EUKARYOTIC PROMOTER DATABASE USER MANUAL
Written by: Philipp Bucher, Rouaida Cavin Périer, Viviane Praz and Christoph Schmid

1 INTRODUCTION

2 PROMOTER SELECTION

1. recognized by eukaryotic RNA POL II,
2. active in a higher eukaryote,
3. experimentally defined, or homologous and sufficiently similar to an experimentally defined promoter,
4. biologically functional,
5. available in the current EMBL release,
6. distinct from other promoters in the database.

1. Transcription by RNA POL II is bona fide assumed for protein coding genes but must be supported by alpha-amanitin data if the end product is an RNA.
2. All eukaryotes except phycophyta, fungi, myxomycetes, and protozoa are considered higher eukaryotes. Note that the expression "active in" does not always refer to the source organism of the promoter (e.g. in viruses). EPD contains currently promoter sequences from 139 different species.
3. A promoter is experimentally determined if a corresponding transcription initiation site is mapped with a precision of +/- 5 bp or higher. Any technique that characterizes the 5'terminus of an in vivo or in vitro generated RNA is acceptable. Single nuclease-protection or primer-extension data must be accompanied by additional evidence unless the gene's intron-exon organization is well established. Similarity is considered "sufficient" if percent identity (as defined in Section 6) is >=60% between -79 and +20 or >=75% between -49 and +10.
4. A promoter is biologically functional if it contributes to the source organism's survival and/or reproduction. This is bona fide assumed except for promoters of pseudogenes, minor transcription initiation sites (<20% of total gene transcripts), promoters giving rise to an unstable RNA product, and mutant promoter.
5. The minimum sequence requirement is 45 bp between -49 and +10.
6. Promoters are considered distinct if they originate from different gene loci or different species. Identity is assumed if two promoters from the same species exhibit >95% similarity between -79 and +20 while their genetic relationship is unknown. Multiple isolates of viruses or transposable elements are considered distinct if at least one promoter region fails to fulfill the above similarity criterion.

3 ASSIGNMENT OF TRANSCRIPTION INITIATION SITE

• S: Single initiation site: >90% of all reported transcripts initiate within 10 bp (the experimental data usually do not allow distinction between a single cap-site and small mRNA 5' heterogeneity).
• M: Multiple initiation sites: >75% of all reported transcripts initiate within 20 bp.
• R: Initiation region: >75% of all reported transcripts initiate within 100 bp.
• U: Undefined transcription initiation pattern, exclusively in 'preliminary' entries in epd_bulk.dat (see next section).

4 FORMAT CONVENTIONS

4.1. The title line

TI   EPD83     Eukaryotic Promoter Database / Release 83              EP

• FPS name and FPS code are used by our data extraction software to generate default names for output files.

4.2. Promoter entries

• Promoter identification and description.
• Machine-readable pointers to the transcription initiation site in corresponding sequence entries.
• Description of the experimental evidence defining the transcription start site.
• Various kinds of promoter classifications useful for extraction of biologically meaningful promoter subsets.
• Information on regulatory properties.
• Cross-references to other databases.
• Bibliographic references.

    ID  - IDentification.
    AC  - ACcession number(s).
    DT  - DaTe.
    DE  - DEscription.
    OS  - Organism Species.
    HG  - Homology Group.
    AP  - Alternative Promoter.
    NP  - Neighbouring Promoter.
    DR  - Database cross-References.
    RN  - Reference Number.
    RX  - Reference cross-references.
    RA  - Reference Authors.
    RT  - Reference Title.
    RL  - Reference Location.
    ME  - MEthods.
    SE  - SEquence.
    FL  - Full Length.
    IF  - Initiation Frequency.
    TX  - TaXonomy.
    KW  - KeyWords.
    FP  - Functional Position.
    DO  - DOcumentation.
    RF  - literature ReFerence.
    //  - Termination line.

