Network propagation

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Unknown (1895)
Genomics (77)
Transcriptomics (76)
Proteomics (27)
Metabolomics (16)
Models (4)
Other (4)
Methylation profiling (2)

Organisms

Homo sapiens (57)
Mus musculus (23)
Andropogon gerardi (20)
Bacteria (20)
Canis lupus familiaris (20)
Cnidaria (20)
Cricetulus griseus (20)
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Vanderwaltozyma polyspora (2)
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Arabidopsis thaliana (2)
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synthetic construct (1)
Eremophila rugosa (1)
Toxoplasma gondii RH (1)

Organisms

Homo sapiens (32)
Mus musculus (10)
Arabidopsis thaliana (2)
Influenza A virus (A/WSN/1933 TS61(H1N1)) (1)
Vanderwaltozyma polyspora (1)
Naumovozyma castellii (1)
Schizosaccharomyces pombe (1)
Triticum aestivum (1)
Rattus norvegicus (1)

Repository

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pride (20)
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Tissue

Cell culture (8)
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T cell (2)
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Lung (1)
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Disease

Disease free (3)
Human immunodeficiency virus infectious disease (2)
Idiopathic dilated cardiomyopathy (1)
Alpha 1-antitrypsin deficiency (1)
COVID-19 (1)

Technology Type

Mass Spectrometry (20)
Bottom-up proteomics (10)
Shotgun proteomics (8)
Mass spectrometry (7)
Data-dependent acquisition (5)
Mass spectrometry assay (4)
Data-independent acquisition (3)
Affinity purification coupled with mass spectrometry proteomics (2)
DiaPASEF (1)
HDMSE (1)
SWATH MS (1)

Instrument Platform

Liquid Chromatography MS - positive - reverse phase (6)
Orbitrap Fusion Lumos (3)
6520A Quadrupole Time-of-Flight LC/MS (2)
LTQ Orbitrap Elite (2)
Liquid Chromatography MS - positive (2)
Liquid Chromatography MS - negative - hilic (2)
Liquid Chromatography MS - positive - hilic (2)
Illumina HiSeq 3000 (1)
NextSeq 500 (1)
MicrOTOF II (1)
Xevo G2 Q-Tof (1)
Impact HD (1)
LTQ Orbitrap Velos (1)
Gas Chromatography MS - - - DSQ II Single Quadrupole GC/MS (Thermo Scientific) (1)
Liquid Chromatography MS - negative (1)
Liquid Chromatography MS - positive - reverse-phase (1)
Liquid Chromatography MS - negative - reverse-phase (1)
Liquid Chromatography MS - negative - reverse phase (1)

Publication Date

2014 (15)
2023 (15)
2024 (13)
2021 (13)
2025 (11)
2013 (10)
2012 (10)
2017 (8)
2026 (8)
2022 (6)
2020 (5)
2016 (5)
2009 (5)
2018 (4)
2019 (4)
2015 (3)
2011 (3)
2010 (3)
2008 (2)
2005 (1)
2007 (1)

UNIPROT ID/AC

P12351 (1)
P40441 (1)
P25601 (1)
P26188 (1)
P14771 (1)
P38830 (1)
P14164 (1)
P50083 (1)
P47098 (1)
P40587 (1)
P39546 (1)
P32896 (1)
P36039 (1)
P42844 (1)
Q03180 (1)
P12294 (1)
Q12088 (1)
O13527 (1)
P48559 (1)
P25561 (1)
P40068 (1)
P36130 (1)
P50273 (1)
P36004 (1)
P40033 (1)
Q06053 (1)
P46993 (1)
P40851 (1)
P14796 (1)
P38248 (1)

