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GeneNet database format
GN_SCHEME_REACTION table
reactions, which have described kinetics
Line code |
Information type |
Example |
| ID |
Identifier |
ID R078 |
| NM |
The reaction name |
NM Mevalonic acid 5-phosphate synthesis |
| SC |
Link to the GN_SCHEME table |
SC SCH7 |
| CO |
Link to the GN_SCHEME_CONSTANT table |
CO C0710 |
| EN |
Link to the GN_SCHEME_ENTITY table |
EN E713 |
| CM |
Description of the reaction |
CM Mevalonic acid ---> Mevalonic acid
5-phosphate |
GN_SCHEME_CONSTANT table
kinetic constants
Line code |
Information type |
Example |
| ID |
Identifier |
ID C0710 |
| NM |
The constant name |
NM KISBme5P |
| SC |
Link to the GN_SCHEME table |
SC SCH7 |
| VL |
The constant value |
VL 1 |
| UN |
Registered parameters |
UN 1/sec |
Line code |
Information type |
Example |
| ID |
GeneNet Identifier |
ID 131 |
| IC |
IdCode:
<Species abbreviation>:<gene abbreviation> |
IC Hs:AGG |
| DT |
Entry info:
<date>; <expert name>; <created/updated> |
DT 15.01.98; Ananko E.; created. |
| OS |
Species:
<Latin name> (<English name>) |
OS Homo sapiens (human). |
| SN |
Gene short name |
SN AGG |
| NM |
Gene full name |
NM Agamma globin |
| SY |
Gene name synonim |
SY hemoglobin gamma chain |
| SO |
Link to the GeneNet CELL table
<Cell identifier> |
SO Hs:K562 |
| CH |
Chromosomal localization |
CH 11, short arm |
| RE |
Inducer/repressor name |
RE erythropoietin |
| PN |
Protein |
PN Hs:AGG |
| DR |
Database link
<database name>; <database first AC>; <database ID> |
DR TRRD; A00297; Hs:AGG |
| RF |
Reference to the paper (GeneNet
BIBLIOGRAPHY table link)
<Paper identifier> |
RF Stamatoyannopoulos G., Nienhis A.W., 1994 |
| CC |
Comments |
CC low level in the adult bone marrow |
Line code |
Information type |
Example |
| ID |
GeneNet Identifier |
ID 25 |
| IC |
:
<Species abbreviation>:<protein abbreviation> |
IC Hs:TfR |
| DT |
Entry info:
<date>; <expert name>; <created/updated> |
DT 03.8.2000.; Stepanenko I.L.;
created. |
| OS |
Species:
<Latin name> (<English name>) |
OS Homo sapiens (human). |
| SN |
RNA short name |
SN TfR |
| NM |
RNA full name |
NM transferrin receptor |
| TP |
RNA type |
TP mRNA |
| GN |
Link to the GeneNet GENE table |
GN Hs:TFREC |
| SY |
RNA name synonim |
SY TfR |
| DR |
Database link
<database name>; <database first AC>; <database ID> |
DR SWISSPROT; P42224; |
| SO |
Link to the GeneNet CELL table
<Cell identifier> |
SO Hs:macrophage |
| RF |
Reference to the paper (GeneNet
BIBLIOGRAPHY table link)
<Paper identifier> |
RF Kim S. and Ponka P., 2000 |
| CC |
Comments |
CC receptor |
Line code |
Information type |
Example |
| ID |
Identifier |
ID 380 |
| IC |
IdCode:
<Species abbreviation>:<protein abbreviation> |
IC Hs:Stat1alpha |
| DT |
Entry info:
<date>; <expert name>; <created/updated> |
DT 09.10.97; Ananko E.; created. |
| OS |
Species:
<Latin name> (<English name>) |
OS Homo sapiens (human). |
| SN |
Protein short name |
SN Stat1alpha |
| NM |
Protein full name |
NM Stat1alpha homodimer |
| SY |
Protein name synonim |
SY p91 |
| DR |
Database link
<database name>; <database first AC>; <database ID> |
DR SWISSPROT; P42224; |
| SO |
Link to the GeneNet CELL table
<Cell identifier> |
SO Hs:macrophage |
| FN |
Functional state
<active/inactive/no data> |
FN active |
| MM |
Multimerization state
<monomer/homodimer/heterodimer/multimer/no data> |
MM homodimer |
| MD |
Protein modifications
<phosphorylated/non-phosphorylated/no data> |
MD phosphorylated |
| RE |
Inducer/repressor name |
RE IFN-gamma |
| GN |
Link to the GeneNet GENE table
<Gene IC> |
GN Hs:Stat1 |
| RF |
Reference to the paper (GeneNet LITER table link)
<Paper identifier> |
RF Kovarik P. et al., 1998 |
| CC |
Comments |
CC transcription factor |
Line code |
Information type |
Example |
| ID |
Identifier |
ID 67 |
| IC |
IdCode: |
IC NO |
| DT |
Entry info:
<date>; <expert name>; <created/updated> |
DT 19.01.2000.; Stepanenko I.L.; updated. |
| SN |
Substance short name |
SN NO |
| NM |
Substance full name |
NM nitric oxide |
| CC |
Comments |
CC NO is detected in the immune, neuronal, and vascular systems and in
many other tissues. |
| RF |
Reference to the paper (GeneNet LITER table link)
<Paper identifier> |
RF Bayon Y. et al., 1998 |
Line code |
Information type |
Example |
| ID |
Identifier |
ID 32 |
| IC |
IdCode:
<Species abbreviation>:<cell abbreviation> |
IC Gg:Eryth Prog |
| DT |
Entry info:
<date>; <expert name>; <created/updated> |
DT 19.06.1999.; Podkolodnaya O.A.; created. |
| OS |
Species:
<Latin name> (<English name>) |
OS Gallus gallus (chicken). |
| SN |
Cell short name |
SN EP |
| NM |
Cell full name |
NM Erythroid progenitor cells |
| RF |
Reference to the paper (GeneNet LITER table link)
<Paper identifier> |
RF Briegel K, et al. 1996 |
| CC |
Comments |
CC Normal SCF-depemdent erythrpoid progenitor cells were pepared by
cultivating bone marrow
CC cells from 3- to 7-day old SPAFAS chicks in modified CFU-E medium supplemented
CC with 100ng/ml of recombinant avian stem cell factor |
Line code |
Information type |
Example |
| ID |
Identifier |
ID 22 |
| IC |
IdCode |
IC Principal cell of CCD |
| DT |
Entry info:
<date>; <expert name>; <created/updated> |
DT 29.02.2000.; Ignatieva E.V.; updated. |
| CC |
Comments |
CC Principal cell of Cortical Collecting Duct |
Line code |
Information type |
Example |
| ID |
GeneNet Identifier |
ID 41 |
| IC |
IdCode
<Latin name> |
IC Ovis aries |
| AC |
Species English name |
AC sheep |
| SN |
Cell short name |
SN Oa |
| OC |
The organism taxonomic classification. The classification is listed
top-down as nodes in a taxonomic tree in which the most general grouping is given first.
