関: EST

WordNet

without unnecessary stops; "an express train"; "an express shipment"
rapid transport of goods (同)expressage
public transport consisting of a fast train or bus that makes only a few scheduled stops; "he caught the express to New York" (同)limited
mail that is distributed by a rapid and efficient system (同)express mail
give expression to; "She showed her disappointment" (同)show, evince
indicate through a symbol, formula, etc.; "Can you express this distance in kilometers?" (同)state
articulate; either verbally or with a cry, shout, or noise; "She expressed her anger"; "He uttered a curse" (同)verbalize, verbalise, utter, give tongue to
by express; "please send the letter express"
manifest the effects of (a gene or genetic trait); "Many of the laboratory animals express the trait"
not tacit or implied; "her express wish"
send by rapid transport or special messenger service; "She expressed the letter to Florida"
touch a player while he is holding the ball
(sports) the act of touching a player in a game (which changes their status in the game)
a game in which one child chases the others; the one who is caught becomes the next chaser
a label written or printed on paper, cardboard, or plastic that is attached to something to indicate its owner, nature, price, etc. (同)ticket
a label associated with something for the purpose of identification; "semantic tags were attached in order to identify different meanings of the word"
attach a tag or label to; "label these bottles" (同)label, mark
provide with a name or nickname
supply (blank verse or prose) with rhymes
determine the order of constituents in; "They sequenced the human genome"
a following of one thing after another in time; "the doctor saw a sequence of patients" (同)chronological sequence, succession, successiveness, chronological succession
film consisting of a succession of related shots that develop a given subject in a movie (同)episode
serial arrangement in which things follow in logical order or a recurrent pattern; "the sequence of names was alphabetical"; "he invented a technique to determine the sequence of base pairs in DNA"
several repetitions of a melodic phrase in different keys
arrange in a sequence
communicated in words; "frequently uttered sentiments" (同)uttered, verbalized, verbalised

PrepTutorEJDIC

(言葉で)〈思想・感情など〉‘を'『表現する』,言い表す,述べる / (言葉以外で)…‘を'『示す』,表す(indicate);〈数字・記号・式などが〉…‘を'表す / 《英》〈荷物など〉‘を'至急便で送る / (…から)〈果汁など〉‘を'絞り出す《+『名』+『from』+『名』》 / 特別の,特定の / はっきりした,明白な / 『至急便の』,急行の / 至急便で,急行で / 〈U〉(手紙・荷物などの)『至急便』 / 〈C〉(至急便を扱う)通運会社 / 〈C〉(列車・バスなどの)『急行』
(名前・番号・定価などを記した)札,下げ札,荷札 / (服などの)切れて垂れ下がった端;(靴ひもなどの)先金 / (特にラテン語引用句の)きまり文句 / =question tag / …‘に'下げ札をつける / (…に)…‘を'つける,加える《+名+on(to)+名》 / 〈人〉‘に'(…の)レッテルをはる《+名+as+名(形)》 / 人の後にくっついて行く《+along》;(人の)すぐ後について行く《+after(behind)+名》
鬼ごっこ / (野球で)タッチアウトにすること / (鬼ごっこで)〈相手〉‘を'捕まえる / (野球で)〈ランナー〉‘を'タッチアウトにする《+out+名,+名+out》
〈U〉〈C〉(時間の上の,また因果関係のつながりによる)『連続』,続き / 〈C〉《a~》(…の)一連のもの《+『of』+『名』》 / 〈U〉(起こる)『順序』(order),筋道 / 〈C〉(…に対する)結果《+『to』+『名』》
配列,接続;(特に時間の)調整

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2017/04/16 22:03:42」(JST)

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In genetics, an expressed sequence tag or EST is a short sub-sequence of a cDNA sequence.^[1] ESTs may be used to identify gene transcripts, and are instrumental in gene discovery and in gene-sequence determination.^[2] The identification of ESTs has proceeded rapidly, with approximately 74.2 million ESTs now available in public databases (e.g. GenBank 1 January 2013, all species).

An EST results from one-short sequencing of a cloned cDNA. The cDNAs used for EST generation are typically individual clones from a cDNA library. The resulting sequence is a relatively low-quality fragment whose length is limited by current technology to approximately 500 to 800 nucleotides. Because these clones consist of DNA that is complementary to mRNA, the ESTs represent portions of expressed genes. They may be represented in databases as either cDNA/mRNA sequence or as the reverse complement of the mRNA, the template strand.

One can map ESTs to specific chromosome locations using physical mapping techniques, such as radiation hybrid mapping, Happy mapping, or FISH. Alternatively, if the genome of the organism that originated the EST has been sequenced, one can align the EST sequence to that genome using a computer.