CHEBI ID

CHEBI:16247 (2)
CHEBI:15848 (1)
CHEBI:15863 (1)
CHEBI:15705 (1)
CHEBI:17118 (1)
CHEBI:32988 (1)
CHEBI:16468 (1)
CHEBI:17478 (1)
CHEBI:15914 (1)
CHEBI:4280 (1)
CHEBI:28401 (1)
CHEBI:18338 (1)
CHEBI:28260 (1)
CHEBI:18290 (1)
CHEBI:33199 (1)
CHEBI:35910 (1)
CHEBI:16385 (1)
CHEBI:2405 (1)
CHEBI:17106 (1)
CHEBI:25805 (1)
CHEBI:30413 (1)
CHEBI:15954 (1)
CHEBI:16211 (1)
CHEBI:18371 (1)
CHEBI:36241 (1)
CHEBI:17505 (1)
CHEBI:17530 (1)
CHEBI:2070 (1)
CHEBI:18062 (1)
CHEBI:15678 (1)

Metabolite Name

Tris(2-butoxyethyl) phosphate (3)
Cholic acid (3)
(2S,3S,4S,5R,6R)-6-[[(3S,4S,6aR,6bS,8aR,9R,12aS,14bR)-9-hydroxy-4-(hydroxymethyl)-4,6a,6b,8a,11,11,14b-heptamethyl-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl]oxy]-5-[(2S,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxy-3,4-dihydroxyoxane-2-carboxylic acid (2)
Dibutyl phthalate (DBP) (2)
Lyso-PC(16:0) (2)
NCGC00385123-01_C22H30O6_7b,9-Dihydroxy-3-(hydroxymethyl)-1,1,6,8-tetramethyl-5-oxo-1,1a,1b,4,4a,5,7a,7b,8,9-decahydro-9aH-cyclopropa[3,4]benzo[1,2-e]azulen-9a-yl acetate (2)
Alpha-linolenic acid|linolenic acid|(9Z,12Z,15Z)-octadeca-9,12,15-trienoic acid (2)
1-({[2-(2-furylmethyl)-5-methylpyrrolidinyl]amino}methylene)-7-[8-({[2-(2-fury lmethyl)pyrrolidinyl]amino}methylene)-1,6-dihydroxy-3-methyl-5-(methylethyl)-7 -oxo(2-naphthyl)]-3,8-dihydroxy-6-methyl-4-(methylethyl)naphthalen-2-one (2)
Threonylleucine (2)
2,6-Di-tert-butyl-4-hydroxymethylphenol (2)
Taurocholic acid (2)
1-Stearoyl-2-hydroxy-sn-glycero-3-phosphocholine (2)
Trans-EKODE-(E)-Ib (2)
Monoolein (2)
Methionine (2)
Elaidic acid (2)
9(10)-EpOME (2)
2-(2,6-Diaminohexanoylamino)-3-methylbutanoic acid (1)
[D-Asp3]MC-LR (1)
Microcystin LY (1)
N-gamma-Glutamylmethionine (1)
N-acetyl-?-D-mannosamine (1)
Alanylphenylalanine (1)
N-(Carboxymethyl)-3-(dodecanoylamino)-N,N-dimethylpropan-1-aminium (1)
2-Amino-6-propanoylpteridin-4(1H)-one (1)
15-benzyl-18-[(1E,3E)-6-methoxy-3,5-dimethyl-7-phenylhepta-1,3-dienyl]-1,5,12,19-tetramethyl-2-methylidene-8-(2-methylpropyl)-3,6,9,13,16,20,25-heptaoxo-1,4,7,10,14,17,21-heptazacyclopentacosane-11,22-dicarboxylic acid (1)
(NAG)(NAM)-AqmA (1)
(2R,3S)-2-[[3-(carboxymethylimino)-5-hydroxy-5-(hydroxymethyl)-2-methoxycyclohexen-1-yl]amino]-3-hydroxybutanoic acid (1)
Alpha aminoadipic acid (1)
DL-2-Aminobutyric acid (1)

First Public Date

2014 (11)
2023 (7)
2025 (6)
2019 (6)
2026 (5)
2024 (5)
2021 (5)
2022 (4)
2018 (4)
2017 (3)
2013 (3)
2020 (1)

