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Literature DB >> 14681468

LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system.

Detlev Bannasch¹, Alexander Mehrle, Karl-Heinz Glatting, Rainer Pepperkok, Annemarie Poustka, Stefan Wiemann.

Abstract

We have implemented LIFEdb (http://www.dkfz.de/LIFEdb) to link information regarding novel human full-length cDNAs generated and sequenced by the German cDNA Consortium with functional information on the encoded proteins produced in functional genomics and proteomics approaches. The database also serves as a sample-tracking system to manage the process from cDNA to experimental read-out and data interpretation. A web interface enables the scientific community to explore and visualize features of the annotated cDNAs and ORFs combined with experimental results, and thus helps to unravel new features of proteins with as yet unknown functions.

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Year: 2004 PMID： 14681468 PMCID： PMC314201 DOI： 10.1093/nar/gkh022

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

21 in total

1. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing.

Authors: J C Simpson; R Wellenreuther; A Poustka; R Pepperkok; S Wiemann
Journal: EMBO Rep Date: 2000-09 Impact factor: 8.807

2. Initial sequencing and analysis of the human genome.

Authors: E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal: Nature Date: 2001-02-15 Impact factor: 49.962

3. The EMBL Nucleotide Sequence Database.

Authors: Guenter Stoesser; Wendy Baker; Alexandra van den Broek; Evelyn Camon; Maria Garcia-Pastor; Carola Kanz; Tamara Kulikova; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Nicole Redaschi; Peter Stoehr; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

4. Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.

Authors: T Nagase; M Nakayama; D Nakajima; R Kikuno; O Ohara
Journal: DNA Res Date: 2001-04-27 Impact factor: 4.458

5. TRIPLES: a database of gene function in Saccharomyces cerevisiae.

Authors: A Kumar; K H Cheung; P Ross-Macdonald; P S Coelho; P Miller; M Snyder
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

6. YPL.db: the Yeast Protein Localization database.

Authors: Georg Habeler; Klaus Natter; Gerhard G Thallinger; Matthew E Crawford; Sepp D Kohlwein; Zlatko Trajanoski
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

7. Microarrays of cells expressing defined cDNAs.

Authors: J Ziauddin; D M Sabatini
Journal: Nature Date: 2001-05-03 Impact factor: 49.962

8. The sequence of the human genome.

Authors: J C Venter; M D Adams; E W Myers; P W Li; R J Mural; G G Sutton; H O Smith; M Yandell; C A Evans; R A Holt; J D Gocayne; P Amanatides; R M Ballew; D H Huson; J R Wortman; Q Zhang; C D Kodira; X H Zheng; L Chen; M Skupski; G Subramanian; P D Thomas; J Zhang; G L Gabor Miklos; C Nelson; S Broder; A G Clark; J Nadeau; V A McKusick; N Zinder; A J Levine; R J Roberts; M Simon; C Slayman; M Hunkapiller; R Bolanos; A Delcher; I Dew; D Fasulo; M Flanigan; L Florea; A Halpern; S Hannenhalli; S Kravitz; S Levy; C Mobarry; K Reinert; K Remington; J Abu-Threideh; E Beasley; K Biddick; V Bonazzi; R Brandon; M Cargill; I Chandramouliswaran; R Charlab; K Chaturvedi; Z Deng; V Di Francesco; P Dunn; K Eilbeck; C Evangelista; A E Gabrielian; W Gan; W Ge; F Gong; Z Gu; P Guan; T J Heiman; M E Higgins; R R Ji; Z Ke; K A Ketchum; Z Lai; Y Lei; Z Li; J Li; Y Liang; X Lin; F Lu; G V Merkulov; N Milshina; H M Moore; A K Naik; V A Narayan; B Neelam; D Nusskern; D B Rusch; S Salzberg; W Shao; B Shue; J Sun; Z Wang; A Wang; X Wang; J Wang; M Wei; R Wides; C Xiao; C Yan; A Yao; J Ye; M Zhan; W Zhang; H Zhang; Q Zhao; L Zheng; F Zhong; W Zhong; S Zhu; S Zhao; D Gilbert; S Baumhueter; G Spier; C Carter; A Cravchik; T Woodage; F Ali; H An; A Awe; D Baldwin; H Baden; M Barnstead; I Barrow; K Beeson; D Busam; A Carver; A Center; M L Cheng; L Curry; S Danaher; L Davenport; R Desilets; S Dietz; K Dodson; L Doup; S Ferriera; N Garg; A Gluecksmann; B Hart; J Haynes; C Haynes; C Heiner; S Hladun; D Hostin; J Houck; T Howland; C Ibegwam; J Johnson; F Kalush; L Kline; S Koduru; A Love; F Mann; D May; S McCawley; T McIntosh; I McMullen; M Moy; L Moy; B Murphy; K Nelson; C Pfannkoch; E Pratts; V Puri; H Qureshi; M Reardon; R Rodriguez; Y H Rogers; D Romblad; B Ruhfel; R Scott; C Sitter; M Smallwood; E Stewart; R Strong; E Suh; R Thomas; N N Tint; S Tse; C Vech; G Wang; J Wetter; S Williams; M Williams; S Windsor; E Winn-Deen; K Wolfe; J Zaveri; K Zaveri; J F Abril; R Guigó; M J Campbell; K V Sjolander; B Karlak; A Kejariwal; H Mi; B Lazareva; T Hatton; A Narechania; K Diemer; A Muruganujan; N Guo; S Sato; V Bafna; S Istrail; R Lippert; R Schwartz; B Walenz; S Yooseph; D Allen; A Basu; J Baxendale; L Blick; M Caminha; J Carnes-Stine; P Caulk; Y H Chiang; M Coyne; C Dahlke; A Deslattes Mays; M Dombroski; M Donnelly; D Ely; S Esparham; C Fosler; H Gire; S Glanowski; K Glasser; A Glodek; M Gorokhov; K Graham; B Gropman; M Harris; J Heil; S Henderson; J Hoover; D Jennings; C Jordan; J Jordan; J Kasha; L Kagan; C Kraft; A Levitsky; M Lewis; X Liu; J Lopez; D Ma; W Majoros; J McDaniel; S Murphy; M Newman; T Nguyen; N Nguyen; M Nodell; S Pan; J Peck; M Peterson; W Rowe; R Sanders; J Scott; M Simpson; T Smith; A Sprague; T Stockwell; R Turner; E Venter; M Wang; M Wen; D Wu; M Wu; A Xia; A Zandieh; X Zhu
Journal: Science Date: 2001-02-16 Impact factor: 47.728

9. Large-scale identification of mammalian proteins localized to nuclear sub-compartments.

Authors: H G Sutherland; G K Mumford; K Newton; L V Ford; R Farrall; G Dellaire; J F Cáceres; W A Bickmore
Journal: Hum Mol Genet Date: 2001-09-01 Impact factor: 6.150

Review 10. Being in the right location at the right time.

Authors: R Pepperkok; J C Simpson; S Wiemann
Journal: Genome Biol Date: 2001-08-29 Impact factor: 13.583

19 in total

1. High-throughput protein analysis integrating bioinformatics and experimental assays.

Authors: Coral del Val; Alexander Mehrle; Mechthild Falkenhahn; Markus Seiler; Karl-Heinz Glatting; Annemarie Poustka; Sandor Suhai; Stefan Wiemann
Journal: Nucleic Acids Res Date: 2004-02-03 Impact factor: 16.971

2. EAnnot: a genome annotation tool using experimental evidence.

Authors: Li Ding; Aniko Sabo; Nicolas Berkowicz; Rekha R Meyer; Yoram Shotland; Mark R Johnson; Kymberlie H Pepin; Richard K Wilson; John Spieth
Journal: Genome Res Date: 2004-12 Impact factor: 9.043

3. From ORFeome to biology: a functional genomics pipeline.

Authors: Stefan Wiemann; Dorit Arlt; Wolfgang Huber; Ruth Wellenreuther; Simone Schleeger; Alexander Mehrle; Stephanie Bechtel; Mamatha Sauermann; Ulrike Korf; Rainer Pepperkok; Holger Sültmann; Annemarie Poustka
Journal: Genome Res Date: 2004-10 Impact factor: 9.043

4. Intracellular localization of GASP/ECOP/VOPP1.

Authors: Alexander Baras; Christopher A Moskaluk
Journal: J Mol Histol Date: 2010-06-23 Impact factor: 2.611

5. Crystal structure of Homo sapiens PTD012 reveals a zinc-containing hydrolase fold.

Authors: Babu A Manjasetty; Konrad Büssow; Martin Fieber-Erdmann; Yvette Roske; Johan Gobom; Christoph Scheich; Frank Götz; Frank H Niesen; Udo Heinemann
Journal: Protein Sci Date: 2006-03-07 Impact factor: 6.725

6. LOCATE: a mouse protein subcellular localization database.

Authors: J Lynn Fink; Rajith N Aturaliya; Melissa J Davis; Fasheng Zhang; Kelly Hanson; Melvena S Teasdale; Chikatoshi Kai; Jun Kawai; Piero Carninci; Yoshihide Hayashizaki; Rohan D Teasdale
Journal: Nucleic Acids Res Date: 2006-01-01 Impact factor: 16.971

7. The LIFEdb database in 2006.

Authors: Alexander Mehrle; Heiko Rosenfelder; Ingo Schupp; Coral del Val; Dorit Arlt; Florian Hahne; Stephanie Bechtel; Jeremy Simpson; Oliver Hofmann; Winston Hide; Karl-Heinz Glatting; Wolfgang Huber; Rainer Pepperkok; Annemarie Poustka; Stefan Wiemann
Journal: Nucleic Acids Res Date: 2006-01-01 Impact factor: 16.971