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Literature DB >> 15590942

Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags.

Simon J Hubbard¹, Darren V Grafham, Kevin J Beattie, Ian M Overton, Stuart R McLaren, Michael D R Croning, Paul E Boardman, James K Bonfield, Joan Burnside, Robert M Davies, Elizabeth R Farrell, Matthew D Francis, Sam Griffiths-Jones, Sean J Humphray, Christopher Hyland, Carol E Scott, Haizhou Tang, Ruth G Taylor, Cheryll Tickle, William R A Brown, Ewan Birney, Jane Rogers, Stuart A Wilson.

Abstract

We present an analysis of the chicken (Gallus gallus) transcriptome based on the full insert sequences for 19,626 cDNAs, combined with 485,337 EST sequences. The cDNA data set has been functionally annotated and describes a minimum of 11,929 chicken coding genes, including the sequence for 2260 full-length cDNAs together with a collection of noncoding (nc) cDNAs that have been stringently filtered to remove untranslated regions of coding mRNAs. The combined collection of cDNAs and ESTs describe 62,546 clustered transcripts and provide transcriptional evidence for a total of 18,989 chicken genes, including 88% of the annotated Ensembl gene set. Analysis of the ncRNAs reveals a set that is highly conserved in chickens and mammals, including sequences for 14 pri-miRNAs encoding 23 different miRNAs. The data sets described here provide a transcriptome toolkit linked to physical clones for bioinformaticians and experimental biologists who wish to use chicken systems as a low-cost, accessible alternative to mammals for the analysis of vertebrate development, immunology, and cell biology.

Entities: Chemical

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Year: 2004 PMID： 15590942 PMCID： PMC540287 DOI： 10.1101/gr.3011405

Source DB: PubMed Journal: Genome Res ISSN： 1088-9051 Impact factor: 9.043

38 in total

1. RefSeq and LocusLink: NCBI gene-centered resources.

Authors: K D Pruitt; D R Maglott
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

2. Ensembl 2004.

Authors: E Birney; D Andrews; P Bevan; M Caccamo; G Cameron; Y Chen; L Clarke; G Coates; T Cox; J Cuff; V Curwen; T Cutts; T Down; R Durbin; E Eyras; X M Fernandez-Suarez; P Gane; B Gibbins; J Gilbert; M Hammond; H Hotz; V Iyer; A Kahari; K Jekosch; A Kasprzyk; D Keefe; S Keenan; H Lehvaslaiho; G McVicker; C Melsopp; P Meidl; E Mongin; R Pettett; S Potter; G Proctor; M Rae; S Searle; G Slater; D Smedley; J Smith; W Spooner; A Stabenau; J Stalker; R Storey; A Ureta-Vidal; C Woodwark; M Clamp; T Hubbard
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

3. The Gene Ontology (GO) database and informatics resource.

Authors: M A Harris; J Clark; A Ireland; J Lomax; M Ashburner; R Foulger; K Eilbeck; S Lewis; B Marshall; C Mungall; J Richter; G M Rubin; J A Blake; C Bult; M Dolan; H Drabkin; J T Eppig; D P Hill; L Ni; M Ringwald; R Balakrishnan; J M Cherry; K R Christie; M C Costanzo; S S Dwight; S Engel; D G Fisk; J E Hirschman; E L Hong; R S Nash; A Sethuraman; C L Theesfeld; D Botstein; K Dolinski; B Feierbach; T Berardini; S Mundodi; S Y Rhee; R Apweiler; D Barrell; E Camon; E Dimmer; V Lee; R Chisholm; P Gaudet; W Kibbe; R Kishore; E M Schwarz; P Sternberg; M Gwinn; L Hannick; J Wortman; M Berriman; V Wood; N de la Cruz; P Tonellato; P Jaiswal; T Seigfried; R White
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

4. The EMBL Nucleotide Sequence Database.

Authors: Tamara Kulikova; Philippe Aldebert; Nicola Althorpe; Wendy Baker; Kirsty Bates; Paul Browne; Alexandra van den Broek; Guy Cochrane; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; Maria Garcia-Pastor; Nicola Harte; Carola Kanz; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Michelle McHale; Francesco Nardone; Ville Silventoinen; Peter Stoehr; Guenter Stoesser; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