The classification may be distributed over several OC lines, but nodes are not split
hyphenated between lines. The individual items are separated by semicolons and the list is
terminated by a period. |
OC EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; TETRAPODA; MAMMALIA;
OC EUTHERIA; ARTIODACTYLA. |
Line code |
Information type |
Example |
| ID |
GeneNet Identifier |
ID 53 |
| IC |
IdCode |
IC dehydration |
| DT |
Entry info:
<date>; <expert name>; <created/updated> |
DT 08-Feb-99.; Tana; created. |
| NM |
process name |
NM dehydration |
| CC |
Comments |
CC An embryo is stabilized by dehydration and may stay in the dormancy
stage for a long period of time. |
Line code |
Information type |
Example |
| ID |
GeneNet Identifier |
ID R135 |
| DT |
Entry info:
<date>; <expert name>; <created/updated> |
DT 03.8.2000.; Stepanenko I.L.; created. |
| IN |
Input entity |
IN <gene>Hs:ferrL^nucleus |
| TY |
Relation class
<control/reaction> |
TY reaction |
| OU |
Output entity |
OU <RNA>Mm:ferritin^cytoplasm |
| CO |
Code of the controlled relation
<<type of the component entering into reaction>><component
identifier>^<component localisation> -> <<type of the
component that is product of the reaction>><component
identifier>^<component localisation> |
CO
<substance>Corticosterone^mitochondria ->
<substance>Aldosterone^mitochondria |
| EF |
Reaction type
<direct/indirect> |
EF direct |
| AT |
Influence type
<increase/decrease/switch on/switch off> |
AT increase |
| RF |
Reference to the paper (GeneNet
BIBLIOGRAPHY table link)
<Paper identifier> |
RF Antonson P. and Xanthopoulos K.G., 1995 |
| CC |
Comments |
CC small intestine, colon, high |
Line code |
Information type |
Example |
| ID |
GeneNet identifier |
ID SCH10 |
| NM |
Gene network name |
NM Macrophage activation (model) |
| DT |
Entry info:
<date>; <expert name>; <created/updated> |
DT 28.06.2001; Nedosekina E.A.; updated. |
| MD |
Link to the GeneNet dynamic model |
MD GeneNet Dynamic Model: Macrophage
activation (model) |
| TP |
Level of the gene network representation
<cell/organism> |
TP cell |
| EN |
Link to the list of entities included in
the gene network |
EN List
of Entities |
| RA |
Link to the list of reactions in the gene
network |
RA List
of Reactions |
| RE |
Link to the list of regulatory events in
the gene network |
RE List
of Regulatory Events |
| DE |
Gene network description |
DE Macrophage activation: the core of the
mathematical model |
| OS |
Species:
<Latin name> (<English name>) |
OS Gallus gallus (chicken). |
| RF |
Reference to the paper (GeneNet
BIBLIOGRAPHY table link)
<Paper identifier> |
RF Amura C.R. et al., 1998 |
| DR |
Database link
<database name>; <database first AC>; <database ID> |
DR SWISSPROT; P42224; |
Line code |
Information type |
Example |
| ID |
GeneNet identifier: |
ID 955 |
| IC |
IdCode:
<name of the first author> et al., <year> |
IC Zhou M. et al., 1996 |
| DT |
Entry info:
<date>; <expert name>; <created/updated> |
DT 20.7.2000.; Stepanenko I.L.; created. |
| TI |
Title of the paper |
TI Evidence that a rapidly turning over protein, normally degraded
TI by proteasomes, regulates hsp72 gene transcription in HepG2 cells. |
| SO |
Journal name |
SO J.Biol.Chem. |
| VL |
Volume number |
VL 271 |
| YR |
Year |
YR 1996 |
| PG |
Pages |
PG 24769-24775 |
| ML |
MEDLINE link
<MEDLINE UI> |
ML 96394641 |
Line code |
Information type |
Example |
| ID |
GeneNet identifier |
ID 1 |
| IC |
Abbreviation of the annotator |
IC Ananko E. |
| NM |
Name of the annotator |
NM Ananko Elena Anatolievna |
| LB |
Laboratory/Department |
LB Laboratory of theoretical genetics |
| OR |
Institute |
OR Institute of Cytology & Genetics |
| EM |
e-mail address |
EM eananko@bionet.nsc.ru |
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