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Transcriptomics (1616)
Unknown (746)
Genomics (538)
Proteomics (308)
Models (8)
Genomic (1)
Methylation profiling (1)
Other (1)
Multiomics (1)
Metabolomics (1)

Organisms

Mus musculus (670)
Homo sapiens (619)
Danio rerio (61)
Rattus norvegicus (45)
Drosophila melanogaster (34)
Sus scrofa (30)
Bos taurus (29)
Gallus gallus (29)
Caenorhabditis elegans (19)
Saccharomyces cerevisiae (16)
Schizosaccharomyces pombe (12)
Heterocephalus glaber (10)
Arabidopsis thaliana (10)
Macaca mulatta (9)
Equus caballus (9)
Callithrix jacchus (7)
Chlorocebus sabaeus (7)
Hordeum vulgare (7)
Canis lupus familiaris (6)
Zea mays (6)
Macaca fascicularis (5)
Pan troglodytes (4)
Monodelphis domestica (4)
Gasterosteus aculeatus (4)
Salmo trutta (3)
Triticum turgidum subsp. durum (3)
Ornithorhynchus anatinus (3)
Mus musculus domesticus (3)
Oryctolagus cuniculus (3)
Bathyergus suillus (2)

Organisms

Mus musculus (144)
Homo sapiens (130)
Danio rerio (17)
Bos taurus (11)
Rattus norvegicus (11)
Gallus gallus (10)
Sus scrofa (7)
Drosophila melanogaster (3)
Equus caballus (3)
Ovis aries (3)
Triticum turgidum subsp. durum (2)
Astyanax mexicanus (2)
Canis lupus familiaris (2)
Caenorhabditis elegans (2)
Tursiops truncatus (1)
Chlorocebus aethiops (1)
Mustela putorius furo (1)
Sarcophilus harrisii (1)
Myodes glareolus (1)
Anolis carolinensis (1)
Culex quinquefasciatus (1)
Botrytis cinerea (1)
Cavia porcellus (1)
Mus (1)
Gasterosteus aculeatus (1)
Mus musculus domesticus (1)
Macaca mulatta (1)
Macaca fascicularis (1)
Xenopus laevis (1)
Fusarium graminearum PH-1 (1)

Repository

biostudies-arrayexpress (1543)
ENA (437)
pride (296)
geo (168)
BioModels (8)
EGA (8)
MassIVE (8)
jPOST (2)
dbGaP (1)
EVA (1)
iProX (1)
MetaboLights (1)

Tissue

Cell culture (42)
Brain (26)
Epithelial cell (26)
Liver (21)
Blood (15)
B cell (13)
Blood plasma (12)
Lung (12)
Plant cell (11)
Heart (10)
Kidney (8)
Testis (8)
Blood serum (7)
Inner ear (7)
Leaf (7)
Leukocyte (7)
Utricle (7)
Blood cell (6)
Primary cell (6)
Retina (6)
T cell (6)
Urine (6)
Bone marrow (5)
Permanent cell line cell (5)
Small intestine (5)
Spleen (5)
Cell suspension culture (4)
Colon (4)
Fibroblast (4)
Hepatocyte (4)

Disease

Disease free (14)
Acute leukemia (12)
Lung cancer (10)
Melanoma (7)
Breast cancer (3)
Chronic lymphocytic leukemia (3)
Colon cancer (3)
Non-small cell lung carcinoma (3)
Acute stress disorder (2)
Alzheimer's disease (2)
Brain cancer (2)
Brain glioblastoma multiforme (2)
Lung adenocarcinoma (2)
Osteosarcoma (2)
Ovarian cancer (2)
Permanent neonatal diabetes mellitus (2)
Severe acute respiratory syndrome (2)
Skin melanoma (2)
Small intestine neuroendocrine neoplasm (2)
Uveitis (2)
Hepatitis C infected (1)
Follicular lymphoma (1)
Breast adenocarcinoma (1)
Normal (1)
Acute myeloid leukemia (1)
Adenocarcinoma (1)
Anal gland adenocarcinoma (1)
Atrial fibrillation (1)
Autoimmune disease of eyes (1)
Autoimmune uveitis (1)

Technology Type

Mass Spectrometry (296)
Shotgun proteomics (179)
Bottom-up proteomics (58)
Data-dependent acquisition (35)
Affinity purification coupled with mass spectrometry proteomics (23)
Gel-based experiment (15)
Data-independent acquisition (14)
SWATH MS (10)
All-ion fragmentation (6)
Top-down proteomics (6)
Chemical cross-linking coupled with mass spectrometry proteomics (2)
Immunopeptidomics (2)
MSE (2)
RNA mass spectrometry (2)
SRM/MRM (2)
Illumina HiSeq 2000 (1)
Mass spectrometry (1)
Affinity proteomics (1)
DiaPASEF (1)
Proteogenomics (1)

