Sengupta2015 - Knowledge base model of human energy pool network (HEPNet)

  public model
Model Identifier
BIOMD0000000579
Short description
Sengupta2015 - Knowledge base model of human energy pool network (HEPNet)

This model is described in the article:

Sengupta A, Grover M, Chakraborty A, Saxena S.
PLoS ONE 2015; 10(6): e0127918

Abstract:

HEPNet is an electronic representation of metabolic reactions occurring within human cellular organization focusing on inflow and outflow of the energy currency ATP, GTP and other energy associated moieties. The backbone of HEPNet consists of primary bio-molecules such as carbohydrates, proteins and fats which ultimately constitute the chief source for the synthesis and obliteration of energy currencies in a cell. A series of biochemical pathways and reactions constituting the catabolism and anabolism of various metabolites are portrayed through cellular compartmentalization. The depicted pathways function synchronously toward an overarching goal of producing ATP and other energy associated moieties to bring into play a variety of cellular functions. HEPNet is manually curated with raw data from experiments and is also connected to KEGG and Reactome databases. This model has been validated by simulating it with physiological states like fasting, starvation, exercise and disease conditions like glycaemia, uremia and dihydrolipoamide dehydrogenase deficiency (DLDD). The results clearly indicate that ATP is the master regulator under different metabolic conditions and physiological states. The results also highlight that energy currencies play a minor role. However, the moiety creatine phosphate has a unique character, since it is a ready-made source of phosphoryl groups for the rapid synthesis of ATP from ADP. HEPNet provides a framework for further expanding the network diverse age groups of both the sexes, followed by the understanding of energetics in more complex metabolic pathways that are related to human disorders.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Format
SBML (L2V4)
Related Publication
  • HEPNet: A Knowledge Base Model of Human Energy Pool Network for Predicting the Energy Availability Status of an Individual.
  • Sengupta A, Grover M, Chakraborty A, Saxena S
  • PloS one , 0/ 2015 , Volume 10 , pages: e0127918 , PubMed ID: 26053019
  • Amity Institute of Biotechnology, Amity University Uttar Pradesh, U.P., India.
  • HEPNet is an electronic representation of metabolic reactions occurring within human cellular organization focusing on inflow and outflow of the energy currency ATP, GTP and other energy associated moieties. The backbone of HEPNet consists of primary bio-molecules such as carbohydrates, proteins and fats which ultimately constitute the chief source for the synthesis and obliteration of energy currencies in a cell. A series of biochemical pathways and reactions constituting the catabolism and anabolism of various metabolites are portrayed through cellular compartmentalization. The depicted pathways function synchronously toward an overarching goal of producing ATP and other energy associated moieties to bring into play a variety of cellular functions. HEPNet is manually curated with raw data from experiments and is also connected to KEGG and Reactome databases. This model has been validated by simulating it with physiological states like fasting, starvation, exercise and disease conditions like glycaemia, uremia and dihydrolipoamide dehydrogenase deficiency (DLDD). The results clearly indicate that ATP is the master regulator under different metabolic conditions and physiological states. The results also highlight that energy currencies play a minor role. However, the moiety creatine phosphate has a unique character, since it is a ready-made source of phosphoryl groups for the rapid synthesis of ATP from ADP. HEPNet provides a framework for further expanding the network diverse age groups of both the sexes, followed by the understanding of energetics in more complex metabolic pathways that are related to human disorders.
Contributors
Submitter of the first revision: Abhishek Sengupta
Submitter of this revision: Abhishek Sengupta
Modellers: Abhishek Sengupta

Metadata information

is
BioModels Database MODEL1507210000
BioModels Database BIOMD0000000579
isDescribedBy
PubMed 26053019
hasTaxon
Taxonomy Homo sapiens
hasProperty
Mathematical Modelling Ontology Ordinary differential equation model