      ID   HS_MYC_2     standard; single; VRT.
      XX
      AC   EP11148;
      XX
      DT   ??-APR-1987 (Rel. 11, created)
      DT   07-MAR-2005 (Rel. 82, Last annotation update).
      XX
      DE   c-myc (cellular homologue of myelocytomatosis virus 29 oncogene),
      DE   promoter 2.
      OS   Homo sapiens (human)
      XX
      HG   Homology group 53; Mammalian c-myc proto-oncogene, promoter 2
      AP   Alternative promoter #2 of 2; exon 1; site 2; major promoter.
      NP   none.
      XX
      DR   GENOME; NT_008046.15; NT_008046; [-41966656, 15188617].
      DR   EPD; EP11146; HS_MYC_1; alternative promoter; [-162; +].
      DR   CLEANEX; HS_MYC.
      DR   EMBL; AC103819.3; [-87815, 60206].
      DR   EMBL; X00364.2; [-2489, 8507].
      DR   EMBL; D10493.1; [-2487, 5569].
      DR   EMBL; K01910.1; [-2451, 49].
      DR   EMBL; M16261.1; [-1843, 1048].
      DR   EMBL; J03253.1; [-1759, 461].
      DR   EMBL; L00057.1; [-810, 2795].
      DR   EMBL; K03015.1; [-555, 458].
      DR   EMBL; X00196.1; [-532, 2792].
      DR   EMBL; M12026.1; [-511, 678].
      DR   EMBL; K01708.1; [-410, 500].
      DR   EMBL; K00559.1; [-345, 1020].
      DR   EMBL; K02280.1; [-302, 178].
      DR   EMBL; K01909.1; [-266, 1365].
      DR   EMBL; S65124.1; [-266, 1023].
      DR   EMBL; M14206.1; [-266, 446].
      DR   EMBL; M20013.1; [-240, 982].
      DR   EMBL; AF111270.1; [-142, 264].
      DR   EMBL; K02275.1; [-96, 780].
      DR   EMBL; X00675.1; [-96, 404].
      DR   EMBL; K02277.1; [-96, 157].
      DR   SWISS-PROT; P01106; MYC_HUMAN.
      DR   TRANSFAC; R01157; HS$CMYC_01; [-211, -189]; by position.
      DR   TRANSFAC; R01158; HS$CMYC_02; [-168, -145]; by position.
      DR   TRANSFAC; R01804; HS$CMYC_04; [-300, -283]; by position.
      DR   TRANSFAC; R01851; HS$CMYC_05; [-65, -57]; by position.
      DR   TRANSFAC; R01852; HS$CMYC_06; [-42, -34]; by position.
      DR   TRANSFAC; R04076; HS$CMYC_12; [-251, -228]; by position.
      DR   TRANSFAC; R04076; HS$CMYC_12; [-252, -229]; by position.
      DR   TRANSFAC; R04076; HS$CMYC_12; [-253, -230]; by position.
      DR   TRANSFAC; R04621; HS$CMYC_17; [-313, -262]; by position.
      DR   TRANSFAC; R08503; HS$CMYC_18; [-50, -41]; by position.
      DR   TRANSFAC; R16688; HS$CMYC_24; [-7, 41]; by position.
      DR   TRANSFAC; R16689; HS$CMYC_25; [-7, 41]; by position.
      DR   TRANSFAC; R17051; HS$CMYC_30; [-510, -480]; by position.
      DR   TRANSFAC; R18503; HS$CMYC_31; [-185, -170]; by position.
      DR   TRANSFAC; R18504; HS$CMYC_32; [-153, -168]; by position.
      DR   RefSeq; NM_002467.
      DR   MIM; 190080.
      XX
      RN   [1]
      RX   MEDLINE; 84026482.
      RA   Battey J., Moulding C., Taub R., Murphy W., Stewart T., Potter H.,
      RA   Lenoir G., Leder P.;
      RT   "The human c-myc oncogene: structural consequences of
      RT   translocation into the IgH locus in Burkitt lymphoma";
      RL   Cell 34:779-787(1983).
      RN   [2]
      RX   MEDLINE; 84131953.
      RA   Bernard O.D., Cory S., Gerondakis S., Webb E., Adams J.M.;
      RT   "Sequence of the murine and human cellular myc oncogenes and two
      RT   modes of myc transcription resulting from chromosome translocation
      RT   in B lymphoid tumours";
      RL   EMBO J. 2:2375-2383(1983).
      RN   [3]
      RX   MEDLINE; 87257828.
      RA   Lipp M., Schilling R., Wiest S., Laux G., Bornkamm G.W.;
      RT   "Target sequences for cis-acting regulation within the dual
      RT   promoter of the human c-myc gene.";
      RL   Mol. Cell. Biol. 7:1393-1400(1987).
      RN   [4]
      RX   MEDLINE; 88038843.
      RA   Broome H.E., Reed J.C., Godillot E.P., Hoover R.G.;
      RT   "Differential promoter utilization by the c-myc gene in mitogen-
      RT   and interleukin-2-stimulated human lymphocytes.";
      RL   Mol. Cell. Biol. 7:2988-2993(1987).
      XX
      ME   Nuclease protection [1,4].
      ME   Nuclease protection; transfected or transformed cells [3].
      ME   Length measurement of an RNA product; low-precision data [1].
      XX
      SE   agggagggatcgcgctgagtataaaagccggttttcggggctttatctaACTCGCTGTAG
      XX
      TX   6. Vertebrate promoters
      TX   6.1. Chromosomal genes
      TX   6.1.5. Hormones, growth factors, regulatory proteins
      TX   6.1.5.16. Various cellular protooncogenes
      XX
      KW   Proto-oncogene, Nuclear protein, DNA-binding, Glycoprotein,
      KW   Transcription regulation.
      XX
      FP   Hs c-myc         P2+:+S  EU:NC_000008.9       1+ 128817660; 11148.053 010*2
      XX
      DO        Experimental evidence: 4,4#,2l
      DO        Expression/Regulation: +mitogen
      RF        Cell34:779     EMBOJ2:2375    MCB7:1393      MCB7:2988
      //