Instrument Platform

Illumina NovaSeq 6000 (143)
NextSeq 500 (131)
Illumina HiSeq 2500 (114)
Illumina HiSeq 2000 (70)
Illumina HiSeq 4000 (62)
Illumina NovaSeq X (29)
NextSeq 2000 (29)
NextSeq 550 (19)
Illumina HiSeq 1500 (11)
DNBSEQ-G400 (10)
Illumina Genome Analyzer IIx (9)
Illumina HiSeq 3000 (9)
Ion Torrent Proton (5)
PromethION (4)
Illumina Genome Analyzer II (4)
N/A (4)
10x Chromium Controller (3)
Linux computer (3)
Racham server on Uppmax, NAISS (3)
FACS Aria-III (3)
Illumina MiSeq (3)
Pacbio Revio (2)
MA900, Sony (2)
10x Chromium (2)
10X Genomics Chromium (2)
BD FACS Aria III (2)
Fluidigm C1 (2)
None (2)
Linux Beowulf cluster; AMD Opteron Linux Beowulf cluster; AMD Opteron 6168 (2)
454 GS FLX+ (2)

Publication Date

2015 (261)
2014 (206)
2016 (203)
2013 (153)
2026 (130)
2024 (112)
2025 (111)
2021 (110)
2022 (105)
2023 (92)
2020 (90)
2012 (85)
2019 (82)
2018 (80)
2017 (80)
2011 (56)
2010 (38)
2009 (10)
2005 (9)
2008 (9)
2007 (3)
2004 (1)
2003 (1)

ENSEMBL ID

ENSBTAG00000027439.2 (1)
ENSBTAG00000019002.3 (1)
ENSBTAG00000039197.1 (1)
ENSBTAG00000016592.4 (1)
ENSBTAG00000038586.1 (1)
ENSBTAG00000035544.2 (1)
ENSBTAG00000016679.4 (1)
ENSBTAG00000011545.3 (1)
ENSBTAG00000001124.4 (1)
ENSBTAG00000011197.4 (1)
ENSBTAG00000016432.4 (1)
ENSBTAG00000014841.4 (1)
ENSBTAG00000015596.4 (1)
ENSBTAG00000014775.4 (1)
ENSBTAG00000020902.4 (1)
ENSBTAG00000030358.2 (1)
ENSBTAG00000006463.4 (1)
ENSBTAG00000006029.3 (1)
ENSBTAG00000014179.4 (1)
ENSBTAG00000021417.4 (1)
ENSBTAG00000001299.4 (1)
ENSBTAG00000004059.3 (1)
ENSBTAG00000015188.3 (1)
ENSBTAG00000008567.4 (1)
ENSBTAG00000015164.4 (1)
ENSBTAG00000012858.3 (1)
ENSBTAG00000007228.4 (1)
ENSBTAG00000006066.4 (1)
ENSBTAG00000030852.2 (1)
ENSBTAG00000008636.4 (1)

CHEBI ID

CHEBI:85684 (1)
CHEBI:85721 (1)
CHEBI:87239 (1)
CHEBI:85682 (1)
CHEBI:142374 (1)
CHEBI:167289 (1)
CHEBI:167288 (1)
CHEBI:167293 (1)
CHEBI:167291 (1)
CHEBI:167292 (1)
CHEBI:142372 (1)
CHEBI:167290 (1)
CHEBI:136199 (1)
CHEBI:136202 (1)
CHEBI:140496 (1)
CHEBI:167287 (1)
CHEBI:167285 (1)
CHEBI:167286 (1)
CHEBI:167283 (1)
CHEBI:167284 (1)
CHEBI:140354 (1)
CHEBI:138905 (1)
CHEBI:131536 (1)
CHEBI:131540 (1)
CHEBI:167035 (1)
CHEBI:155818 (1)
CHEBI:155817 (1)
CHEBI:141312 (1)
CHEBI:138916 (1)
CHEBI:167041 (1)

Metabolite Name

PE P-18:0/22:5 (1)
PE P-18:0/22:6 (1)
PE P-18:0/20:1 (1)
PE P-18:0/20:2 (1)
PE P-18:0/20:3 (1)
PE P-18:0/20:5 (1)
PE P-18:0/18:1 (1)
PE P-18:0/18:2 (1)
PE P-18:1/22:5 (1)
PE P-18:1/22:6 (1)
PE P-18:1/20:2 (1)
PE P-18:1/20:3 (1)
PE P-16:0/22:1 (1)
PE P-16:0/22:2 (1)
PE P-16:0/22:3 (1)
PE P-16:0/22:4 (1)
PE P-16:0/22:6 (1)
PE P-16:0/20:1 (1)
PE P-16:0/20:3 (1)
PE P-16:0/20:5 (1)
PE P-16:0/18:1 (1)
PE P-16:0/18:2 (1)
PE P-18:0/22:4 (1)
PE P-16:0/20:4 (1)
PE P-18:0/20:4 (1)
PE P-18:1/20:4 (1)
PE P-18:1/18:2 (1)
PE P-18:1/18:1 (1)

