Sengupta2015 - Knowledge base model of human energy pool network (HEPNet)
This model is described in the article:
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.
This model is hosted on BioModels Database and identified by: BIOMD0000000579.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.
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.
-
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.
Metadata information
| Name | Description | Size | Actions |
|---|---|---|---|
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.sci | Auto-generated Scilab file | 154.00 Bytes | Preview | Download |
| BIOMD0000000579_urn.xml | Auto-generated SBML file with URNs | 1.22 MB | 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.vcml | Auto-generated VCML file | 52.00 Bytes | Preview | Download |
| BIOMD0000000579.m | Auto-generated Octave file | 76.75 KB | Preview | Download |
| 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.svg | Auto-generated Reaction graph (SVG) | 630.32 KB | Preview | Download |
| BIOMD0000000579.xpp | Auto-generated XPP file | 60.78 KB | Preview | Download |
- Model originally submitted by : Abhishek Sengupta
- Submitted: 21-Jul-2015 18:52:50
- Last Modified: 08-Apr-2016 19:17:35
Revisions
-
Version: 2
- Submitted on: 08-Apr-2016 19:17:35
- Submitted by: Abhishek Sengupta
- With comment: Current version of Sengupta2015 - Knowledge base model of human energy pool network (HEPNet)
-
Version: 1
- Submitted on: 21-Jul-2015 18:52:50
- 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
of this model will only be shown to the submitter and their collaborators.
: Variable used inside SBML models
| Species | Initial Concentration/Amount |
|---|---|
| s355 NAD+ ; NAD(+) |
24.0 mol |
| s351 NADH ; NADH |
22.0 mol |
| s381 NADH ; NADH |
22.0 mol |
| s14 L-Alanine ; L-alanine |
333.0 mol |
| Reactions | Rate | Parameters |
|---|---|---|
| s355 => s355; s355 | s355*k1 | k1=1.0 substance |
| s9 + s355 => s50 + s351 + s361; s28, s9 | v1*s9/(k1+s9) | k1=3.8E-4 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 |
| s5 + s350 + s355 => s6 + s349 + s351 + s361; s57, s5 | v1*s5/(k1+s5) | k1=490.0 substance; v1=1.0 substance |
| s72 + s355 => s80 + s351 + s361; s366, s72 | v1*s72/(k1+s72) | k1=34.5 substance; v1=1.0 substance |
| s96 + s355 => s89 + s351 + s361; s366, s96 | v1*s96/(k1+s96) | k1=34.5 substance; v1=1.0 substance |
| s99 + s355 => s100 + s351 + s361; s366, s99 | v1*s99/(k1+s99) | k1=34.5 substance; v1=1.0 substance |
| s112 + s355 => s111 + s351 + s361; s366, s112 | v1*s112/(k1+s112) | k1=34.5 substance; v1=1.0 substance |
| s115 + s355 => s116 + s351 + s361; s366, s115 | v1*s115/(k1+s115) | k1=34.5 substance; v1=1.0 substance |
| s351 => s381; s351 | s351*k1 | k1=1.0 substance |
| s11 => s14; s11 | s11*k1 | k1=1.0 substance |
(added: 07 Aug 2015, 16:25:48, updated: 07 Aug 2015, 16:25:48)