Integration transcriptomics and proteomics

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Unknown (258)
Proteomics (166)
Transcriptomics (90)
Genomics (50)
Metabolomics (9)
Other (7)
Models (1)

Organisms

Homo sapiens (133)
Bombyx mori (75)
Schizosaccharomyces pombe (75)
Human immunodeficiency virus 1 (75)
Oryza sativa Indica Group (75)
Sinorhizobium meliloti BL225C (75)
Sus scrofa domesticus (75)
Ostreococcus tauri (75)
Saccharomyces cerevisiae (75)
Vitis vinifera (75)
Staphylococcus aureus (75)
Rattus norvegicus (75)
Escherichia coli (75)
Mus musculus (18)
Geobacter sulfurreducens PCA (3)
Saccharomyces cerevisiae (3)
Sus scrofa (3)
Danio rerio (3)
Ixodes scapularis (2)
Thermoplasma acidophilum DSM 1728 (1)
Arabidopsis thaliana (1)
Streptomyces rimosus subsp. rimosus (1)
Cunninghamia lanceolata (1)
Neurospora crassa (1)
Escherichia coli K-12 (1)
Bos taurus (1)
Nannochloropsis oceanica strain IMET1 (1)
Epinephelus fuscoguttatus x Epinephelus lanceolatus (1)
Rattus rattus (1)
Haemaphysalis longicornis (1)

Organisms

Homo sapiens (22)
Mus musculus (8)
Danio rerio (3)
Streptomyces rimosus subsp. rimosus (1)
Ixodes scapularis (1)
Neurospora crassa (1)
Cunninghamia lanceolata (1)
Escherichia coli K-12 (1)

Repository

pride (75)
geo (65)
PeptideAtlas (63)
ENA (46)
biostudies-arrayexpress (33)
iProX (13)
MassIVE (9)
MetaboLights (9)
PAXDB (4)
EGA (2)
PanoramaPublic (2)
BioModels (1)
GPMDB (1)

Tissue

Others (29)
Cell culture (15)
Brain (11)
Male Reproductive System (8)
Digestive System (8)
Female Reproductive System (7)
Liver (6)
Lung (5)
Epithelial cell (5)
Fibroblast (4)
Spleen (3)
Liver (3)
Embryonic stem cell (3)
Blood plasma (3)
Stem cell (3)
Extracellular vesicle (2)
Skeletal muscle (2)
Root (2)
Seminal plasma (2)
Leaf (2)
Blood cell (2)
Lung (1)
Pancreas (1)
Brain (1)
Adrenal Gland (1)
Kidney (1)
Brown fat cell differentiation (1)
Segmented neutrophil of bone marrow (1)
Neutrophilic promyelocyte (1)
Neutrophilic metamyelocyte (1)

Disease

Azoospermia (2)
Oligoasthenoteratozoospermia (2)
Skeletal muscle atrophy (2)
Brain glioblastoma multiforme (2)
Cervix carcinoma (2)
Disease free (2)
Not Available (1)
Developmental and epileptic encephalopathy 9 (1)
Toxic encephalopathy (1)
Organic acidemia (1)
Rhabdomyosarcoma (1)
Mitochondrial complex I deficiency (1)
Lung carcinoma in situ (1)
Lipid metabolism disorder (1)
Idiopathic pulmonary fibrosis (1)
Stroke (1)
Human granulocytic anaplasmosis (1)
Prostate adenocarcinoma (1)
Liver disease (1)
Mixed disorder as reaction to stress (1)
Prostate cancer (1)
Renal fibrosis (1)
Atrial fibrillation (1)
Osteoarthritis (1)
Brain cancer (1)
Alzheimer's disease (1)
Urinary bladder cancer (1)
Type 2 diabetes mellitus (1)
Burkitt lymphoma (1)
Colon cancer (1)

Technology Type

Mass Spectrometry (75)
Shotgun proteomics (41)
Bottom-up proteomics (19)
Mass spectrometry (9)
SWATH MS (7)
Data-dependent acquisition (6)
Data-independent acquisition (3)
Gel-based experiment (3)
Mass spectrometry imaging (2)
All-ion fragmentation (2)
Affinity purification coupled with mass spectrometry proteomics (2)
Metaproteomics (1)
Proteogenomics (1)
Immunopeptidomics (1)
MSE (1)
Top-down proteomics (1)

