Expressed sequence tag

In 1979, teams at Harvard and Caltech extended the basic idea of making DNA copies of mRNAs in vitro to amplifying a library of such in bacterial plasmids. In 1982, the idea of selecting random or semi-random clones from such a cDNA library for sequencing was explored by Greg Sutcliffe and coworkers. In 1983, Putney et al. sequenced 178 clones from a rabbit muscle cDNA library. In 1991, Adams and co-workers coined the term EST and initiated more systematic sequencing as a project (starting with 600 brain cDNAs). == Sources of data and annotations ==

dbEST The is a division of Genbank established in 1992. As for GenBank, data in is directly submitted by laboratories worldwide and is not curated. EST contigs Because of the way ESTs are sequenced, many distinct expressed sequence tags are often partial sequences that correspond to the same mRNA of an organism. In an effort to reduce the number of expressed sequence tags for downstream gene discovery analyses, several groups assembled expressed sequence tags into EST contigs. Example of resources that provide EST contigs include: TIGR gene indices, Unigene, and STACK Constructing EST contigs is not trivial and may yield artifacts (contigs that contain two distinct gene products). When the complete genome sequence of an organism is available and transcripts are annotated, it is possible to bypass contig assembly and directly match transcripts with ESTs. This approach is used in the TissueInfo system (see below) and makes it easy to link annotations in the genomic database to tissue information provided by EST data. Tissue information High-throughput analyses of ESTs often encounter similar data management challenges. A first challenge is that tissue provenance of EST libraries is described in plain English in . This makes it difficult to write programs that can unambiguously determine that two EST libraries were sequenced from the same tissue. Similarly, disease conditions for the tissue are not annotated in a computationally friendly manner. For instance, cancer origin of a library is often mixed with the tissue name (e.g., the tissue name "glioblastoma" indicates that the EST library was sequenced from brain tissue and the disease condition is cancer). With the notable exception of cancer, the disease condition is often not recorded in entries. The TissueInfo project was started in 2000 to help with these challenges. The project provides curated data (updated daily) to disambiguate tissue origin and disease state (cancer/non cancer), offers a tissue ontology that links tissues and organs by "is part of" relationships (i.e., formalizes knowledge that hypothalamus is part of brain, and that brain is part of the central nervous system) and distributes open-source software for linking transcript annotations from sequenced genomes to tissue expression profiles calculated with data in . == See also ==