The current understanding of the human set of genes (as of 2006^[update]) includes the existence of thousands of genes based solely on EST evidence. In this respect, ESTs have become a tool to refine the predicted transcripts for those genes, which leads to the prediction of their protein products and ultimately of their function. Moreover, the situation in which those ESTs are obtained (tissue, organ, disease state - e.g. cancer) gives information on the conditions in which the corresponding gene is acting. ESTs contain enough information to permit the design of precise probes for DNA microarrays that then can be used to determine the gene expression.

Some authors use the term "EST" to describe genes for which little or no further information exists besides the tag.^[3]

Nagaraj et al. (2007) have reviewed the significance of ESTs, their properties, methods to analyze EST datasets and their applications in various areas of biology.^[4]

History

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^[5]

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.^[6]

In 1983, Putney et al. sequenced 178 clones from a rabbit muscle cDNA library^[7]

In 1991 Adams and co-workers coined the term EST and initiated more systematic sequencing as a project (starting with 600 brain cDNAs).^[2]

Sources of data and annotations

dbEST

dbEST is a division of Genbank established in 1992. As for GenBank, data in dbEST 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,^[8] Unigene,^[9] and STACK ^[10]

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 dbEST.^[11] 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).^[12] With the notable exception of cancer, the disease condition is often not recorded in dbEST 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 dbEST.^[13]

References

^ ESTs Factsheet. National Center for Biotechnology Information.
^ ^a ^b Adams MD, Kelley JM, Gocayne JD, et al. (Jun 1991). "Complementary DNA sequencing: expressed sequence tags and human genome project". Science. 252 (5013): 1651–6. doi:10.1126/science.2047873. PMID 2047873. Archived from the original on August 29, 2007.
^ dbEST
^ Nagaraj SH, Gasser RB, Ranganathan S (Jan 2007). "A hitchhiker's guide to expressed sequence tag (EST) analysis". Brief. Bioinformatics. 8 (1): 6–21. doi:10.1093/bib/bbl015. PMID 16772268.
^ Sim GK, Kafatos FC, Jones CW, Koehler MD, Efstratiadis A, Maniatis T (December 1979). "Use of a cDNA library for studies on evolution and developmental expression of the chorion multigene families". Cell. 18 (4): 1303–16. doi:10.1016/0092-8674(79)90241-1.
^ Sutcliffe JG, Milner RJ, Bloom FE, Lerner RA (August 1982). "Common 82-nucleotide sequence unique to brain RNA". Proc Natl Acad Sci U S A. 79 (16): 4942–6. doi:10.1073/pnas.79.16.4942.
^ Putney SD, Herlihy WC, Schimmel P (1983). "A new troponin T and cDNA clones for 13 different muscle proteins, found by shotgun sequencing". Nature. 302: 718–21. doi:10.1038/302718a0.
^ Lee Y, Tsai J, Sunkara S, et al. (Jan 2005). "The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes". Nucleic Acids Res. 33 (Database issue): D71–4. doi:10.1093/nar/gki064. PMC 540018. PMID 15608288.
^ Stanton JA, Macgregor AB, Green DP (2003). "Identifying tissue-enriched gene expression in mouse tissues using the NIH UniGene database". Appl Bioinform. 2 (3 Suppl): S65–73. PMID 15130819.
^ Christoffels A, van Gelder A, Greyling G, Miller R, Hide T, Hide W (Jan 2001). "STACK: Sequence Tag Alignment and Consensus Knowledgebase". Nucleic Acids Res. 29 (1): 234–8. doi:10.1093/nar/29.1.234. PMC 29830. PMID 11125101.
^ Skrabanek L, Campagne F (Nov 2001). "TissueInfo: high-throughput identification of tissue expression profiles and specificity". Nucleic Acids Res. 29 (21): E102–2. doi:10.1093/nar/29.21.e102. PMC 60201. PMID 11691939.
^ Campagne F, Skrabanek L (2006). "Mining expressed sequence tags identifies cancer markers of clinical interest". BMC Bioinformatics. 7: 481. doi:10.1186/1471-2105-7-481. PMC 1635568. PMID 17078886.
^ :institute for computational biomedicine::TissueInfo Archived June 4, 2008, at the Wayback Machine.

External links

ESTs Factsheet from NCBI, a good and easy to read introduction to ESTs.
The NCBI Handbook, Part 3, Chapter 21 has a very nice overview.
ECLAT a server for the classification of ESTs from mixed EST pools (from fungus infected plants) using codon usage.
The current number of EST sequences in the GenBank division dbEST.
Web Resources for EST data and analysis
[1] TissueInfo project: Curated EST tissue provenance, tissue ontology, open-source software.
http://www.estinformatics.org/ Web resource contains all publicly available ESTs which has been processed through various cleaning steps where contaminating DNA e.g. vector, E coli and short sequences (<100bp) removed.

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リンク元	「EST」「発現遺伝子配列断片」「発現配列タグ」
関連記事	「sequence」「express」「tag」「sequencing」「TAG」