Instrument Platform

LTQ Orbitrap Velos (37)
LTQ Orbitrap Elite (28)
QExactive (6)
Illumina HiSeq 2000 (3)
Illumina NovaSeq 6000 (2)
Q Exactive (2)
Gas Chromatography MS - positive (2)
Liquid Chromatography MS - positive - hilic (2)
Liquid Chromatography MS - positive - reverse phase (2)
Liquid Chromatography MS - negative - reverse phase (2)
Coulter Automated Workstation Biomek i7 Hybrid (1)
RNeasy 96-well plate kit (1)
None (1)
NextSeq 2000 (1)
DNBSEQ-G400 (1)
Instrument (1)
Q Exactive Plus (1)
Gas Chromatography MS - (1)
Liquid Chromatography MS - (1)
Exactive (Thermo Scientific) (1)
Liquid Chromatography MS - alternating - reverse phase (1)
Liquid Chromatography MS - negative - HILIC (1)
Liquid Chromatography MS - positive - HILIC (1)
Liquid Chromatography MS - negative - hilic (1)
LTQ Orbitrap (1)

Publication Date

2014 (63)
2025 (42)
2024 (25)
2026 (17)
2023 (13)
2016 (12)
2022 (12)
2020 (12)
2010 (11)
2021 (11)
2019 (10)
2015 (9)
2017 (8)
2018 (7)
2009 (4)
2013 (3)
2011 (3)
2006 (1)
2005 (1)

UNIPROT ID/AC

LAMB3_MOUSE (2)
COLQ_MOUSE (2)
CFA53_MOUSE (2)
MMP9_MOUSE (2)
S6A14_MOUSE (2)
LOXL3_MOUSE (2)
CFA57_MOUSE (2)
SG3A2_MOUSE (2)
ABCA5_MOUSE (2)
CC151_MOUSE (2)
Q80UR4_MOUSE (2)
SPAT6_MOUSE (2)
S39A8_MOUSE (2)
MCPT8_MOUSE (2)
SP17_MOUSE (2)
VGFR1_MOUSE (2)
DLRB2_MOUSE (2)
LFNG_MOUSE (2)
PAR6B_MOUSE (2)
D3YVL2_MOUSE (2)
MIEAP_MOUSE (2)
GRAA_MOUSE (2)
CFA69_MOUSE (2)
C1QT2_MOUSE (2)
CLC1A_MOUSE (2)
M4A4D_MOUSE (2)
MUC1_MOUSE (2)
SPA6L_MOUSE (2)
CC181_MOUSE (2)
SEM3E_MOUSE (2)

ENSEMBL ID

ENSG00000170477 (56)
ENSG00000229353 (44)
ENSG00000147251 (22)
ENSG00000247315 (13)
ENSG00000176092 (3)
ENSG00000204131 (3)

CHEBI ID

CHEBI:28842 (3)
CHEBI:15428 (3)
CHEBI:15741 (3)
CHEBI:18012 (3)
CHEBI:15756 (3)
CHEBI:42111 (2)
CHEBI:33508 (2)
CHEBI:17822 (2)
CHEBI:17234 (2)
CHEBI:17148 (2)
CHEBI:17754 (2)
CHEBI:16119 (2)
CHEBI:6650 (2)
CHEBI:16196 (2)
CHEBI:7916 (2)
CHEBI:16010 (2)
CHEBI:15843 (2)
CHEBI:15971 (2)
CHEBI:32816 (2)
CHEBI:30915 (2)
CHEBI:17351 (2)
CHEBI:30769 (2)
CHEBI:194570 (1)
CHEBI:191920 (1)
CHEBI:194568 (1)
CHEBI:194564 (1)
CHEBI:194560 (1)
CHEBI:194571 (1)
CHEBI:194569 (1)
CHEBI:194567 (1)