5. The InterPro Database, 2003 brings increased coverage and new features.

Authors: Nicola J Mulder; Rolf Apweiler; Teresa K Attwood; Amos Bairoch; Daniel Barrell; Alex Bateman; David Binns; Margaret Biswas; Paul Bradley; Peer Bork; Phillip Bucher; Richard R Copley; Emmanuel Courcelle; Ujjwal Das; Richard Durbin; Laurent Falquet; Wolfgang Fleischmann; Sam Griffiths-Jones; Daniel Haft; Nicola Harte; Nicolas Hulo; Daniel Kahn; Alexander Kanapin; Maria Krestyaninova; Rodrigo Lopez; Ivica Letunic; David Lonsdale; Ville Silventoinen; Sandra E Orchard; Marco Pagni; David Peyruc; Chris P Ponting; Jeremy D Selengut; Florence Servant; Christian J A Sigrist; Robert Vaughan; Evgueni M Zdobnov
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

6. The small RNA profile during Drosophila melanogaster development.

Authors: Alexei A Aravin; Mariana Lagos-Quintana; Abdullah Yalcin; Mihaela Zavolan; Debora Marks; Ben Snyder; Terry Gaasterland; Jutta Meyer; Thomas Tuschl
Journal: Dev Cell Date: 2003-08 Impact factor: 12.270

7. A microRNA array reveals extensive regulation of microRNAs during brain development.

Authors: Anna M Krichevsky; Kevin S King; Christine P Donahue; Konstantin Khrapko; Kenneth S Kosik
Journal: RNA Date: 2003-10 Impact factor: 4.942

8. A series of normal stages in the development of the chick embryo.

Authors: V HAMBURGER; H L HAMILTON
Journal: J Morphol Date: 1951-01 Impact factor: 1.804

9. The nuclear RNase III Drosha initiates microRNA processing.

Authors: Yoontae Lee; Chiyoung Ahn; Jinju Han; Hyounjeong Choi; Jaekwang Kim; Jeongbin Yim; Junho Lee; Patrick Provost; Olof Rådmark; Sunyoung Kim; V Narry Kim
Journal: Nature Date: 2003-09-25 Impact factor: 49.962

10. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection.

Authors: Koji Numata; Akio Kanai; Rintaro Saito; Shinji Kondo; Jun Adachi; Laurens G Wilming; David A Hume; Yoshihide Hayashizaki; Masaru Tomita
Journal: Genome Res Date: 2003-06 Impact factor: 9.043

29 in total

1. Does the human X contain a third evolutionary block? Origin of genes on human Xp11 and Xq28.

Authors: Margaret L Delbridge; Hardip R Patel; Paul D Waters; Daniel A McMillan; Jennifer A Marshall Graves
Journal: Genome Res Date: 2009-05-13 Impact factor: 9.043

2. Non-coding RNAs revealed during identification of genes involved in chicken immune responses.

Authors: Marie-Laure Endale Ahanda; Thomas Ruby; Håkan Wittzell; Bertrand Bed'Hom; Anne-Marie Chaussé; Veronique Morin; Anne Oudin; Catherine Chevalier; John R Young; Rima Zoorob
Journal: Immunogenetics Date: 2008-11-14 Impact factor: 2.846

3. Telomerase gene expression in the chicken: Telomerase RNA (TR) and reverse transcriptase (TERT) transcript profiles are tissue-specific and correlate with telomerase activity.

Authors: Thomas H O'Hare; Mary E Delany
Journal: Age (Dordr) Date: 2006-02-17

4. Large-scale collection and annotation of gene models for date palm (Phoenix dactylifera, L.).

Authors: Guangyu Zhang; Linlin Pan; Yuxin Yin; Wanfei Liu; Dawei Huang; Tongwu Zhang; Lei Wang; Chengqi Xin; Qiang Lin; Gaoyuan Sun; Mohammed M Ba Abdullah; Xiaowei Zhang; Songnian Hu; Ibrahim S Al-Mssallem; Jun Yu
Journal: Plant Mol Biol Date: 2012-06-27 Impact factor: 4.076

5. MicroRNA-221 regulates chondrogenic differentiation through promoting proteosomal degradation of slug by targeting Mdm2.

Authors: Dongkyun Kim; Jinsoo Song; Eun-Jung Jin
Journal: J Biol Chem Date: 2010-06-24 Impact factor: 5.157