data from published biological literature, including phenotype, gene expression, interactions (genetic and physical), gene ontology (GO) information and many others. These data are organized in ∼31 different data-type reports such as the Gene Report or the Allele Report. The range of data we provide increases and changes as new types of data become available. Whether you are using the fruit fly Drosophila melanogaster as an experimental system or wish to understand Drosophila biological knowledge in relation to human disease or to other model systems, FlyBase can help you successfully find the information you are looking for.
GXD / Gene eXpression Database
Offers an extensive and well-curated community resource of mouse developmental expression information. GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments through curation of the scientific literature and by collaborations with large-scale expression projects. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches. GXD includes over 1.5 million expression results and more than 300 000 images, all annotated with detailed and standardized metadata.
ReCount
Summarizes analysis-ready expression data for genes, exons, exon–exon splice junctions and base-level coverage. ReCount is an online resource that uses analysis pipelines that are annotation agnostic to process and summarize samples. The data provided allow multiple downstream analyses, including testing for differential expression of potentially unannotated transcribed sequence, enabling studies that individual laboratories would otherwise not have the resources to undertake.
PATRIC / Pathosystems Resource Integration Center
Aims to assist scientists in infectious-disease research. PATRIC is a National Institute of Health (NIH) supported bioinformatics resource center that has been built to enable comparative genomic analysis of bacterial pathogens. The database provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Tools and services for bacterial infectious disease research are also available.
BCaPE / Breast Cancer PDTX Encyclopaedia
A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. BCaPE provides tools for visualizing, querying and downloading data from a large collection of highly molecularly annotated breast cancer patient-derived tumour xenografts (PDTX). The biobank represents a powerful resource for pre-clinical breast cancer pharmacogenomic studies, including identification of biomarkers of response or resistance.
Expression Atlas
Provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. Expression Atlas consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Expression Atlas search interface allows for querying one or more genes or proteins from a selected species. The user can also add search filters for sample attributes and experimental factors, taking full advantage of ontology-driven query expansion.
PED / Pancreatic Expression database
Provides functions to extract, analyze, and integrate publicly available multi-omics datasets. PED is developed as a data repository to provide researchers with a single-entry point from which to manipulate, mine and integrate the heterogeneous and isolated findings into their own research. It incorporates published findings on pancreatic precursor lesions, including pancreatic intraepithelial neoplasias (PanINs), intraductal papillary mucinous neoplasms (IPMNs) and mucinous cystic neoplasms (MCNs).
BrainTx / Brain Transcriptome Database
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Provides data on the transcriptome related to mouse cerebellar development. BrainTx is a neuroinformatics database that contains gene expression information related to various stages and states of the brain. This online resource assigns parent ID number to each gene as described above and classifies different expression data for each gene, which are obtained from different transcripts of a gene or obtained by different probes of a gene.
Nematode.net
Consists of a community resource dedicated to the study of parasitic nematodes. Nematode.net is a publicly available resource that provides access to annotation of genomes, expression and related genome-scale data, as well as data-mining tools and their comparative data products. NemaGene hosts annotation for almost 1.1 million genes and transcripts spanning 67 nematode species and NemaBrowse allows displaying of SnpEff-annotated variants from isolates with different phenotypes. The database is a part of Helminth.net, an evolving collection of databases hosting resources for helminths.
OASIS
Provides a central repository and a web-based analytical platform for cancer multi-omics data. OASIS contains sample-level annotations and gene level mutation, copy number variation (CNV) and expression data on primary tumor, normal samples and cell lines across cancers and tissues from The Cancer Genome Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE), the Genotype-Tissue Expression (GTE) project and four published genomics studies of liver, gastric and breast cancers. It also provides a suite of easy-to-use analytical features to help wet-lab biologists perform exploratory analysis of the data.
BloodSpot
Provides an expression plot of genes in healthy and cancerous haematopoietic cells at specific differentiation stages. BloodSpot facilitates the easy assessment of gene-expression data and how this links to patient survival, investigation of gene-expression signatures, as well as analysis of user generated data and export of data and figures. Focusing on simplicity, BloodSpot has features that allow clinicians or biologists to quickly retrieve relevant information on the expression of specific genes/pathways, and further explore co-regulated patterns of gene-expression as well as impact on patient survival.
MEPD / Medaka Expression Pattern Database
A repository of medaka expression data for the scientific community. In this update we present two main improvements. First, we have changed the previous clone-centric view for in situ data to a gene-centric view. This is possible because now we have linked all the data present in MEPD to the medaka gene annotation in ENSEMBL. In addition, we have also connected the medaka genes in MEPD to their corresponding orthologous gene in zebrafish, again using the ENSEMBL database. Based on this, we provide a link to the Zebrafish Model Organism Database (ZFIN) to allow researches to compare expression data between these two fish model organisms. As a second major improvement, we have modified the design of the database to enable it to host regulatory elements, promoters or enhancers, expression patterns in addition to gene expression.
RSIADB
A collective resource for rice sheath blight pathogen, Rhizoctonia solani AG1 IA genome and transcritome. RSIADB enables users to search, browse, and download gene sequences for R. solani AG1 IA, and mine the data using BLAST, sequence extractor, browse and construction diagram tools that were integrated into the database. RSIADB is an important genomic resource for scientists working with R. solani AG1 IA and will assist researchers in analysing the annotated genome and transcriptome of this pathogen. This resource facilitates studies on gene function, pathogenesis factors and secreted proteins, as well as provide an avenue for comparative analyses of genes expressed during different stages of infection.
SZGR / Schizophrenia Gene Resource
A database for candidate variants and genes for schizophrenia. SZGR covers genetic, epigenetic, transcriptomic, translational and many other types of evidence. This tool provides a onestop shop of schizophrenia variants and genes and their function and regulation, providing an important resource in the schizophrenia and other mental disease community. To facilitate interpretation, SZGR includes various functional annotation data, especially brain eQTL (expression quantitative trait loci), methylation QTL, brain expression featured in deep categorization of brain areas and developmental stages and brain-specific promoter and enhancer annotations.
diArk
Aims to provide access to all available assembled genomes and transcriptomes. In September 2014, diArk contains about 2600 eukaryotes with 6000 genome and transcriptome assemblies, of which 22% are not available via NCBI/ENA/DDBJ. Several indicators for the quality of the assemblies are provided to facilitate their comparison for selecting the most appropriate dataset for further studies. diArk has a user-friendly web interface with extensive options for filtering and browsing the sequenced eukaryotes.
ANISEED
A sophisticated information system dedicated to the biology of ascidians, and which consists of two classes of inter-linked databases. The Developmental Browser formalizes, integrates and displays an extensive set of complementary and inter-related molecular and anatomical data for each species, which can be explored via four main menus giving access to functional annotations of genes and cis-regulatory sequences, to descriptions of anatomical entities, to gene expression data and to literature articles. Dedicated Genome Browsers complement this information by providing a visualization of genetic elements in their chromosomal context. One of the originalities of the system is to go beyond the classical hierarchical textual representation of anatomical entities found in most model organism databases and to provide a description of the shapes, neighborhood and area of cell contacts up to the early gastrula stage.
FlyAtlas
Compiles expression of the genes of Drosophila melanogaster in different tissues. FlyAtlas includes data obtained by hybridization of messenger RNA to Affymetrix Drosophila Genome 2 microarrays. It displays information related to the expression of individual transcripts, microRNAs, and separates data for male and female flies in adult somatic tissues. Results can be browsed by gene, tissue and category and users can also to query a specific gene for finding those with a similar pattern of expression across the different tissues.
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