Learn to use the DataBase of Transcriptional Start Sites, DBTSS, a public resource for the analysis of promoter regions. It contains data on all transcriptional start sites that have been reported for a particular gene, compiling data from its own experimental sources as well as other genome databases. Important additional annotations such as transcription factor binding sites and SNPs can be visualized.
You will learn:
This tutorial is a part of the tutorial group Advanced Analysis and Queries. You might find the other tutorials in the group interesting:
BioMart: Management and querying of many types of biological data
UniProt: UniProt, Universal Protein Resource
ENCODE Data at UCSC: ENCODE Data at UCSC
Galaxy: Analysis tools for researchers
This tutorial is a part of the tutorial group Expression resources. You might find the other tutorials in the group interesting:
Functional Glycomics Gateway: The home for Functional Glycomics research
CleanEx: A Database of Heterogeneous Gene Expression Data Based on A Consistent Gene Nomenclature
Allen Mouse Brain Atlas: Mapped gene expression data in mouse brain
miRBase: microRNA sequences, targets and gene nomenclature
Alternative Splicing and Transcript Diversity (ASTD) database: A bioinformatics resource for alternative splice events and transcripts for human, mouse, and rat
GENSAT: Provides an extensive amount of high quality images of gene expression in the central nervous system of the mouse.
Gene Expression Omnibus (GEO): A gene expression/molecular abundance repository and a curated, online resource for gene expression data
ArrayExpress: A public repository for microarray gene expression data at the EBI
Expression : This category may contain various expression data collections, annotation tools, or repositories of expression data.
Nucleotides : Tools that are primarily used in the storage, retrieval, or exploration of nucleotide-based data. Some tools may also involve protein sequence information.
Video Tip of the Week: Let Allie help you figure out those acronyms : Just ask Allie. As I mentioned in a post nearly 5 years ago, I dislike acronyms. From my time in the army, which speaks in a language of acronyms, they've made me cringe. Of course, genomics databases...
NAR database issue (always a treasure trove): The advance access release of most of the NAR database issue articles is out. As usual, this this database issue includes a wealth of new and updated data repositories and analysis tools. We'll be wri...
Updated Online Tutorials for DBTSS, Pfam and PDB: Seattle, WA (PRWEB) October 29, 2008 -- OpenHelix today announced the availability of newly updated tutorial suites on the DataBase of Transcriptional Start Sites (DBTSS), Pfam and the Protein Databan...
Recent BioMed Central research articles citing this resource
Acevedo-Luna Natalia et al., Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules Sequence analysis (applications). BMC Bioinformatics (2016) doi:10.1186/s12859-016-1354-5
Lizio Marina et al., Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biology (2015) doi:10.1186/s13059-014-0560-6
Mao Ai-Ping et al., Expression and regulation of long noncoding RNAs in TLR4 signaling in mouse macrophages. BMC Genomics (2015) doi:10.1186/s12864-015-1270-5
Sahlén Pelin et al., Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution. Genome Biology (2015) doi:10.1186/s13059-015-0727-9
Maekawa Sho et al., Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance Human and rodent genomics. BMC Genomics (2015) doi:10.1186/s12864-015-1358-y