Phenome - OmicsDI

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Organisms

Homo sapiens (37)
Mus musculus (16)
Aerococcus urinae NBRC 15544 = CCUG 36881 (12)
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Ectopseudomonas oleovorans CECT 5344 (12)
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Human immunodeficiency virus 1 (12)
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Methylohalobius crimeensis 10Ki (12)
Miscanthus x giganteus (12)
Mus musculus (12)
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Organisms

Homo sapiens (89)
Mus musculus (17)
Drosophila serrata (1)
Cryptococcus neoformans H99 (1)
Canis lupus familiaris (1)
mollusc metagenome (1)
Candida albicans (1)
Danio rerio (1)

Repository

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pride (12)
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Tissue

Cell culture (4)
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Root (1)
Urine (1)
Yeast (1)

Disease

Cryptococcosis (2)
Gonorrhea (1)

Technology Type

Mass Spectrometry (12)
Mass spectrometry assay (6)
Bottom-up proteomics (6)
Mass spectrometry (5)
Shotgun proteomics (4)
NMR spectroscopy (2)
Data-independent acquisition (2)
Illumina MiSeq, ILLUMINA (1)
Illumina HiSeq 2000, Ion Torrent PGM (1)
AB SOLiD 4 System (1)
Illumina HiSeq 2000 (1)
NMR spectroscopy assay (1)
SWATH MS (1)
Top-down proteomics (1)

Instrument Platform

Liquid Chromatography MS - negative - reverse phase (7)
Liquid Chromatography MS - positive - reverse phase (6)
Illumina HiSeq 2000 (5)
Liquid Chromatography MS - positive - hilic (4)
Illumina HiSeq 2500 (3)
Illumina NovaSeq 6000 (3)
Xevo G2-S Tof (2)
Nuclear Magnetic Resonance (NMR) - (2)
Liquid Chromatography MS - negative - hilic (2)
- (1)
Flow injection analysis MS - negative (1)
Direct infusion MS - negative (1)
Liquid Chromatography MS - Positive (LC-MS (Positive)) (1)
Nuclear Magnetic Resonance (NMR) (1)
Direct infusion MS - positive (1)
MS Imaging - (1)
Liquid Chromatography MS - alternating - reverse phase (1)
Liquid Chromatography MS - positive - HILIC (1)

Publication Date

2026 (14)
2022 (9)
2021 (9)
2024 (8)
2018 (5)
2016 (5)
2025 (5)
2017 (3)
2015 (3)
2020 (3)
2013 (2)
2009 (2)
2008 (2)
2007 (2)
2023 (2)
2019 (2)
2014 (1)
2006 (1)

CHEBI ID

CHEBI:82912 (2)
CHEBI:17768 (2)
CHEBI:26271 (2)
CHEBI:15978 (2)
CHEBI:22660 (2)
CHEBI:22653 (2)
CHEBI:28044 (2)
CHEBI:10072 (2)
CHEBI:30763 (2)
CHEBI:17509 (2)
CHEBI:21547 (2)
CHEBI:17405 (2)
CHEBI:32805 (2)
CHEBI:16737 (2)
CHEBI:16020 (2)
CHEBI:18344 (2)
CHEBI:178204 (1)
CHEBI:27020 (1)
CHEBI:39919 (1)
CHEBI:178200 (1)
CHEBI:38034 (1)
CHEBI:38705 (1)
CHEBI:178208 (1)
CHEBI:155822 (1)
CHEBI:178205 (1)
CHEBI:178201 (1)
CHEBI:229948 (1)
CHEBI:89110 (1)
CHEBI:89348 (1)
CHEBI:178211 (1)

