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FANTOM / Functional ANnoTation Of the Mammalian genome
Contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors (TF) and enhancers across the FANTOM atlas. FANTOM is a worldwide collaborative project aiming at identifying all functional elements in mammalian genomes. The object of the project is moving steadily up the layers in the system of life, progressing thus from an understanding of the ‘elements’ to an understanding of the ‘system’.
UCbase
A web tool dedicated to the analysis of ultraconserved sequences (UCRs). UCRs are 481 sequences >200 bases sharing 100% identity among human, mouse and rat genomes. They are frequently located in genomic regions known to be involved in cancer or differentially expressed in human leukemias and carcinomas. UCbase is a platform-independent web resource that includes the updated version of the human genome annotation (hg19), information linking disorders to chromosomal coordinates based on the Systematized Nomenclature of Medicine classification, a query tool to search for single nucleotide polymorphisms (SNPs) and a new text box to directly interrogate the database using a MySQL interface. To facilitate the interactive visual interpretation of UCR chromosomal positioning, UCbase includes a graph visualization interface directly linked to UCSC genome browser.
UCNEbase
Provides information on the evolution and genomic organization of ultra-conserved non-coding elements (UCNEs) in multiple vertebrate species. UCNEbase currently covers 4,351 such elements in 18 different species. Around half of these elements are located within intergenic regions (2,139) and the rest are located within non-coding parts of genes: introns (1,713) and UTRs (499). The majority of UCNEs are supposed to be transcriptional regulators of key developmental genes. As it relies on the UCSC genome browser as visualization platform, a large part of its data content is also available as browser viewable custom track files. UCNEbase is potentially useful to any computational, experimental or evolutionary biologist interested in conserved non-coding DNA elements in vertebrates.
ECRbase
Provides users with detailed synteny structure interconnecting pair of genomes. ECRbase is a portal to pre-computed, post-processed whole-genome comparative data that allows the extraction of evolutionary conserved regions (ECRs). It promotes sequences as well as the transcription factor binding sites (TFBSs) associated with them, for all available vertebrate genomes. This resource allows for constant growth to accommodate the dynamic nature of genome research where newly emerging genomes.
BacterialID?
Identifies uniquely conserved regions (UCRs) as candidate diagnostic targets for a selected group of organisms solely from their genomic sequences. Using a sequence-indexing algorithm to identify UCRs and a k-mer integer-mapping model for computational efficiency, this method has successfully identified UCRs within the bacteria domain for 15 test groups, including pathogenic, probiotic, commensal and extremophilic bacterial species or strains. The UCRs identified for the 15 bacterial species are freely available.
EnhancerAtlas
An interactive database which contains an atlas of 2,534,123 enhancers for 105 cell/tissue types. A consensus enhancer annotation was obtained for each cell by summation of independent experimental datasets with the relative weights derived from a cross-validation approach. Moreover, EnhancerAtlas provides a set of useful analytic tools that allow users to query and compare enhancers in a particular genomic region or associated with a gene of interest, and assign enhancers and their target genes from a custom dataset.
C-It-Loci
A tool to explore and to compare the expression profiles of conserved loci among various tissues in three organisms. Conversed loci are pairs of adjacent homologous protein-coding genes shared between one or more species. Expression profiles are based on RNA-seq data from many sources to derive tissue enrichment or specificity. Classifications of transcripts are based on the latest release of ENSEMBL, which will be updated in a timely manner. In addition to protein-coding genes, expression profiles of yet-to-be-characterized long non-coding RNAs (lncRNAs) are included.
CONDOR
A resource dealing with conserved non-coding elements (CNEs) identified through targeted multiple alignments of orthologous DNA sequence between the Fugu genome and a number of mammalian genomes. CNEs identified in this way are likely to have been conserved in all vertebrate genomes and cluster almost exclusively around genes involved with regulation of early vertebrate development. These sequences are likely to represent distal cis-regulatory elements such as enhancers and silencers essential for the correct spatial/temporal expression of early developmental regulators. This resource is designed both for the increasing number of experimental groups interested in prioritising a set of elements for experimental verification and computational users interested in training sets with high regulatory potential.
DENdb / Dragon Enhancers database
A centralized on-line repository of predicted enhancers derived from multiple human cell-lines. DENdb integrates enhancers predicted by five different methods (ChromHMM, Segway, RFECS, CSI-ANN, and ENCODE integrated annotation) generating an enriched catalogue of enhancers for each of the analyzed cell-lines. DENdb contains overlap of enhancers with DNase I hypersensitive regions, and transcription factor binding sites. It also provides means to investigate enhancer interactions with DNA using several chromatin interaction assays, and the ability to explore genes neighbouring enhancers.
DG-CST / Disease Gene - Conserved Sequence Tags
Obsolete
Collects human–mouse conserved elements associated to disease genes. DG-CST is an annotated collection of conserved sequences related to genes involved in genetic diseases. The database contains a large number of annotations and is designed to allow easy retrieval of conserved sequence tag (CST) information. It can be useful for investigators interested in studying the molecular mechanisms that underlie genetic diseases and may help in deciphering the spectrum of pathogenetic mutations that determine genetic diseases.
CEGA / Conserved Elements from Genomic Alignments
Obsolete
Aims to provide an easy access to unbiased and comprehensive sets of conserved non-coding sequences (CNCs) at distinct levels of the vertebrate lineage. The sets were computed based on a strategy to be as comprehensive and sensitive as possible, while keeping scalability in mind. CEGA provides a convenient access using dynamic webpages to all elements within a genomic interval or close to a particular gene. Quick visualization of relevant biological data in relation to the conserved elements is also provided and can help prioritize the in-depth investigation of a sub-group of elements. Therefore elements can be selected and downloaded in various formats: as bed-file for visualization and for finding overlaps with other features, as multiple alignments in Fasta format for phylogenetic studies or single sequence Fasta for further studies and comparisons.
UCDB / Ulcerative Colitis Database
Obsolete
Catalogs the genes showing evidence in ulcerative colitis (UC) pathogenesis (UC GENE), drugs used in chemotherapy (UC DRUG), UC susceptibility single nucleotide polymorphism (SNP) loci (UC LOCUS), and microarray data (UC ANALYSIS). UCDB provides search facility for querying the database. It also contains tools for various analysis such as gene expression correlation, clustering, differential expression, and gene set enrichment analysis (GSEA).
TFCONES / Transcription Factor genes & associated COnserved Noncoding ElementS
Obsolete
Contains all human, mouse and fugu TF-encoding genes and conserved noncoding elements (CNEs) associated with them. The CNEs were identified by gene-by-gene alignments of orthologous TF-encoding gene loci using MLAGAN. The conserved noncoding elements identified in TFCONES represent a catalog of highly prioritized putative cis-regulatory elements of TF-encoding genes and are candidates for functional assay.
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