pathway reconstruction

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Unknown (1293)
Genomics (154)
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Organisms

Homo sapiens (54)
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Drosophila melanogaster (8)
Escherichia coli str. K-12 substr. MG1655 (5)
Methanosarcina barkeri (4)
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cellular organisms (1)
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Organisms

Homo sapiens (28)
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Hippeastrum (2)
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Caenorhabditis elegans (2)
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unclassified Narcissus (1)
uncultured Bacillota bacterium (1)
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Galanthus elwesii (1)
Crinum x powellii (1)
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Instrument Platform

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2009 (2)
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2006 (1)

UNIPROT ID/AC

Q06187 (1)
P08571 (1)
Q99683 (1)
Q8N5C8 (1)
Q07890 (1)
Q12933 (1)
Q15628 (1)
Q13546 (1)
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CHEBI ID

CHEBI:30769 (7)
CHEBI:30915 (6)
CHEBI:30887 (4)
CHEBI:18021 (4)
CHEBI:352 (3)
CHEBI:44863 (3)
CHEBI:18705 (3)
CHEBI:10728 (3)
CHEBI:27047 (3)
CHEBI:42610 (3)
CHEBI:24075 (3)
CHEBI:569217 (3)
CHEBI:5140 (3)
CHEBI:1785 (3)
CHEBI:11960 (3)
CHEBI:20316 (3)
CHEBI:21312 (3)
CHEBI:13108 (3)
CHEBI:6230 (3)
CHEBI:13113 (3)
CHEBI:42741 (3)
CHEBI:22373 (3)
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CHEBI:28972 (3)
CHEBI:28061 (3)
CHEBI:32889 (3)
CHEBI:40752 (3)
CHEBI:2351 (3)
CHEBI:13231 (3)

Metabolite Name

Fumaric acid (3)
L-tyrosine (3)
Ala-Met (2)
D-Ornithine (2)
Capillarisin (2)
Alpha-ketoglutaric acid (2)
Phosphoenolpyruvate (2)
L-leucine (2)
Tyramine (2)
N-Oleoylethanolamine (2)
L-alanine (2)
Citric acid (2)
Beta-alanine (2)
Spermidine (2)
L-threonine (2)
L-valine (2)
L-glutamic acid (2)
N6-Acetyl-L-lysine (2)
Lumichrome (2)
L-Lysine (2)
Diethanolamine (2)
5'-Methylthioadenosine (2)
5-Hydroxy-L-tryptophan (2)
Piperidine (2)
L-lysine (2)
Pyridoxine (2)
Adenosine (2)
Guanine (2)
Cytosine (2)
L-methionine (2)

First Public Date

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2019 (7)
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2014 (6)
2020 (5)
2017 (5)
2023 (3)
2021 (3)
2013 (2)
2016 (1)
2015 (1)

Modelling Approach

Constraint-based model (13)
Ordinary differential equation model (8)
Other (1)
Metabolic network (1)

Lab affiliation

1. Division of Radiation Health, 2. Department of Pharmaceutical Sciences, 3. Neurobiology & Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR (1)
Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon (1)
Department of Biotechnology, TU Delft, The Netherlands (1)
Department of Ecogenomics and Systems Biology, Division Molecular Systems Biology, University of Vienna, Austria (1)
Department of Ophthalmology University Medical Center Mainz Germany (1)
HUN-REN–SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Pharmahungary Group, Záhony utca 7, 1031 Budapest, Hungary (1)
Institute of Biomedical Chemistry, Group of Biobamking, Department of Proteomic Research; 119121 Moscow, 10 Pogodinskaya str., bld. 8, Russian Federation (1)
Institute of Hydrobiology, Chinese Academy of Sciences (1)
King's BHF Centre, King's College London, London, UK (1)
Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (1)
Microbiology Department, The Ohio State University, United States of America (1)
No. 72 Binhai Road, Qingdao, Shandong Province, 266237, P.R. China (1)
Proteomics core facility, Seoul National University Hospital (1)
Proteomics lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay (1)
School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia. (1)
Third Hospital of Hebei Medical University (1)

IsPrivate

False (30)

Model Flag

Non Kinetic (13)

Submitter Keywords

FROG (6)
Not Peer Reviewed (1)

Classification

bacteria (2)

Study type

Transcription profiling by array (36)
RNA-seq of coding RNA (26)
RNA-seq of non coding RNA (6)
Transcription profiling by SAGE (2)
ChIP-chip by tiling array (2)
Transcription profiling by tiling array (2)
ChIP-chip by array (2)
ChIP-seq (2)
RNA-seq of coding RNA from single cells (2)
Unknown experiment type (1)
Animal - High-throughput sequencing (1)
DNA-seq (1)

Release Date

2025 (204)
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2023 (110)
2019 (76)
2020 (75)
2016 (73)
2018 (72)
2015 (57)
2014 (53)
2026 (51)
2017 (50)
2012 (38)
2013 (35)
2010 (34)
2011 (23)
2009 (22)
2008 (15)
2007 (13)
2006 (11)
2004 (8)
2002 (4)
2005 (3)
2001 (2)

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Phenotypes and Multi—omics Reveal Changes and Molecular Mechanism of Suspension Adaptation of HEK293 Cells Structural Remodelling, Metabolic Reconstruction and Stress Resistance

Human embryonic kidney 293 (HEK293) cells have been successfully adapted from adherent to suspension culture and have been widely applied in both scientific research and the pharmaceutical industry. However, the alterations in cells during the adaptation have not been well described, which raise ...

2025-12-16 | MTBLS13517 | MetaboLights

Reconstruction of signaling networks regulating fungal morphogenesis by transcriptomics

Reconstruction of signaling networks regulating fungal morphogenesis by the expression profiling of wild-type and the temperature sensitive morphological ramosa-1 mutant. Aspergillus niger wildtype versus Ramosa mutant for 1h at 37 under controlled growth condition in 5L bioreactor

ORGANISM(S): Aspergillus niger

2010-05-05 | E-GEOD-17641 | biostudies-arrayexpress

Reconstruction of the human nigrostriatal pathway in vitro reveals target-dependent dopamine neuron maturation

PRJNA1374099 | ENA

Reconstruction of the decidual pathway in human endometrial cells using single-cell RNA-Seq

PRJNA525821 | ENA

Comparing Bayesian-Based Reconstruction Strategies in Topology-Based Pathway Enrichment Analysis.

Not available

S-EPMC9313337 | biostudies-literature

From injury to recovery: Spatiotemporal dynamics of the visual pathway during spontaneous structural and functional regeneration after optic nerve transection in zebrafish.

Not available

S-EPMC12464375 | biostudies-literature