Genetic interaction network

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Unknown (3156)
Transcriptomics (1805)
Genomics (388)
Proteomics (191)
Metabolomics (82)
Other (24)
Models (17)
Methylation profiling (4)
Multiomics (3)
Genomic (1)

Organisms

Homo sapiens (811)
Mus musculus (465)
Arabidopsis thaliana (117)
Saccharomyces cerevisiae (71)
Rattus norvegicus (48)
Drosophila melanogaster (45)
Escherichia coli (23)
Caenorhabditis elegans (22)
Bos taurus (20)
Danio rerio (18)
Candida albicans (15)
Medicago truncatula (13)
Sus scrofa (13)
Methanococcus maripaludis S2 (10)
Thermus thermophilus HB8 (10)
Glycine max (10)
Schizosaccharomyces pombe (10)
synthetic construct (9)
Entamoeba histolytica (8)
Gallus gallus (8)
Xenopus laevis (7)
Plasmodium falciparum (7)
Zea mays (7)
Staphylococcus aureus (6)
Oryza sativa Japonica Group (6)
Macaca mulatta (5)
Helicobacter pylori (4)
Arabidopsis (3)
cellular organisms (3)
Mammalia (1)

Organisms

Homo sapiens (61)
Mus musculus (29)
Saccharomyces cerevisiae (10)
Drosophila melanogaster (5)
Arabidopsis thaliana (5)
Sus scrofa (4)
Danio rerio (4)
Rattus norvegicus (4)
Escherichia coli (3)
Brachypodium distachyon (2)
Strongylocentrotus purpuratus (2)
Nicotiana tabacum (2)
Pestalotiopsis fici (1)
Klebsiella pneumoniae subsp. pneumoniae ATCC 43816 (1)
Saccharomyces cerevisiae W303 (1)
Anas platyrhynchos (1)
Ailuropoda melanoleuca (1)
Macaca fascicularis (1)
Brassica napus (1)
Aspergillus fumigatus (1)
Marchantia polymorpha (1)
Schizosaccharomyces pombe (1)
Citrus sinensis (1)
Malus domestica (1)
Candida albicans (1)
Solanum lycopersicum (1)
human gut metagenome (1)
Vitis vinifera (1)
Gossypium hirsutum (1)
Bos taurus (1)

Repository

biostudies-arrayexpress (1841)
ENA (200)
geo (141)
pride (86)
MetaboLights (81)
MassIVE (51)
EGA (42)
iProX (26)
PAXDB (11)
BioModels (10)
jPOST (9)
Cell Collective (7)
PanoramaPublic (5)
GPMDB (3)
dbGaP (1)
GNPS (1)
PeptideAtlas (1)

Tissue

Cell culture (26)
Brain (9)
Epithelial cell (7)
Leaf (4)
Permanent cell line cell (4)
Blood serum (3)
Embryo (3)
Liver (3)
Lung (3)
Blood plasma (2)
Heart (2)
Kidney (2)
Primary cell (2)
Stem cell (2)
Adipose tissue (1)
B cell (1)
Blood cell (1)
CNS neuron (sensu Vertebrata) (1)
Cartilage (1)
Cell suspension culture (1)
Colorectal adenocarcinoma cell line (1)
Dendritic cell (1)
Early embryonic cell (1)
Embryonic cell (1)
Fibroblast (1)
Hepatocyte (1)
Hippocampus (1)
Kidney cell (1)
Monocyte (1)
T cell (1)

Disease

Normal (4)
Not Available (3)
Neuroblastoma (2)
Peptic ulcer disease (1)
Duodenal ulcer (1)
Congential heart disease (1)
Polycystic Lipomembranous Osteodysplasia with Sclerosing Leukoencephalopathy (1)
Ewing family tumor (1)
4T1 tumor-bearing (1)
Alopecia (1)
Uninfected (1)
Lymphoma (1)
Keratoconus (1)
HIV (1)
HHV-6B infected (1)
Xoo inoculated (1)
Hutchinson-Gilford Progeria Syndrome (1)
Apparently healthy (1)
Dystrophic (1)
Raji Burkitt's lymphoma (1)
Cancer cell line pool (1)
ARR1-SRDX (1)
Familial adenomatous polyposis (FAP) (1)
T-cell acute lymphoblastic leukemia (1)
Infertility (1)
Glioblastoma (1)
None (1)
Neurofibromatosis type 1 (1)
Control (1)
Cervical cancer (1)

