Guidelines and Procedures for Establishing and Maintaining EPD Cross-References

Purpose of this document:

The purpose of this document is to make clear for each type of Cross-references:

The type-specific format of the cross-reference.
The biological meaning of the cross-reference.
The conditions and rules for establishing and maintaining of a cross-reference.
The strategies for identifying new targets.
The procedures for storage, update, verification of existing cross-references.

`DR EPD`

1. Format:

DR   EPD; "AC"; "ID"; "definition"; "position; direction"

"AC"	string	EPD accession number.
"ID"	string	EPD identification.
"definition"	keyword	alternative promoter
"position; direction"	seq_pos	Position and direction relative to the transcription initiation site.

2. Biological meaning:

Multiple initiation sites preceding the same structural gene appear as alternative promoters if they are clearly separated from each other or differentially regulated.

3. Conditions and rules:

The minimum distance required between two alternative initiation sites is 20 bp.

4. Target identification:
5. Storage, maintenance and verification:

`DR EMBL`

1. Format:

DR   EMBL; "SV"; "ID"; "position".

"SV"	string	EMBL sequence version.
"ID"	string	EMBL identification.
"position"	seq_pos	Position of the EPD transcription initiation site.

Note: seq_pos is a positional sequence object represented according to the Milano convention.

2. Biological meaning:
3. Conditions and rules:
4. Target identification:
5. Storage, maintenance and verification:

`DR SWISS-PROT`

1. Format:

DR   SWISS-PROT; "AC"; "ID".

"AC"	string	SWISS-PROT accession number.
"ID"	string	SWISS-PROT identification.

2. Biological meaning:
3. Conditions and rules:
4. Target identification:
5. Storage, maintenance and verification:

`DR TRANSFAC`

1. Format:

DR   TRANSFAC; "AC"; "ID"; "position"; "type".

"AC"	string	TransFac accession number.
"ID"	string	Transfac identification.
"position"	seq_pos	Position of site relative to the EPD initiation site.
"type"	keyword	Type of initiation sites.

Notes:
seq_pos is a positional sequence object represented according to
the Milano convention.

Valid keywords for "type" are: "by position", "by function".

2. Biological meaning:

There are two types of cross-references, distuinguished by the keywords "by position" and "by function". "By position" means that the site described in TRANSFAC falls withing the range [-500,+100] of the initiation sites. "By function" means that the site has been reported to regulate transcription from the initiation site described by the EPD entry. "By position" cross-references are typically generated by an automatic procedure. "By function" cross-references are established by literature scanning. "By position" generally does not exclude "by function"; it simply means that a functional relationship has not (yet) come to the attention of the EPD curator.

3. Conditions and rules:

Rule 2: For a given pair of a TRANSFAC and an EPD entry, there can be at most one cross-reference for each SQ line in the TRANSFAC entry. A cross-reference can only be created for an SQ line, if the sequence matches a range of an EMBL sequence indicated

4. Target identification:

TRANSFAC entries containing multiple SQ lines with identical sequences may cause promblems to automatic procedures for establishing "by position" cross-references. There is a program for identification of such entries which can be used in the following way:

   g77 -fno-automatic /home/epd/src/find_difficult_sites.f 
   ./a.out < /db/transfac/site.dat

   R00052(not in 61)
   R00281  
   R00470  
   R00603  
   R00825(not in 61) 
   R00826 "
   R02711  
   R02728 " 
   R03466 "
   R03715  
   R03735 "

Verification of positions:

Examples:

1. EPD on + strand, TRANSFAC site on + strand:
EPD: | ID AD2_DNBI standard; single; VRT. | AC EP07159; | DE Major late promoter | OS Human adenovirus type 2 e1,e2 | DR EMBL; J01917; HACG; g209811; [-6038, 29899]. p1,p2 | DR TRANSFAC; R03156; AD$MLP_39; [-31,-24]; automatic. SE gtgttcctgaaggggggctataaaagggggtgggggcgcgttcgtcctcACTCTCTTCCG TRANSFAC: | AC R03156 | ID AD$MLP_39 | DE MLP (major late promoter); G000010. | SQ TATAAAA. t1,t2 | DR EMBL: J01917; HACG(6008:6014).
Conversion arithmetics:
p1 = e1 + t1 - 1 p2 = e1 + t2 t1 = p1 - e1 + 1 t2 = p2 - e1

5. Storage, maintenance and verification:

`DR FLYBASE`

1. Format:

DR   FLYBASE; "ID"; "symbol".

"ID"	string	FlyBase identification
"symbol"	string	FlyBase symbol.

2. Biological meaning:
3. Conditions and rules:
4. Target identification:
5. Storage, maintenance and verification:

`DR MIM`

1. Format:

DR   FLYBASE; "ID"; "symbol".

"ID"	string	FlyBase identification
"symbol"	string	FlyBase symbol.

2. Biological meaning:
3. Conditions and rules:
4. Target identification:
5. Storage, maintenance and verification:

`DR MGD`

1. Format:

DR   MGD; "MGI:ACID"; "symbol".

"ACID"	string	MGD accession identification
"symbol"	string	MGD symbol.

2. Biological meaning:
3. Conditions and rules:
4. Target identification:
5. Storage, maintenance and verification:

APPENDICES

A1 Representation of Positional Sequence Objects Convention:

1. The Milano convention

The Milano convention for defining the position of SEQUENCES relative to a transcription inititation SITE (or another physiological sites wich logically falls between adjacent bases) is ilustrated by the following example.

           -15       -10        -5         0         5               
     ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' '       
      a C C C G C C t g c a c c c g a t t c a t g t g a g a a        
       <----------->                       |                         
       TRANSFAC entry R99999/ET$SITE_1     +---> EPD entry EP99999   
                                                                     
     <------------------------------------------------------->       
     EMBL entry ZZ999999.1/HS28BP                                    



                                                                     
     DR   EMBL; ZZ999999.1; HS28BP; [-19, 9].                        
     DR   TRANSFAC; R99999; ET$SITE_1; [-18,-12], by position.

TRANSFAC applies the EMBL feature table numbering system for indicating a SITE or SUBSEQUENCE within a SEQUENCE. (Note that this problem is slightly different from the problem of indicating the position of a SEQUENCE relative to a SITE.) The FP lines of EPD follow the EMBL convention by referring to the first base of the transcript as the transcription initiation site.

     1       5        10        15        20        25               
     ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' '         
     a C C C G C C t g c a c c c g a t t c A T G T G A G A A         
       <--------->                         |                         
      TRANSFAC entry R99999/ET$SITE_1      EPD entry EP99999         
                                                                     
     <----------------------------------------------------->        
     EMBL entry ZZ999999.1/HS28BP                                     




     AC   R99999;                                                     
     ID   ET$SITE_1;                                                   
     DR   EMBL: ZZ999999; HS28BP(2:7)                                   
                                                                      
     FP   ET strange promoter :-S  ETL:R99999.1   1+      20; 99999.

2. Format for sequence object positions

["begin","end"]