Literature DB >> 10592205

The TIGR gene indices: reconstruction and representation of expressed gene sequences.

J Quackenbush1, F Liang, I Holt, G Pertea, J Upton.   

Abstract

Expressed sequence tags (ESTs) have provided a first glimpse of the collection of transcribed sequences in a variety of organisms. However, a careful analysis of this sequence data can provide significant additional functional, structural and evolutionary information. Our analysis of the public EST sequences, available through the TIGR Gene Indices (TGI; http://www.tigr.org/tdb/tdb.html ), is an attempt to identify the genes represented by that data and to provide additional information regarding those genes. Gene Indices are constructed for selected organisms by first clustering, then assembling EST and annotated gene sequences from GenBank. This process produces a set of unique, high-fidelity virtual transcripts, or tentative consensus (TC) sequences. The TC sequences can be used to provide putative genes with functional annotation, to link the transcripts to mapping and genomic sequence data, and to provide links between orthologous and paralogous genes.

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Year:  2000        PMID： 10592205      PMCID： PMC102391          DOI： 10.1093/nar/28.1.141

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  22 in total

1.  The construction of Arabidopsis expressed sequence tag assemblies. A new resource to facilitate gene identification.

Authors:  S D Rounsley; A Glodek; G Sutton; M D Adams; C R Somerville; J C Venter; A R Kerlavage
Journal:  Plant Physiol       Date:  1996-11       Impact factor: 8.340

Review 2.  A gene map of the human genome.

Authors:  G D Schuler; M S Boguski; E A Stewart; L D Stein; G Gyapay; K Rice; R E White; P Rodriguez-Tomé; A Aggarwal; E Bajorek; S Bentolila; B B Birren; A Butler; A B Castle; N Chiannilkulchai; A Chu; C Clee; S Cowles; P J Day; T Dibling; N Drouot; I Dunham; S Duprat; C East; C Edwards; J B Fan; N Fang; C Fizames; C Garrett; L Green; D Hadley; M Harris; P Harrison; S Brady; A Hicks; E Holloway; L Hui; S Hussain; C Louis-Dit-Sully; J Ma; A MacGilvery; C Mader; A Maratukulam; T C Matise; K B McKusick; J Morissette; A Mungall; D Muselet; H C Nusbaum; D C Page; A Peck; S Perkins; M Piercy; F Qin; J Quackenbush; S Ranby; T Reif; S Rozen; C Sanders; X She; J Silva; D K Slonim; C Soderlund; W L Sun; P Tabar; T Thangarajah; N Vega-Czarny; D Vollrath; S Voyticky; T Wilmer; X Wu; M D Adams; C Auffray; N A Walter; R Brandon; A Dehejia; P N Goodfellow; R Houlgatte; J R Hudson; S E Ide; K R Iorio; W Y Lee; N Seki; T Nagase; K Ishikawa; N Nomura; C Phillips; M H Polymeropoulos; M Sandusky; K Schmitt; R Berry; K Swanson; R Torres; J C Venter; J M Sikela; J S Beckmann; J Weissenbach; R M Myers; D R Cox; M R James; D Bentley; P Deloukas; E S Lander; T J Hudson
Journal:  Science       Date:  1996-10-25       Impact factor: 47.728

3.  Yeast genes and human disease.

Authors:  D E Bassett; M S Boguski; P Hieter
Journal:  Nature       Date:  1996-02-15       Impact factor: 49.962

Review 4.  Molecular linguistics: extracting information from gene and protein sequences.

Authors:  D Botstein; J M Cherry
Journal:  Proc Natl Acad Sci U S A       Date:  1997-05-27       Impact factor: 11.205

5.  Why map the rat?

Authors:  M R James; K Lindpaintner
Journal:  Trends Genet       Date:  1997-05       Impact factor: 11.639

6.  Sequence mapping by electronic PCR

Authors:  Gregory D Schuler
Journal:  Genome Res       Date:  1997-05       Impact factor: 9.043

7.  Distinguishing homologous from analogous proteins.

Authors:  W M Fitch
Journal:  Syst Zool       Date:  1970-06

8.  Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence.

Authors:  M D Adams; A R Kerlavage; R D Fleischmann; R A Fuldner; C J Bult; N H Lee; E F Kirkness; K G Weinstock; J D Gocayne; O White
Journal:  Nature       Date:  1995-09-28       Impact factor: 49.962

9.  A survey of expressed genes in Caenorhabditis elegans.

Authors:  R Waterston; C Martin; M Craxton; C Huynh; A Coulson; L Hillier; R Durbin; P Green; R Shownkeen; N Halloran
Journal:  Nat Genet       Date:  1992-05       Impact factor: 38.330

10.  Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues.