Technology Type

Mass Spectrometry (86)
Mass spectrometry (50)
Shotgun proteomics (41)
Mass spectrometry assay (27)
Affinity purification coupled with mass spectrometry proteomics (20)
Bottom-up proteomics (18)
Data-independent acquisition (6)
NMR spectroscopy (4)
Data-dependent acquisition (4)
Illumina HiSeq 2000 (3)
Top-down proteomics (3)
Affinity proteomics (2)
ILLUMINA, Illumina HiSeq 2500 (1)
Illumina HiSeq 3000 (1)
Illumina Genome Analyzer II (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
HDMSE (1)
Immunopeptidomics (1)
SRM/MRM (1)
SWATH MS (1)

Instrument Platform

Illumina HiSeq 2000 (19)
Illumina NovaSeq 6000 (14)
Illumina HiSeq 4000 (13)
Illumina HiSeq 2500 (10)
NextSeq 500 (10)
Agilent Technologies G2565CA microarray scanner (6)
NextSeq 2000 (4)
Beadarray reader (2)
ScanArray 4000 [PerkinElmer] (2)
Illumina Genome Analyzer II (2)
ScanArray 6000 [Perkin Elmer] (2)
Illumina NovaSeq X (2)
NextSeq 550 (2)
Illumina HiSeq 3000 (2)
Coulter Automated Workstation Biomek i7 Hybrid (1)
RNeasy 96-well plate kit (1)
NextSeq 500, 75 bp single end lane (1)
STAR v2.5.3a, rpkmforgenes, RSeQC 2.6.1 (1)
Illumina Nextera XT index kits (Set A–D) (1)
Oligo(dT) primer and SuperScript II reverse transcriptase (ThermoFisher Scientific), TapeStation 4200 or 2100 Bioanalyzer with a DNA High Sensitivity chip (Agilent Biotechnologies) (1)
Aria III (BD Biosciences) (1)
Dr. Tom Multi-omics Data Mining System (1)
Animal Experiment Facility (1)
SPF Animal Room (1)
PCR Thermocycler, Fragment Analyzer (1)
Centrifuge, Nucleic Acid Quantification Instrument (1)
Biosafety Cabinet, Liquid Nitrogen Tank, -80°C Freezer (1)
Genomics Core Shared Resources at Augusta University (RRID: SCR_026483) (1)
RNeasy Mini Kit (Qiagen) (1)
GentleMACS Octo Dissociator with Heaters (Miltenyi Biotec, Cat. No. 130-096-427) together with the Human Tumor Dissociation Kit (Miltenyi Biotec, Cat. No. 130-095-929), (1)

Publication Date

2013 (268)
2010 (243)
2012 (215)
2014 (213)
2011 (212)
2015 (185)
2008 (125)
2009 (119)
2016 (107)
2025 (81)
2026 (76)
2024 (57)
2007 (52)
2022 (47)
2021 (44)
2020 (41)
2023 (39)
2017 (36)
2018 (25)
2019 (25)
2005 (23)
2006 (16)
2004 (3)
2003 (3)
2027 (1)

UNIPROT ID/AC

Q93WK5 (3)
Q8L500 (3)
Q9LKL2 (3)
O81713 (3)
Q9UUB7 (1)
Q5AFP3 (1)
Q22197 (1)
Q9LIE5 (1)
O24646 (1)
Q9FFA7 (1)
Q9LTJ6 (1)
Q9FN03 (1)
Q8LGH4 (1)
Q9M086 (1)
Q9SYX2 (1)
P43254 (1)
P28700 (1)
P70284 (1)
Q64729 (1)
Q9WVS0 (1)
Q04683 (1)
Q9ES17 (1)
P18893 (1)
P07750 (1)
P04351 (1)
P42232 (1)
Q60636 (1)
P41183 (1)
P06332 (1)
P34057 (1)

ENSEMBL ID

ENSMUSG00000027651 (1)
ENSMUSG00000072849 (1)
ENSMUSP00000141097 (1)

CHEBI ID

CHEBI:17568 (17)
CHEBI:15741 (16)
CHEBI:30769 (16)
CHEBI:16708 (15)
CHEBI:15428 (15)
CHEBI:28044 (15)
CHEBI:16335 (15)
CHEBI:18186 (14)
CHEBI:16811 (14)
CHEBI:6650 (14)
CHEBI:18012 (14)
CHEBI:22653 (13)
CHEBI:17154 (13)
CHEBI:18211 (13)
CHEBI:17895 (13)
CHEBI:17822 (12)
CHEBI:26271 (12)
CHEBI:22660 (12)
CHEBI:27570 (12)
CHEBI:28300 (12)
CHEBI:17533 (12)
CHEBI:32816 (12)
CHEBI:30887 (12)
CHEBI:16027 (12)
CHEBI:17552 (8)
CHEBI:33699 (4)
CHEBI:16356 (1)
CHEBI:36080 (1)
CHEBI:29108 (1)
CHEBI:15996 (1)