4.2.1. The ID line

ID   ENTRY_NAME data class; initiation site type; TAXONOMIC DIVISION.

• ENTRY_NAME is a unique entry identifier "HS_MYC_2" which obeys rigorous naming conventions. It contains 2 or 3 fields, the first is the species identification code at most 4 alphanumeric characters representing the biological source of the promoter. The second field uses for gene identification the protein code of SWISS-PROT ID (if available). For human EPD entries, instead of the SwissProt ID the official gene symbol approved by the HUGO nomenclature committee (if available) is used. The third field is optional, it is either a number which represents alternative promoters or a letter for promoters of duplicated genes. The `_' sign serves as a separator.
• The data class field relates to the quality of the information: "standard" means that the information is complete and correct according the standards laid down in this document; "preliminary" means that the entry has not yet undergone all quality checks necessary for being classified as "standard".
• The initiation site type is either "single", "multiple", "region" as defined in Section 3.
• TAXONOMIC DIVISION are
• PLN for plant
• NEM for nematode
• ART for arthropode
• MLS for mollusc
• ECH for echinoderm
• VRT for vertebrates.
Note that these codes relate to the organism in which the promoter is expressed, not to the source organism in which the promoter is replicated as defined on the OS line.

4.2.2. The AC line

AC   EP11148;

4.2.3. The DT line

DT   DD-MMM-YEAR (Rel. XX, Comment)

• The first DT line indicates when the entry first appeared in the database.
• The second DT line indicates when the promoter data was last modified. It is terminated by a period.

4.2.4. The DE line

DE   c-myc (cellular homologue of myelocytomatosis virus 29 oncogene),
DE   promoter 2.

4.2.5. The OS line

OS   Mus musculus (house mouse)

4.2.6. The HG line

HG   Homology group 53; Mammalian c-myc proto-oncogene, promoter 2

4.2.7. The AP line

AP   Alternative promoter #2 of 2; 5' exon 1; site 2; major promoter.

descriptive text fields followed by

• Two numbers indicating, respectively, the promoter's relative position along the gene, and the total number of alternative promoters of the gene. Promoters are numbered in the 5' to 3' directions starting with one.
• A number referring to the exon preceded by the promoters. Note that multiple promoters may be associated with the same (3'-coterminal) exon or with different exons. Known exons are numbered in 5' to 3' direction starting with one.

Note that the nomenclature of 5'-exons in EPD may differ from the usage in the literature.
• A number indicating the promoter's relative position among the subset of promoters preceeding the same exon.
• An optional keyword indicating major promoters.

4.2.8. The NP line

NP   Neighbouring Promoter; EP23008; MM_H2B1; [-209; -].

