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.
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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.
Submitter of this revision: Abhishek Sengupta
Modellers: Abhishek Sengupta
Metadata information
Connected external resources
Name | Description | Size | Actions |
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Model files |
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BIOMD0000000579_url.xml | SBML L2V4 representation of Sengupta2015 - Knowledge base model of human energy pool network (HEPNet) | 1.45 MB | Preview | Download |
Additional files |
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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
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Version: 2
- 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)
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Version: 1
- Submitted on: Jul 21, 2015 6:52:50 PM
- Submitted by: Abhishek Sengupta
- With comment: Original import of BIOMD0000000579.xml.origin
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: Variable used inside SBML models
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 | 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 |
(added: 07 Aug 2015, 16:25:48, updated: 07 Aug 2015, 16:25:48)