Metabolite Name

Adenosine (15)
Thymine (14)
Choline (14)
Proline (14)
Uridine (14)
Hypoxanthine (14)
Oleamide (13)
Uric acid (13)
L-Tyrosine (13)
L-Threonine (12)
Phenylalanine (12)
Adenine (12)
Guanosine (12)
Creatine (12)
Inosine (12)
Histidine (11)
Uracil (11)
Glutathione (11)
Pantothenic acid (11)
Indole (11)
Methionine (11)
Xanthosine (11)
Creatinine (11)
L-Valine (11)
Glycine (10)
Betaine (10)
Benzoic acid (10)
Succinic acid (10)
Pyridoxine (10)
Pyridoxamine (10)

First Public Date

2025 (34)
2024 (26)
2026 (25)
2014 (25)
2023 (15)
2019 (14)
2021 (13)
2020 (12)
2022 (8)
2018 (7)
2016 (7)
2013 (7)
2015 (4)
2017 (3)

Modelling Approach

Ordinary differential equation model (9)

Lab affiliation

Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China. (2)
First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (2)
Shanghai Jiao Tong University (2)
UCSF (2)
Associate Professor Bioinformatics, UCD School of Medicine, Conway Institute, Systems Biology Ireland, University College Dublin. (1)
Associate Professor of Systems Biology Department of Molecular Medicine University of Pavia 9, via A Ferrata/ 27100 Pavia / Italy (1)
BRIC-National Centre for Cell Science, Inside Pune Univesrity, Ganeshkhind, Pune, India, 411007 (1)
Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China (1)
Biology Department University of Massachusetts Boston Boston, USA (1)
CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China (1)
Capital Institute of Pediatrics, Beijing (1)
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria (1)
Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women’s and Children’s Health, Karolinska Institute, Region Stockholm, Stockholm, Sweden Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden (1)
Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, China; (1)
Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Québec, QC, Canada Centre de recherche sur le cancer de l’Université Laval, Québec, QC, Canada PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada (1)
Centre for MND Research, Macquarie Medical School, Faculty of Medicine Health and Human Sciences, Macquarie University, North Ryde NSW 2109 Australia (1)
Clinical Medical Research Center of Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, No.1017, Dongmen North Road, Luohu District, Shenzhen 518020, China. (1)
College of Agronomy, Northwest A&F University, Shaanxi, Yangling 712100, China. (1)
Core Facility for Medical Bioanalytics Proteomics Platform Tübingen (PxP) Institute for Ophthalmic Research Eberhard-Karls University of Tuebingen Elfriede-Aulhorn-Str. 7 D-72076 Tuebingen. Germany. (1)
Dame Kate Campbell Fellow Department of Surgery| Melbourne Medical School Department of Anatomy and Physiology| School of Biomedical Sciences Faculty of Medicine, Dentistry and Health Sciences Medical Building (#181), Grattan Street The University of Melbourne, Victoria 3010 Australia P: +61 3 9035 5464 E: apebay@unimelb.edu.au W: https://medicine.unimelb.edu.au/school-structure/surgery W: https://biomedicalsciences.unimelb.edu.au/departments/anatomy-and-physiology (1)
Department of Bacterial Molecular Genetics University of Gdansk (1)
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, United States (1)
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA (1)
Department of Biomedical Sciences, Affiliated with The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen. (1)
Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay (IITB), Powai, Mumbai, Maharashtra - 400076 (1)
Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke (1)
Department of Microbiology & Immunology Stanford University School of Medicine (1)
Department of Molecular Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland (1)
Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences (1)
Department of Pediatrics, Shengjing Hospital of China Medical University (1)

IsPrivate

False (10)

Model Flag

Non Kinetic (1)

Submitter Keywords

TransQST (1)

Classification

bacteria (4)
fungi (2)