• The EPD accession number of the neighbouring promoter.
• The EPD identifier of the neighbouring promoter.
• The last field indicates, respectively, the position and the direction of the neighbouring promoter relative to the transcription initiation site given in the promoter entry.
• Negative numbers indicate the upstream region of this entry and positive ones indicate the downstream region.
• The sign indicates the transcription direction of the neighbouring promoter relative to the promoter entry:

"+" means same direction
"-" means opposite direction

4.2.9. The DR line

     DR   GENOME; NT_037436.1; NT_037436; [-14139754, 9212459].
     DR   EPD; EP11146; HS_MYC_1; alternative promoter; [-162; +].
     DR   EMBL; J00120.1; [-2489, 8507].
     DR   SWISS-PROT; P01106; MYC_HUMAN.
     DR   SPTREMBL; Q8IQL1.
     DR   FLYBASE; FBgn0013718; nuf.
     DR   TRANSFAC; R01804; HS$CMYC_04; [-300, -283]; by position.
     DR   MIM; 190080.
     DR   RefSeq; NM_003529.
     DR   MGD; MGI:88468; Cola2.
     DR   ENSEMBL; CG32140.
     DR   TRANSCRIPTOME; DMe000571.

• The first item on the DR line is the abbreviated name of the data collection to which reference is made. The currently defined data bank identifiers are the following:



GENOME	NCBI Reference Sequence (RefSeq) of genomic sequence contigs
EPD	Eukaryotic Promoter Database: alternative promoters of the same gene
CLEANEX	Gene expression database for human EPD promoters
EMBL	Nucleotide sequence database of the EMBL
SWISS_PROT	Protein sequence database
SPTREMBL	Subset of protein sequence database TrEMBL. It contains the entries which should be eventually incorporated into SWISS-PROT. SWISS-PROT accession numbers have been assigned for all SP-TrEMBL entries
FLYBASE	Drosophila genome database
TRANSFAC	Transcription factor (TF) database
MIM	Mendelian Inheritance in Man Database
RefSeq	Reference Sequence Database
MGD	Mouse Genome Database
ENSEMBL	Metazoan genome annotation
TRANSCRIPTOME	Catalog of transcripts and their mapping onto the genome (LICR Lausanne branch)
TIGR	'gene identifiers' from the 'Rice Genome Annotation' project at TIGR

• The second item is the primary accession number (or an equivalent unique identifier of another data banks) of the entry to which reference is made.
• The third item (if it exists) is a secondary idientifier or name for the cross-referenced database entry.
• The fourth item for EMBL and Transfac indicates the location and extension of the sequences given in these entries relative to the transcription initiation site given in the promoter entry. Negative numbers indicate the upstream region of this site and positive ones indicate the downstream part.
• The fifth item
• in the EPD line, indicates the position and the direction of the alternative promoter as it is defined for the neighbouring promoter in the NP line last field
• in the TRANSFAC line, designates the criteria used to collect the TF entry:

- by position: The TF binding site is situated between -500 and + 100, +1 being the transcription initiation site
- by function: The TF binding site is known to regulate the corresponding promoter.

4.2.10. The RN, RX, RA, RT and RL lines

RN   [1]
RX   MEDLINE; 84026482.
RA   Battey J., Moulding C., Taub R., Murphy W., Stewart T., Potter H.,
RA   Lenoir G., Leder P.;
RT   "The human c-myc oncogene: structural consequences of
RT   translocation into the IgH locus in Burkitt lymphoma";
RL   Cell 34:779-787(1983).

4.2.10.1. The RN line

4.2.10.2 The RX line

4.2.10.3 The RA line

4.2.10.4 The RT line

4.2.10.5 The RL line

4.2.11. The ME line

ME   Method_description [; Qualifier...] [n,...].

ME   Nuclease protection [1,4].
ME   Nuclease protection; transfected or transformed cells [3].
ME   Length measurement of an RNA product; low-precision data [1].

4.2.12. The SE line

4.2.13. The FL line

4.2.13. The IF line

4.2.14. The TX line

4.2.15. The KW line

4.2.16. The FP, DO and RF lines

4.2.17. The // line

4.3. Line types retained from the old format

FP   Hs c-myc         P2+:+S  EU:NC_000008.9       1+ 128817660; 11148.053 010*2
XX
DO        Experimental evidence: 4,4#,<2>
DO        Expression/Regulation: +mitogen
RF        Cell34:779     EMBOJ2:2375    MCB7:1393      MCB7:2988
//