Metabolite Name

Glyceric acid (2)
PS(DiMe(11,3)/DiMe(11,5)) (2)
DG(14:0/19:0/0:0) (2)
Postin (2)
Glyuranolide (2)
Simvastatin hydroxy acid (2)
Deoxycholic acid glycine conjugate (2)
Americine (2)
Hordatine A (2)
Sulfolithocholylglycine (2)
Chenodeoxycholic acid sulfate (2)
PE(18:0/20:5(5Z,8Z,11Z,14Z,17Z)) (2)
LysoPE(0:0/22:1(13Z)) (2)
1-Oleoylglycerophosphoserine (2)
PS(15:0/22:1(13Z)) (2)
PA(14:1(9Z)/14:0) (2)
Dynorphin B (6-9) (2)
Gamma-Linolenic acid (2)
Gentamicin (2)
Serine (2)
Glycine (2)
Glycerol (2)
Succinic acid (2)
Fumaric acid (2)
Malic acid (2)
Lithocholic acid glycine conjugate (2)
Dehydroepiandrosterone sulfate (2)
3a,7a,12b-Trihydroxy-5b-cholanoic acid (2)
Taurocholic acid (2)
Docosahexaenoic acid (2)

First Public Date

2024 (13)
2025 (12)
2026 (6)
2023 (5)
2022 (3)
2020 (3)
2021 (2)
2017 (1)
2016 (1)

Modelling Approach

Ordinary differential equation model (1)

Lab affiliation

Systems Biology Ireland, University College Dublin (3)
Functional Proteomics Lab, Dpt. Life Sciences, University of Siena, Italy (2)
Department of Inflammation and Immunity, Gastroenterology and Hepatology. Cleveland Clinic, Cleveland Ohio, USA (2)
Department of Ecogenomics and Systems Biology, Division Molecular Systems Biology, University of Vienna, Austria (1)
Laboratory of Experimental Hematology, Vaccine and Infectious Disease Institute (Vaxinfectio), University of Antwerp, 2610 Wilrijk, Belgium (1)
European Molecular Biology Laboratory (EMBL) Meyerhofstr 17 69117 Heidelberg Germany (1)
Helmholtz Zentrum München, Institute of Lung Biology and Disease, Member of the German Center for Lung Research (DZL), Munich, Germany (1)
The Australian Wine Research Insistute (1)
University of Melbourne, Melbourne, Australia (1)
CeBiTec, Bielefeld University (1)
Histone Modifications Group Zentrallabor für Proteinanalytik BioMedical Center Faculty of Medicine Ludwig-Maximilians-University of Munich Großhadernerstr. 9 82152 Planegg-Martinsried GERMANY (1)
Department of Clinical and Experimental Medicine (1)
Pulmonary, Critical Care, and Sleep Medicine Veterans Affairs Medical Center, Minneapolis, MN Pulmonary, Critical Care, and Sleep Medicine University of Minnesota, Minneapolis, MN (1)
Department of Physiology and Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea Immune-network pioneer research center, Ajou University School of Medicine, Suwon, Republic of Korea (1)
Neurovascular Research Laboratory, Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. Institute de Biomedicine of Seville, IBiS/Hospital Universitario Virgen del Rocío/CSIC/University of Seville & Department of Neurology, Hospital Universitario Virgen Macarena, Seville. (1)
Brain tumor translational targets German Cancer Research Center (DKFZ) Im Neuenheimer Feld 580 69120 Heidelberg Germany (1)
VIB Proteomics Core, VIB, Ghent, Belgium (1)
Institute of Cancer Research, London & Wellcome Trust Sanger Institute, Cambridge (1)
Lab head's proteomics and metabolomics program basic research 57357 (1)
Epithelial Systems Biology Laboratory National Heart, Lung, and Blood Institute National Institutes of Health U.S.A. (1)
New York University Abu Dhabi, Division of Biology, Saadiyaat Island, Abu Dhabi, United Arab Emirates New York University Abu Dhabi, Center of Genomics and System Biology, Saadiyaat Island, Abu Dhabi, United Arab Emirates (1)
Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 751 23 Uppsala, Sweden (1)
University of Vienna, Austria (1)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen Current affiliation: Evosep Aps, Denmark (1)
Parasitology Laboratory, Institute of Natural Resources and Agrobiology (IRNASA, CSIC). Cordel de Merinas, 40-52, 37008 Salamanca, Spain. (1)
Institute for Maternal and Child Health-IRCCS "Burlo Garofolo" (1)
Department of Molecular and Cellular Hemostasis, Sanquin Research Amsterdam, NL (1)
Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain; Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain. (1)
Weill Cornell Medical College in Qatar (1)
Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University (1)