Curation status
Curated


Original model(s)
HEPNET:Human Energy Pool Network

Tags

Connected external resources

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Model files

BIOMD0000000579_url.xml SBML L2V4 representation of Sengupta2015 - Knowledge base model of human energy pool network (HEPNet) 1.45 MB Preview | Download

Additional files

BIOMD0000000579-biopax2.owl Auto-generated BioPAX (Level 2) 406.04 KB Preview | Download
BIOMD0000000579-biopax3.owl Auto-generated BioPAX (Level 3) 625.90 KB Preview | Download
BIOMD0000000579.m Auto-generated Octave file 76.75 KB Preview | Download
BIOMD0000000579.pdf Auto-generated PDF file 1.23 MB Preview | Download
BIOMD0000000579.png Auto-generated Reaction graph (PNG) 9.32 MB Preview | Download
BIOMD0000000579.sci Auto-generated Scilab file 154.00 Bytes Preview | Download
BIOMD0000000579.svg Auto-generated Reaction graph (SVG) 630.32 KB Preview | Download
BIOMD0000000579.vcml Auto-generated VCML file 52.00 Bytes Preview | Download
BIOMD0000000579.xpp Auto-generated XPP file 60.78 KB Preview | Download
BIOMD0000000579_urn.xml Auto-generated SBML file with URNs 1.22 MB Preview | Download

  • Model originally submitted by : Abhishek Sengupta
  • Submitted: Jul 21, 2015 6:52:50 PM
  • Last Modified: Apr 8, 2016 7:17:35 PM
Revisions
  • Version: 2 public model Download this version
    • Submitted on: Apr 8, 2016 7:17:35 PM
    • Submitted by: Abhishek Sengupta
    • With comment: Current version of Sengupta2015 - Knowledge base model of human energy pool network (HEPNet)
  • Version: 1 public model Download this version
    • Submitted on: Jul 21, 2015 6:52:50 PM
    • Submitted by: Abhishek Sengupta
    • With comment: Original import of BIOMD0000000579.xml.origin

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models


Species
Species Initial Concentration/Amount
s136 43.0 mol
s7

Succinate ; succinic acid
0.0 mol
s267 0.0 mol
s334

NADP+ ; NADP(+)
0.0 mol
s355

NAD+ ; NAD(+)
24.0 mol
s347

H2O ; water
5.5E7 mol
s329

H+ ; hydron
0.0 mol
s361

H+ ; hydron
0.0 mol
s51

sn-Glycerol 3-phosphate ; sn-glycerol 3-phosphate
30.0 mol
Reactions
Reactions Rate Parameters
s370 => s65 + s136; s124, s370 s370*k1 k1=1.0 substance
s6 + s352 => s7 + s345 + s350; s58, s6 v1*s6/(k1+s6) k1=0.09 substance; v1=1.0 substance
s358 => s267; s358 s358*k1 k1=1.0 substance
s234 + s334 => s181 + s185; s186, s333, s234 v1*s234/(k1+s234) k1=0.04 substance; v1=1.0 substance
s323 + s351 + s361 => s325 + s355; s330, s323 v1*s323/(k1+s323) v1=1.0 substance; k1=12.6 substance
s347 => s258; s347 s347*k1 k1=1.0 substance
s74 + s67 + s329 => s35 + s44 + s93; s85, s74 v1*s74/(k1+s74) k1=33.0 substance; v1=1.0 substance
s52 + s355 => s5 + s349 + s351 + s361; s56, s52 v1*s52/(k1+s52) k1=73.0 substance; v1=1.0 substance
s112 + s355 => s111 + s351 + s361; s366, s112 v1*s112/(k1+s112) k1=34.5 substance; v1=1.0 substance
s293 => s51; s293 s293*k1 k1=1.0 substance
Curator's comment:
(added: 07 Aug 2015, 16:25:48, updated: 07 Aug 2015, 16:25:48)
Figure 5A of the reference publication has been reproduced using SBML odeSolver.