4.3.1. The FP line

• The promoter name begins with a species code usually followed by a gene locus or gene product name. Species codes consist of the initials of genus and species name. Occasionally, three characters are required to generate unique codes. Standard abbreviations identify viruses. The full names of the organisms are given in appendix B.1. Subspecies or strains are specified in parentheses. Chromosomal locations (genetic or cytogenetic loci, genomic map units, etc.) may appear in square brackets immediately following species codes. Many gene products are referred to by abbreviations explained in appendix B.3. Alternative promoters are identified by right-justified "P" and a digit indicating the corresponding initiation site numbered sequentially from 5' to 3'. An optional "E" and digit refers to the corresponding 5'exons, if known. Identical numbers indicate 3'co-terminal exons. The strongest initiation site is marked by trailing + if known (see also List of alternative promoters)
• genome db codes currently used are 'EM' for EMBL database, and 'EU' for genome contigs or chromosomal genome assemblies of the RefSeq database.
• The EMBL accession number always relates to the first EMBL cross-reference. This one is usually the longest promoter region except when the entry is cancelled from the EMBL database, but still present in GenBank or DDBJ.
• The sequence type indicates whether the sequence is circular or linear. A sequence comprising exactly one repeat unit of a tandem repeat cluster is also considered circular. Note that the annotation as circular or linear sequences in EPD is not always in agreement with the corresponding annotation in EMBL.
• The entry code is a five-digit number which is the only part of a promoter entry that is stable from release to release.
• Alternative promoter identification code: Genes represented by multiple promoter entries in EPD are assigned a promoters group number. The corresponding initiation sites are numbered sequentially from 5' to 3'.

4.3.2. DO lines: Documentation

Special characters appended to the number codes designate an experimental gene expression system where the RNA for the corresponding experiments was synthesized.

• The full-length assumption of a cDNA clone or a proccessed pseudogene is based on consistency with accompanying nuclease-protection or primer extension data or, alternatively, the existence of multiple 5'coterminal clones or pseudogenes.

• Semicolon delimits the two fields : expression and regulation.
• Comma delimits alternative keywords (e.g. liver, kidney)
• "+" means "induced by" or "strongly expressed in".
• "-" means "repressed by" or "weakly expressed in".
• "~" means "modulated by".
• Cell cycle stages are given in square brackets.

4.3.3. RF line: Literature references

They primarily point to the articles where the experimental promoter evidence is presented. Additional potential subjects are homology to other promoters, gene expression and regulation, nomenclature. Papers containing only sequence data are usually not referred to because they are easy to find via the corresponding EMBL sequence entry descriptions.

4.3.4. Miscellaneous

• Greek letters are sometimes represented by corresponding latin letters followed by apostrophe:



a' = alpha	b' = beta	g' = gamma	d' = delta	e' = epsilon
z' = zeta	h' = eta	th'= theta	k' = kappa	l' = lambda
n' = nu	r' = rho

• Sub- and superscripts are sometimes indicated by preceding "_" and "^", respectively.

4.4. Distinct format of 'preliminary' entries in epd_bulk.dat

4.4.1. The title line:

TI   epd83     Bulk Section Eukaryotic Promoter Database / Release 83 EP

4.4.2. The ID line

ID   OS_bAAAA     preliminary; undefined; TAXONOMIC DIVISION.

• An unique entry identifier "OS_bAAAA" is contructed using the species identification code ('OS') with at most 4 alphanumeric characters representing the biological source of the promoter and a 'b' (for bulk) followed by an arbitrary 4 letter code
• "preliminary" data class field indicates that the entry has not (yet) undergone all quality checks necessary for being classified as "standard".
• "undefined" as initiation site type due to insufficient data to define transcription initiation patterns (Section 3).
• TAXONOMIC DIVISION are
• PLN for plant
• NEM for nematode
• ART for arthropode
• MLS for mollusc
• ECH for echinoderm
• VRT for vertebrates.
Note that these codes relate to the organism in which the promoter is expressed, not to the source organism in which the promoter is replicated as defined on the OS line.

4.4.3. The AC line

AC   EP00001;

5 CLASSIFICATION

The entries of the Eukaryotic Promoter Database are embedded in a hierarchical classification system. A promoter's taxonomic location is made clear by interspersed group headings. The example shown below is taken from top of the database. A contrasting format has been chosen to emphasize the very different nature of this information.