IsPrivate

False (1)

Classification

bacteria (1)

Study type

Transcription profiling by array (19)
RNA-seq of coding RNA (8)
Spatial transcriptomics by high-throughput sequencing (2)
ChIP-chip by tiling array (1)
Transcription profiling by tiling array (1)
RNA-seq of coding RNA from single cells (1)
RNA-seq of non coding RNA (1)

Release Date

2025 (53)
2024 (39)
2023 (27)
2021 (25)
2022 (24)
2020 (15)
2026 (14)
2010 (14)
2019 (12)
2018 (11)
2016 (9)
2015 (9)
2017 (9)
2014 (8)
2013 (7)
2011 (4)
2009 (4)
2006 (3)
2012 (3)
2005 (1)

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Integrated metabolomics, transcriptomics and proteomics identifies metabolic pathways affected by Anaplasma phagocytophilum infection in tick cells

Anaplasma phagocytophilum is an emerging zoonotic pathogen that causes human granulocytic anaplasmosis. These intracellular bacteria establish infection by affecting cell function in both the vertebrate host and the tick vector, Ixodes scapularis. Previous studies have characterized the tick transcr...

ORGANISM(S): Ixodes scapularis

2016-01-06 | E-GEOD-68881 | biostudies-arrayexpress

Integration of cell-type resolved spatial proteomics and transcriptomics reveals novel mechanisms in early ovarian cancer

PRJNA1304545 | ENA

Multimodal integration of transcriptomics, proteomics and radiomics improves prediction of recurrence in patients with IDH-mutant Glioma

PRJNA939698 | ENA

Heart-muscle expression ratios in pig obtained by 454-sequencing, iTRAQ-based proteomics and cDNA microarrays

The recent development within high-throughput technologies for expression profiling has allowed for parallel analysis of transcriptomes and proteomes in biological systems such as comparative analysis of transcript and protein levels of tissue regulated genes. Until now, such studies of have only in...

ORGANISM(S): Sus scrofa

2009-01-22 | E-GEOD-10122 | biostudies-arrayexpress

Multi-omics analysis of thermogenic lipolysis in brown adipocytes

The integration of omics technologies into molecular biological research has transformed it into a field where a system can be investigated as a whole by combining information from multiple biochemical layers. This extension of traditional molecular biology, where various data sources are conside...

2025-11-12 | MTBLS12307 | MetaboLights

Identification and quantification of allele specific proteins and homeolog expression bias in an allopolyploid non-model crop by integrating transcriptomics and proteomics.

The fate of doubled genes, from allopolyploid or autopolyploid origin, is controlled at multiple levels within the central dogma: gene loss or silencing, neo- and/or sub functionalization, inter genomic transfer, allele dominance/co-dominance, differences in transcription/translation efficiency, pos...

ORGANISM(S): Musa acuminata subsp. malaccensis

2018-01-29 | PXD006375 | Pride

Integration of transcriptomics, proteomics, phosphoproteomics analysis for characterization of pulmonary arterial hypertension in Chinese people

PRJNA1138715 | ENA

Integration of transcriptomics, proteomics and loss-of-function screening reveals WEE1 as a target for combination with dasatinib against proneural glioblastoma.

Not available

S-EPMC12768573 | biostudies-literature

Integration of transcriptomics, proteomics and metabolomics data to reveal the biological mechanisms of abrin injury in human lung epithelial cells

we performed a comprehensive analysis of transcriptomics, proteomics and metabolomics on the potential mechanism of abrin injury in human lung epithelial cells.

ORGANISM(S): Homo Sapiens

2019-01-18 | PXD012435 |

Integration of cell-type resolved spatial proteomics and transcriptomics reveals novel mechanisms in early ovarian cancer.

Not available

S-EPMC12407665 | biostudies-literature

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581 Results

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