Modelling Approach

Ordinary differential equation model (2)

Lab affiliation

Chair of Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany (4)
Institute for Clinical Biochemistry and Pathobiochemistry German Diabetes Center (DDZ) Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf Auf´m Hennekamp 65 40225 Düsseldorf Germany (2)
1Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA 2Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA 3Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA (1)
Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Canada (1)
Center for Network Systems Biology, Boston University (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)
Chulalongkorn University Systems Bilogy center, Research affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand (1)
Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Germany (1)
EDyP (1)
Functional Proteomics Lab, National Center for Biotechnology (CNB-CSIC) (1)
Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Auf´m Hennekamp 65, 40225 Düsseldorf, Germany (1)
Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, USA Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, LA, USA Molecular Biology Institute, University of California, Los Angeles, USA (1)
Key Laboratory of Zoonotic of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Liaoning Province, Shenyang 110866, P. R. China (1)
Key Laboratory of Zoonotic of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Liaoning Province, Shenyang 110866, P. R. China Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, P. R. China Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology,100029, P. R. China (1)
Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, Campos dos Goytacazes, RJ, Brazil. Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil. (1)
Yale Cancer Biology Institute, Department of Pharmacology, Yale University School of Medicine (1)

IsPrivate

False (3)

Model Flag

Non Kinetic (1)

Classification

viruses (1)

Study type

Transcription profiling by array (24)
RNA-seq of coding RNA (11)
ChIP-seq (4)
Other (2)
RNA-seq of non coding RNA (2)
Transcription profiling by SAGE (1)
Genotyping by array (1)

Release Date

2025 (316)
2024 (214)
2023 (205)
2022 (203)
2021 (198)
2019 (133)
2020 (131)
2018 (96)
2016 (77)
2017 (73)
2015 (58)
2014 (50)
2026 (35)
2013 (34)
2012 (29)
2011 (23)
2010 (21)
2009 (16)
2008 (9)
2007 (8)
2006 (4)
2005 (4)
2004 (1)
2003 (1)
2002 (1)

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The propagation of perturbations in shuffled bacterial gene networks

This dataset contains transcription profiles of TOP10 E.coli transformed with 85 rewired network plasmids first described in: Evolvability and hierarchy in rewired bacterial gene networks. Nature 452:840-5 (2008). The data are described and analysed in an accompanying paper Baumstark et al.,The pr...

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

2015-12-14 | E-MTAB-3233 | biostudies-arrayexpress

Network propagation in the cytoscape cyberinfrastructure.

Not available

S-EPMC5638226 | biostudies-literature

Propagation of transient explosive synchronization in a mesoscale mouse brain network model of epilepsy.

Not available

S-EPMC11398721 | biostudies-literature

Classifying tumors by supervised network propagation.

Not available

S-EPMC6022559 | biostudies-literature

Optimizing network propagation for multi-omics data integration.

Not available

S-EPMC8664198 | biostudies-literature

Identification of a dynamic core transcriptional network in t(8;21) AML regulating differentiation block and self-renewal [ChIP-Seq]

The leukemogenic fusion protein RUNX1/ETO impairs myeloid differentiation and drives malignant self-renewal. Here we use digital footprinting and ChIP-sequencing to identify the core RUNX1/ETO responsive transcriptional network of t(8;21) cells. We show that the transcriptional programme underlying ...

ORGANISM(S): Homo sapiens

2014-09-24 | E-GEOD-60130 | biostudies-arrayexpress

NetCore: a network propagation approach using node coreness.

Not available

S-EPMC7515737 | biostudies-literature

Identification of a dynamic core transcriptional network in t(8;21) AML regulating differentiation block and self-renewal [RNA-Seq]

ORGANISM(S): Homo sapiens

2014-09-24 | E-GEOD-54478 | biostudies-arrayexpress

NPF:network propagation for protein function prediction.

Not available

S-EPMC7430911 | biostudies-literature

NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks.