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Contents

• Description
• Restrictions on Proprietary Data
• A. thaliana
  
• C. elegans
  
• C. jejuni
  
• E. histolytica
  
• E. coli
  
• H. pylori
  
• M. tuberculosis
  
• P. falciparum
  
• S. cerevisiae
  
• S. coelicolor
  
• V. cholerae
  

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Description

This page documents the external sources of annotation used by the database.

Proprietary Data

Please note that some data in the database are proprietary and subject to legal restriction on their use, re-use and distribution. This includes but is not limited to oligonucleotide sequences and patented sequences from:

• Affymetrix (license terms here)
• Agilent

It is the responsibility of the person viewing or downloading such data to ensure that such use does not infringe on the intellectual property rights of others, by agreeing to relevant licenses or obtaining necessary permission.

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Arabidopsis thaliana

For A. thaliana gene and protein annotations we used data found at:

TIGR

Reference:


Sequence and analysis of the Arabidopsis genome.
Bevan, M., Mayer, K., White, O., Eisen, J.A., Preuss, D., Bureau, T., Salzberg, S.L., Mewes, H.
Current Opinion Plant Biology Apr 1;4(2):105-110 (2001) [PubMed] [PDF]

The Arabidopsis Information Resource (TAIR)

Reference:



Huala, E; Dickerman, A; Garcia-Hernandez, M; Weems, D; Reiser, L; LaFond, F; Hanley, D; Kiphart, D; Zhuang, J; Huang, W; Mueller, L; Bhattacharyya, D; Bhaya, D; Sobral, B; Beavis, B, Somerville, C; and Rhee, SY
The Arabidopsis Information Resource (TAIR): A comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant.
Nucleic Acids Res. 2001 Jan 1;29(1):102-5. [PubMed] [PDF]

NCBI

Reference:



Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA.
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res. 2000 Jan 1;28(1):10-4. [PubMed] [PDF]

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Caenorhabditis elegans

For C. elegans gene and protein annotations we used data found at:

WormBase

Reference:


Bieri T, Blasiar D, Ozersky P, Antoshechkin I, Bastiani C, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Han M, Harris TW, Kishore R, Lee R, McKay S, MŸller HM, Nakamura C, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Spooner W, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Durbin R, Stein LD, Sternberg PW, Spieth J. (2007)
WormBase: new content and better access
Nucleic Acids Research 29(1): 75-9. [PubMed] [PDF]

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Campylobacter jejuni

For C. jejuni gene and protein annotations we used data found at:

Sanger Institute

Reference:


J. Parkhill, B.W. Wren, K. Mungall, J.M. Ketley, C. Churcher, D. Basham, T. Chillingworth, R.M. Davies, T. Feltwell, S. Holroyd, K. Jagels, A.V. Karlyshev, S. Moule, M.J. Pallen, C. W. Penn, M.A. Quail, M-A. Rajandream, K.M. Rutherford, A.H.M. van Vliet, S. Whitehead, and B.G. Barrell.
The genome sequence of the foodborne pathogen Campylobacter jejuni reveals hypervariable sequences.
Nature 403, 665-668 (2000). [PubMed] [PDF]

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Entamoeba histolytica

For E. histolytica gene and protein annotations we used data found at:

NCBI GenBank

Reference:


Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA.
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res. 2000 Jan 1;28(1):10-4. [PubMed] [PDF]

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Escherichia coli

For E. coli gene and protein annotations we used data found at:

dbget/GenomeNet

Reference:


Kanehisa, M.: Linking databases and organisms: GenomeNet resources in Japan.
Trends Biochem Sci. 22, 442-444 (1997). [PubMed] [PDF]



Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M.:
DBGET/LinkDB: an integrated database retrieval system.
Pacific Symp. Biocomputing 1998, 683-694 (1997). [PubMed]

EcoCyc/MetaCyc

Reference:

Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Paley, S. and Pellegrini-Toole, A.
EcoCyc: Electronic Encyclopedia of E. coli Genes and Metabolism,
Nucleic Acids Research, 28(1):56 2000. [PubMed] [PDF]

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Helicobacter pylori

For H. pylori gene and protein annotations we used data found at:

TIGR

Reference:


Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Venter JC, et al.
The complete genome sequence of the gastric pathogen Helicobacter pylori.
Nature. 1997 Aug 7;388(6642):539-47. [PubMed] [PDF]

AstraZeneca

Reference:


Alm RA, Ling LS, Moir DT, King BL, Brown ED, Doig PC, Smith DR, Noonan B, Guild BC, deJonge BL, Carmel G, Tummino PJ, Caruso A, Uria-Nickelsen M, Mills DM, Ives C, Gibson R, Merberg D, Mills SD, Jiang Q, Taylor DE, Vovis GF, Trust TJ.
Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori.
Nature. 1999 Jan 14;397(6715):176-80. [PubMed] [PDF]

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Mycobacterium tuberculosis

For M. tuberculosis gene and protein annotations we used data found at:

Sanger Insitute

Reference:


Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S.V., Eiglmeier K., Gas S., Barry C.E.III., Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R., Devlin K., Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L., Oliver K., Osborne J., Quail M.A., Rajandream, M-A., Rogers J., Rutter S., Seeger K., Skelton J., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S. and Barrell, B.G.
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
Nature 393, 537-544 (1998). [PubMed] [PDF]

Institut Pasteur TubercuList

Reference:


Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S.V., Eiglmeier K., Gas S., Barry C.E.III., Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R., Devlin K., Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L., Oliver K., Osborne J., Quail M.A., Rajandream, M-A., Rogers J., Rutter S., Seeger K., Skelton J., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S. and Barrell, B.G.
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
Nature 393, 537-544 (1998). [PubMed] [PDF]

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Plasmodium falciparum

For P. falciparum gene and protein annotations we used data found at:

PlasmoDB

Reference:


Aurrecoechea C, et al.
PlasmoDB: a functional genomic database for malaria parasites.
Nucleic Acids Res. 2008 Oct 31. [PubMed] [PDF]

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Saccharomyces cerevisiae

For S. cerevisiae gene and protein annotations we used data found at:

SGD

Reference:


Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D
Genetic and physical maps of Saccharomyces cerevisiae.
Nature. 1997 May 29;387(6632 Suppl):67-73. [PubMed] [PDF]


Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM.
Integrating functional genomic information into the Saccharomyces genome database.
Nucleic Acids Res. 2000 Jan 1;28(1):77-80. [PubMed] [PDF]

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Streptomyces coelicolor

For S. coelicolor gene and protein annotations we used data found at:

Sanger Institute

Reference:


Bentley SD, Chater KF, Cerde–o-T‡rraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA (2002) Nature 417;141-7. [PubMed] [PDF]

EMBL

Reference:


Stoesser G., Baker W., van den Broek A., Camon E., Garcia-Pastor M., Kanz C., Kulikova T., Lombard V., Lopez R., Parkinson H., Redaschi N., Sterk P., Stoehr P., Tuli MA.:
The EMBL Nucleotide Sequence Database.
Nucleic Acids Res 2001, Vol. 29 (1), 17-21 [PubMed] [PDF]

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Vibrio cholerae

For V. cholerae gene and protein annotations we used data found at:

TIGR

Reference:


Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O.
DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.
Nature. 2000 Aug 3;406(6795):477-83. [PubMed] [PDF]

Please send comments or questions to: array@princeton.edu