*----------------------------------------------------------------------*
*    1. Plant promoters                                                *
*----------------------------------------------------------------------*
*    1.1. Chromosomal genes                                            *
*----------------------------------------------------------------------*
*    1.1.1. Small nuclear RNAs                                         *
*----------------------------------------------------------------------*

6 HOMOLOGOUS PROMOTERS

Gap weight and gap length weight are specified as 3 and 0, respectively. Terminal gaps are ignored. Percent similarity is understood as alignment score divided by segment length, times 100. Groups of homologous promoters are identified by homology group numbers (see 4.2.1.). Definition of these groups is based on similarity scores as defined above and a tree generation method called UPGMA (14). In a few cases, similarities between 50% and 56% were ignored if the protein sequences of the corresponding genes were not related. Similarities were also ignored between alternative promoter sequences that are spaced by less than 50 bp. A subset of "independent" promoters is marked by "+" in column 27 of the FP line. This set contains only one member per homology group (usually, the promoter with the longest upstream sequence available) and is intended to be used for statistical analysis of functional patterns where it is important to avoid bias by multiples of closely related sequences.

7 PROMOTER SEQUENCE RETRIEVAL

8 REFERENCES

1. Bucher, P. & Trifonov, E.N., Compilation and analysis of eukaryotic POL II promoter sequences, Nucl. Acids Res. 14, 10009-10026 (1986). (3808945)


2. Bucher, P. & Bryan, B., Signal search analysis: a new method to localize and characterize functionally important DNA sequences, Nucl. Acids Res. 12, 287-305 (1984). (6546421)


3. Stoesser, G., Tuli,M.A., Lopez, R. and Sterk, P., The EMBL nucleotide sequence database, Nucleic Acids. Res., 27, 18-24 (1999). (9847133)


4. Benson, D.A., Boguski, M.S., Lipman, D.J., Ostell, J., Ouellette B.F.F,  Rapp, B:A: and Wheeler, D.L., GenBank, Nucleic Acids. Res., 27, 12-17 (1999). (9847132)


5. Sugawara,  H., Miyazaki, S., Gojobori, T. and Tateno, Y.,DNA Data Bank of Japan dealing with large-scale data submission, Nucleic Acids. Res., 27, 25-28 (1999). (9847134)


6. Bairoch, A. and Apweiler, R., The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999, Nucleic Acids Res., 27, 49-54 (1999). (9847139)


7. Heinemeyer, T., Chen, X., Karas, H., Kel, A.E., Kel, O.V., Liebich, I., Meinhardt, T., Reuter, I., Schacherer, F. and Wingender, E., Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms, Nucleic Acids. Res., 27, 318-322 (1999). (9847216)


8. The FlyBase consortium, The FlyBase database of the drosophilia genome projects and community litterature, Nucleic Acids. Res., 27,85-88 (1999). (9847148)


9. Pearson, P., Francomano, C., Foster, P., Bocchini, C., Li, P. and McKusick, V., The status of online Mendelian inheritance in man (OMIM) medio 1994, Nucleic Acids Res., 22, 3470-3473 (1994). (7937048)


10. Blake, J.A., Richardson, J.E., Davisson, M.T., Eppig, J.T. and the Mouse Genome Database Group, The Mouse Genome Database (MGD): genetic and genomic information about the laboratory mouse, Nucleic Acids Res., 27, 95-98 (1999). (9847150)


11. Suzuki Y., Yamashita R., Nakai K., Sugano S., DBTSS: database of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res. 30(1):328-331(2002). (11752328)


12. Strausberg, R.L., Feingold, E.A., Klausner, R.D., Collins, F.S., The Mammalian Gene Collection. Science, 286, 455-457 (1999). (10521335)


13. Devereux,J., Haeberli,P., & Smithies,O. A comprehensive set of sequence analysis programs for the VAX, Nucl. Acids Res. 12, 387-395 (1984). (6546423)


14. Sneath,H.A. & Sokal,R.R., Numerical taxonomy, W.H. Freemann, San Francisco, London (1973).


15. Stapleton M., Liao GC., Brokstein P., Hong L., Carninci P., Shiraki T., Hayashizaki Y., Champe M., Pacleb J., Wan K., Yu C., Carlson J., George R., Celniker S., and Rubin GM., The Drosophila Gene Collection: Identification of Putative Full-Length cDNAs for 70% of D. melanogaster Genes. Genome Res., 12:1294-1300 (2002). (12176937)


16. Schmid C.D., Praz V., Delorenzi M., Périer R., and Bucher P., The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Res. 32, D82-5 (2004). (14681364)

 

A.  APPENDIX A : SURVEY OF RELEASE

B.  APPENDIX B : CODES AND ABBREVIATIONS

B.1. SPECIES CODES

B.2. JOURNAL CODES

B.3.  ABBREVIATIONS