Study type

Transcription profiling by array (1216)
RNA-seq of coding RNA (210)
ChIP-seq (106)
Unknown experiment type (56)
RNA-seq of non coding RNA (48)
ChIP-chip by tiling array (33)
Comparative genomic hybridization by array (30)
Transcription profiling by tiling array (24)
Other (21)
Methylation profiling by array (20)
RNA-seq of coding RNA from single cells (15)
ChIP-chip by array (9)
Methylation profiling by high throughput sequencing (9)
RNA-seq of total RNA (7)
Transcription profiling by RT-PCR (5)
High-throughput sequencing (4)
Transcription profiling by SAGE (3)
Animal - High-throughput sequencing (3)
RNAi profiling by array (3)
Genotyping by array (3)
DNA-seq (3)
One-color microarray (2)
Cell line - High-throughput sequencing (1)
Proteomic profiling by mass spectrometer (1)
MicroRNA profiling by high throughput sequencing (1)
ATAC-seq (1)
RIP-seq (1)
ScATAC-seq (1)
MicroRNA profiling by array (1)

Release Date

2022 (409)
2013 (348)
2021 (345)
2025 (330)
2023 (315)
2015 (306)
2014 (306)
2010 (304)
2012 (282)
2011 (275)
2024 (272)
2020 (256)
2016 (224)
2019 (206)
2018 (163)
2017 (158)
2008 (155)
2009 (147)
2007 (73)
2026 (56)
2005 (27)
2006 (26)
2004 (7)
2003 (6)
2002 (1)

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Interaction of Genetic Variants Activates Latent Metabolic Pathways in Yeast

Genetic interactions are fundamental to the architecture of complex traits, yet the molecular mechanisms by which variant combinations influence cellular pathways remain poorly understood. Here, we answer the question of whether interactions between genetic variants can activate unique pathways a...

2025-07-22 | MTBLS12761 | MetaboLights

Metabolic network construction reveals probiotic-specific colonization resistance in a synthetic small intestinal community

The gut microbiota is essential to host health. Probiotics can be used as a microbiota targeted therapy to improve host health. However, probiotic molecular mechanisms of action and probiotics targeting the small intestinal microbiota are often not elucidated. In this study, we construct a three ...

2024-09-26 | MTBLS7370 | MetaboLights

A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation

Histone acetylation and deacetylation are among the principal mechanisms by which chromatin is regulated during transcription, DNA silencing, and DNA repair. We analyzed patterns of genetic interactions uncovered during comprehensive genome-wide analyses in yeast to probe how histone acetyltransfera...

ORGANISM(S): Saccharomyces cerevisiae

2008-06-11 | E-GEOD-9771 | biostudies-arrayexpress

Linking genetic, metabolic and phenotypic diversity 1 among S. cerevisiae strains using multi-omics associations

The selection of bioengineering platform strains and engineering strategies to improve the stress resistance of Saccharomyces cerevisiae remains a pressing need in bio-based chemical production. Thus, a systematic effort to exploit the genotypic and phenotypic diversity to boost yeast’s industrial v...

2019-01-16 | MTBLS780 | MetaboLights

Integrating Network Pharmacology, Microbiomics, and Metabolomics to Uncover the Therapeutic Effect of Liubao Tea on Osteoarthritis

Background: Osteoarthritis (OA) is a debilitating joint disorder with no effective disease-modifying drugs. Liubao tea, a traditional Chinese dark tea, possesses various bioactivities, including anti-inflammatory and gut microbiota-regulating effects. However, its potential therapeutic role and m...

2026-02-18 | MTBLS13905 | MetaboLights

Mapping the Genetic Interaction Network of PARP inhibitor Response

PRJNA1196842 | ENA

The genetic architecture of the human bZIP interaction network

PRJNA1309138 | ENA

Genetic reconstruction of a functional transcriptional regulatory network

Although global analyses of transcription factor binding provide one view of potential transcriptional regulatory networks, regulation also occurs at levels distinct from transcription factor binding. Here, we use a genetic approach to identify targets of transcription factors in yeast and reconstru...

ORGANISM(S): Saccharomyces cerevisiae

2010-07-02 | E-GEOD-4654 | biostudies-arrayexpress

Insight into the complex interaction between vaginal microbiome, metabolome, and host gene expression in cervical cancer progression

This study aimed to highlight the relationships between vaginal microbiome composition, metabolic alterations, and gene expression changes during cervical cancer. Multi-omics analysis for the healthy (Z group), abortion (AB group), HPV infection (HP group), and cervical cancer group (CC group), q...

2025-11-26 | MTBLS10477 | MetaboLights

Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks

Delineating the extracellular interaction network of the cell surface proteotype (the surfaceome) is fundamental to understanding cellular signaling function in health and disease. Here, we developed LUX-MS, an optoproteomic technology that enables the spatiotemporal and proteome-wide study of surfa...

ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) Listeria monocytogenes serotype 4b Listeria phage A500 Escherichia coli

2021-06-14 | PXD020481 | Pride

Lc-ms/ms

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5672 Results

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