Table_2_ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species.xlsx

The availability of genome sequences, annotations, and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in bacteria, archaea, and eukaryotes. When modeled using mathematical representations...

Full description

Bibliographic Details
Main Authors: Eileen Marie Hanna, Xiaokang Zhang, Marta Eide, Shirin Fallahi, Tomasz Furmanek, Fekadu Yadetie, Daniel Craig Zielinski, Anders Goksøyr, Inge Jonassen
Format: Dataset
Language:unknown
Published: 2020
Subjects:
Online Access:https://doi.org/10.3389/fmolb.2020.591406.s002
https://figshare.com/articles/dataset/Table_2_ReCodLiver0_9_Overcoming_Challenges_in_Genome-Scale_Metabolic_Reconstruction_of_a_Non-model_Species_xlsx/13291646
id ftfrontimediafig:oai:figshare.com:article/13291646
record_format openpolar
spelling ftfrontimediafig:oai:figshare.com:article/13291646 2023-05-15T15:27:16+02:00 Table_2_ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species.xlsx Eileen Marie Hanna Xiaokang Zhang Marta Eide Shirin Fallahi Tomasz Furmanek Fekadu Yadetie Daniel Craig Zielinski Anders Goksøyr Inge Jonassen 2020-11-26T05:57:46Z https://doi.org/10.3389/fmolb.2020.591406.s002 https://figshare.com/articles/dataset/Table_2_ReCodLiver0_9_Overcoming_Challenges_in_Genome-Scale_Metabolic_Reconstruction_of_a_Non-model_Species_xlsx/13291646 unknown doi:10.3389/fmolb.2020.591406.s002 https://figshare.com/articles/dataset/Table_2_ReCodLiver0_9_Overcoming_Challenges_in_Genome-Scale_Metabolic_Reconstruction_of_a_Non-model_Species_xlsx/13291646 CC BY 4.0 CC-BY Biochemistry Molecular Biology Structural Biology Enzymes Protein Trafficking Proteomics and Intermolecular Interactions (excl. Medical Proteomics) Receptors and Membrane Biology Signal Transduction Structural Biology (incl. Macromolecular Modelling) Synthetic Biology genome-scale metabolic reconstruction Atlantic cod less-annotated species model curation environmental toxicology Dataset 2020 ftfrontimediafig https://doi.org/10.3389/fmolb.2020.591406.s002 2020-12-02T23:58:57Z The availability of genome sequences, annotations, and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in bacteria, archaea, and eukaryotes. When modeled using mathematical representations, a reconstruction can simulate underlying genotype-phenotype relationships. Accordingly, genome-scale metabolic models (GEMs) can be used to predict the response of organisms to genetic and environmental variations. A bottom-up reconstruction procedure typically starts by generating a draft model from existing annotation data on a target organism. For model species, this part of the process can be straightforward, due to the abundant organism-specific biochemical data. However, the process becomes complicated for non-model less-annotated species. In this paper, we present a draft liver reconstruction, ReCodLiver0.9, of Atlantic cod (Gadus morhua), a non-model teleost fish, as a practicable guide for cases with comparably few resources. Although the reconstruction is considered a draft version, we show that it already has utility in elucidating metabolic response mechanisms to environmental toxicants by mapping gene expression data of exposure experiments to the resulting model. Dataset atlantic cod Gadus morhua Frontiers: Figshare
institution Open Polar
collection Frontiers: Figshare
op_collection_id ftfrontimediafig
language unknown
topic Biochemistry
Molecular Biology
Structural Biology
Enzymes
Protein Trafficking
Proteomics and Intermolecular Interactions (excl. Medical Proteomics)
Receptors and Membrane Biology
Signal Transduction
Structural Biology (incl. Macromolecular Modelling)
Synthetic Biology
genome-scale metabolic reconstruction
Atlantic cod
less-annotated species
model curation
environmental toxicology
spellingShingle Biochemistry
Molecular Biology
Structural Biology
Enzymes
Protein Trafficking
Proteomics and Intermolecular Interactions (excl. Medical Proteomics)
Receptors and Membrane Biology
Signal Transduction
Structural Biology (incl. Macromolecular Modelling)
Synthetic Biology
genome-scale metabolic reconstruction
Atlantic cod
less-annotated species
model curation
environmental toxicology
Eileen Marie Hanna
Xiaokang Zhang
Marta Eide
Shirin Fallahi
Tomasz Furmanek
Fekadu Yadetie
Daniel Craig Zielinski
Anders Goksøyr
Inge Jonassen
Table_2_ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species.xlsx
topic_facet Biochemistry
Molecular Biology
Structural Biology
Enzymes
Protein Trafficking
Proteomics and Intermolecular Interactions (excl. Medical Proteomics)
Receptors and Membrane Biology
Signal Transduction
Structural Biology (incl. Macromolecular Modelling)
Synthetic Biology
genome-scale metabolic reconstruction
Atlantic cod
less-annotated species
model curation
environmental toxicology
description The availability of genome sequences, annotations, and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in bacteria, archaea, and eukaryotes. When modeled using mathematical representations, a reconstruction can simulate underlying genotype-phenotype relationships. Accordingly, genome-scale metabolic models (GEMs) can be used to predict the response of organisms to genetic and environmental variations. A bottom-up reconstruction procedure typically starts by generating a draft model from existing annotation data on a target organism. For model species, this part of the process can be straightforward, due to the abundant organism-specific biochemical data. However, the process becomes complicated for non-model less-annotated species. In this paper, we present a draft liver reconstruction, ReCodLiver0.9, of Atlantic cod (Gadus morhua), a non-model teleost fish, as a practicable guide for cases with comparably few resources. Although the reconstruction is considered a draft version, we show that it already has utility in elucidating metabolic response mechanisms to environmental toxicants by mapping gene expression data of exposure experiments to the resulting model.
format Dataset
author Eileen Marie Hanna
Xiaokang Zhang
Marta Eide
Shirin Fallahi
Tomasz Furmanek
Fekadu Yadetie
Daniel Craig Zielinski
Anders Goksøyr
Inge Jonassen
author_facet Eileen Marie Hanna
Xiaokang Zhang
Marta Eide
Shirin Fallahi
Tomasz Furmanek
Fekadu Yadetie
Daniel Craig Zielinski
Anders Goksøyr
Inge Jonassen
author_sort Eileen Marie Hanna
title Table_2_ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species.xlsx
title_short Table_2_ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species.xlsx
title_full Table_2_ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species.xlsx
title_fullStr Table_2_ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species.xlsx
title_full_unstemmed Table_2_ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species.xlsx
title_sort table_2_recodliver0.9: overcoming challenges in genome-scale metabolic reconstruction of a non-model species.xlsx
publishDate 2020
url https://doi.org/10.3389/fmolb.2020.591406.s002
https://figshare.com/articles/dataset/Table_2_ReCodLiver0_9_Overcoming_Challenges_in_Genome-Scale_Metabolic_Reconstruction_of_a_Non-model_Species_xlsx/13291646
genre atlantic cod
Gadus morhua
genre_facet atlantic cod
Gadus morhua
op_relation doi:10.3389/fmolb.2020.591406.s002
https://figshare.com/articles/dataset/Table_2_ReCodLiver0_9_Overcoming_Challenges_in_Genome-Scale_Metabolic_Reconstruction_of_a_Non-model_Species_xlsx/13291646
op_rights CC BY 4.0
op_rightsnorm CC-BY
op_doi https://doi.org/10.3389/fmolb.2020.591406.s002
_version_ 1766357711552774144