Metabolite Name

Creatinine (2)
N,N,N-Trimethyl-L-alanyl-L-proline betaine (TMAP) (1)
PI(16:0/18:2) (1)
CAR(26:1) (1)
CAR(20:2) (1)
CAR(20:1) (1)
CAR(20:0) (1)
CAR(16:2) (1)
2-Octenoylcarnitine CAR(8:1) (1)
Manghaslin (1)
Mauritianin (1)
3-hydroxy-3-methyl-5-oxo-5-[[3,4,5-trihydroxy-6-[[6-methoxy-2-oxo-3-[(2-oxo-1-benzopyran-7-yl)oxy]-1-benzopyran-7-yl]oxy]-2-oxanyl]methoxy]pentanoic acid (1)
Multinoside A (1)
(+)-syringaresinol beta-D-glucoside (1)
Forsythiaside (1)
Pectolinarin (1)
2''-galloylhyperin (1)
Neohesperidin (1)
Tulipanin (1)
Diosmetin rutinoside (1)
Tribuloside (1)
4-{[(3s,4r,5s)-3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)tetrahydro-3-furanyl]methyl}-2-methoxyphenyl beta-d-glucopyranoside (1)
Vitexin 2''-O-alpha-L-rhamnoside (1)
Kaempferol 3-O-beta-D-glucopyranosyl-7-O-alpha-L-rhamnopyranoside (1)
MCULE-7899134902 (1)
Theaflavin (1)
9-hydroxy-2,6,12-trimethyl-12-[2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyethyl]-15-oxatetracyclo[8.4.1.01,10.02,7]pentadecane-6-carboxylic acid (1)
Quercetin 3-O-(6-O-malonyl-beta-D-glucoside) (1)
UDP-beta-L-rhamnose (1)
(+)-volkensiflavone (1)

IsPrivate

False (3)

Submitter Keywords

FROG (2)

First Public Date

2024 (22)
2025 (18)
2022 (17)
2021 (17)
2023 (15)
2019 (13)
2026 (9)
2020 (7)
2018 (7)
2014 (7)
2016 (6)
2017 (4)
2013 (4)
2015 (1)

Classification

fungi (2)

Modelling Approach

Constraint-based model (2)
Metabolic network (1)

Study type

RNA-seq of coding RNA (10)
Transcription profiling by array (3)
Comparative genomic hybridization by array (2)
Spatial transcriptomics by high-throughput sequencing (1)
ChIP-seq (1)
Methylation profiling by array (1)
RNA-seq of coding RNA from single cells (1)
RNA-seq of non coding RNA (1)

Release Date

2025 (360)
2024 (338)
2023 (305)
2022 (302)
2021 (213)
2020 (131)
2019 (109)
2018 (72)
2017 (51)
2026 (43)
2016 (39)
2015 (32)
2014 (26)
2013 (17)
2009 (11)
2011 (11)
2008 (6)
2012 (6)
2007 (4)
2010 (4)
2006 (4)
2001 (1)

Lab affiliation

Human Phenome Institute,Zhangjiang FudanInternational Innovation Center, Fudan UniversityShanghai, 201203, China. (2)
Molecular and Cellular Biology, University of Guelph, Canada (2)
Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, USA (1)
ETH Zürich (1)
Human Phenome Institute,Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China (1)
Khon Kaen University National Phenome Institute, Regional Science Park Northeast 1, Khon Kaen University, Khon Kaen, 40002, Thailand (1)
Proteomics, Leibniz-Institut für analytische Wissenschaften -ISAS - e.V., Germany (1)
School of BioSciences, The University of Melbourne Parkville VIC 3010, Australia Australian National Phenome Centre, Murdoch University, Murdoch, WA 6150, Australia (1)
State Key Laboratory of Genetic Engineering, Institutes of Biomedical Sciences, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University (1)
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (1)

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Kim2021 - Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917

Escherichia coli Nissle 1917 (EcN) is an intestinal probiotic that is effective for the treatment of intestinal disorders, such as inflammatory bowel disease and ulcerative colitis. EcN is a representative Gram-negative probiotic in biomedical research and is an intensively studied probiotic. Howeve...

2024-10-15 | BIOMD0000001062 | BioModels

FROG