Authors:  W R McCombie; M D Adams; J M Kelley; M G FitzGerald; T R Utterback; M Khan; M Dubnick; A R Kerlavage; J C Venter; C Fields
Journal:  Nat Genet       Date:  1992-05       Impact factor: 38.330
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  119 in total

1.  STACK: Sequence Tag Alignment and Consensus Knowledgebase.

Authors:  A Christoffels; A van Gelder; G Greyling; R Miller; T Hide; W Hide
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes.

Authors:  M Rossberg; K Theres; A Acarkan; R Herrero; T Schmitt; K Schumacher; G Schmitz; R Schmidt
Journal:  Plant Cell       Date:  2001-04       Impact factor: 11.277

3.  Early and multiple Ac transpositions in rice suitable for efficient insertional mutagenesis.

Authors:  R Greco; P B Ouwerkerk; A J Taal; C Favalli; T Beguiristain; P Puigdomènech; L Colombo; J H Hoge; A Pereira
Journal:  Plant Mol Biol       Date:  2001-05       Impact factor: 4.076

4.  Short-chain dehydrogenase/reductase (SDR) relationships: a large family with eight clusters common to human, animal, and plant genomes.

Authors:  Yvonne Kallberg; Udo Oppermann; Hans Jörnvall; Bengt Persson
Journal:  Protein Sci       Date:  2002-03       Impact factor: 6.725

5.  The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome.

Authors:  A A Camargo; H P Samaia; E Dias-Neto; D F Simão; I A Migotto; M R Briones; F F Costa; M A Nagai; S Verjovski-Almeida; M A Zago; L E Andrade; H Carrer; H F El-Dorry; E M Espreafico; A Habr-Gama; D Giannella-Neto; G H Goldman; A Gruber; C Hackel; E T Kimura; R M Maciel; S K Marie; E A Martins; M P Nobrega; M L Paco-Larson; M I Pardini; G G Pereira; J B Pesquero; V Rodrigues; S R Rogatto; I D da Silva; M C Sogayar; M F Sonati; E H Tajara; S R Valentini; F L Alberto; M E Amaral; I Aneas; L A Arnaldi; A M de Assis; M H Bengtson; N A Bergamo; V Bombonato; M E de Camargo; R A Canevari; D M Carraro; J M Cerutti; M L Correa; R F Correa; M C Costa; C Curcio; P O Hokama; A J Ferreira; G K Furuzawa; T Gushiken; P L Ho; E Kimura; J E Krieger; L C Leite; P Majumder; M Marins; E R Marques; A S Melo; M B Melo; C A Mestriner; E C Miracca; D C Miranda; A L Nascimento; F G Nobrega; E P Ojopi; J R Pandolfi; L G Pessoa; A C Prevedel; P Rahal; C A Rainho; E M Reis; M L Ribeiro; N da Ros; R G de Sa; M M Sales; S C Sant'anna; M L dos Santos; A M da Silva; N P da Silva; W A Silva; R A da Silveira; J F Sousa; D Stecconi; F Tsukumo; V Valente; F Soares; E S Moreira; D N Nunes; R G Correa; H Zalcberg; A F Carvalho; L F Reis; R R Brentani; A J Simpson; S J de Souza; M Melo
Journal:  Proc Natl Acad Sci U S A       Date:  2001-10-09       Impact factor: 11.205

6.  Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat.

Authors:  Ramesh V Kantety; Mauricio La Rota; David E Matthews; Mark E Sorrells
Journal:  Plant Mol Biol       Date:  2002 Mar-Apr       Impact factor: 4.076

7.  An optimized protocol for analysis of EST sequences.

Authors:  F Liang; I Holt; G Pertea; S Karamycheva; S L Salzberg; J Quackenbush
Journal:  Nucleic Acids Res       Date:  2000-09-15       Impact factor: 16.971

8.  A semiautomated approach to gene discovery through expressed sequence tag data mining: discovery of new human transporter genes.

Authors:  Shoshana Brown; Jean L Chang; Wolfgang Sadée; Patricia C Babbitt
Journal:  AAPS PharmSci       Date:  2003

9.  The predicted candidates of Arabidopsis plastid inner envelope membrane proteins and their expression profiles.

Authors:  Abraham J K Koo; John B Ohlrogge
Journal:  Plant Physiol       Date:  2002-10       Impact factor: 8.340

10.  PipeOnline 2.0: automated EST processing and functional data sorting.

Authors:  Patricia Ayoubi; Xiaojing Jin; Saul Leite; Xianghui Liu; Jeson Martajaja; Abdurashid Abduraham; Qiaolan Wan; Wei Yan; Eduardo Misawa; Rolf A Prade
Journal:  Nucleic Acids Res       Date:  2002-11-01       Impact factor: 16.971
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