First Public Date

2021 (49)
2024 (45)
2020 (40)
2022 (39)
2026 (37)
2023 (34)
2014 (34)
2025 (32)
2019 (31)
2018 (26)
2017 (25)
2015 (15)
2016 (14)
2013 (11)
2011 (2)
2010 (2)
2012 (1)

Modelling Approach

Constraint-based model (1)

Lab affiliation

Institute of Molecular Biology (IMB) (6)
Dept. Oncology Pathology, Karolinska Institutet, and Scilifelab, Stockholm, Sweden (5)
Research Unit Protein Science, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Germany (5)
Oregon Hearing Research Center Oregon Health & Science University Portland, OR, USA (4)
Center for Systems and Synthetic Biology Institute for Cellular and Molecular Biology Department of Molecular Biosciences University of Texas at Austin (2)
Chair of Physiology, Department of Veterinary Sciences, LMU Munich (2)
Department of Biology, University of Bergen, Bergen, Norway (2)
Department of Oncology Pathology, Karolinska Institute, Solna, Sweden (2)
Department of Oncology-Pathology, Karolinska Institute and Scilifelab, Solna, Sweden (2)
Department of Oncology-Pathology, SciLifeLab, Karolinska Institutet (2)
Department of Plant and Environmental Sciences, Aharoni lab, Weizmann Institute of Science (2)
Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec and Prague, Czech Republic (2)
Dept. Oncology Pathology, Science for Life Laboratory, Karolinska Institutet, Sweden (2)
EMBL-EBI (2)
Faculty of Medicine and University Hospital of Cologne, Institute of Pathology, University of Cologne, Cologne, Germany (2)
Fraunhofer Attract Eco’n’OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Auf dem Aberg 1, 57392 Schmallenberg. (2)
IMB, Ackermannweg 4, 55128 Mainz (2)
Institute of Molecular Biology (IMB) Ackermannweg 4 55128 Mainz (2)
Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems,Germany (2)
Institute of genetics and developmental biology (2)
Karolinska Institutet, Department of Oncology-Pathology (OnkPat) (2)
Microbiologie, Adaptation et Pathogénie, UMR 5240, Univ Lyon, Université Lyon 1, Bayer SAS, Lyon, France. (2)
National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, China (2)
Oregon Hearing Research Center Oregon Health & Science University Portland OR 97239 (2)
Science for Life Laboratory; Department of Oncology Pathology, Karolinska Institute, Stockholm, Sweden (2)
Sun yat-sen university cancer center (2)
TTUHSC Cell Biology and Biochemistry Lubbock, TX, USA (2)
Tongji University (2)
VIB Midical Biotechnology Center, University of Gent, Belgium (2)
1 Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland 2 Faculty of Science, University of Zurich, Zurich, Switzerland (1)

Tags

xref:PubMed:35088629 (3)
xref:PubMed:31168962 (3)
xref:PubMed:32755574 (3)
xref:PubMed:29364867 (3)
xref:PubMed:29986096 (3)
xref:PubMed:33378683 (2)
xref:PubMed:33935720 (2)
xref:PubMed:39706164 (2)
xref:PubMed:36476855 (2)
xref:PubMed:36389786 (2)
xref:PubMed:37702745 (2)
xref:PubMed:29661169 (2)
xref:PubMed:33235333 (2)
xref:PubMed:34197724 (2)
xref:PubMed:37015057 (2)
xref:PubMed:33979605 (2)
xref:PubMed:36289348 (2)
xref:PubMed:33479702 (2)
xref:PubMed:32762937 (2)
xref:PubMed:18776931 (2)
xref:PubMed:24699212 (2)
xref:PubMed:40885711 (2)
xref:PubMed:16925838 (2)
xref:PubMed:38786017 (2)
xref:PubMed:40855070 (2)
xref:PubMed:39093347 (2)
xref:PubMed:25402615 (2)
xref:ArrayExpress:E-MTAB-3188 (1)
xref:ArrayExpress:E-MTAB-975 (1)
xref:ArrayExpress:E-MTAB-831 (1)

IsPrivate

False (8)

Model Flag

Non Kinetic (7)

Submitter Keywords

FROG (1)

Classification

fungi (1)

Modification

2x(15)N labeled L-lysine (2)
4x(15)N labeled L-arginine (2)
4-tetrahydrothiazine-3-carboxylic acid (1)

Study type

RNA-seq of coding RNA (935)
Transcription profiling by array (158)
RNA-seq of coding RNA from single cells (122)
ChIP-seq (70)
RNA-seq of non coding RNA (59)
RNA-seq of total RNA (39)
Other (23)
Animal - High-throughput sequencing (16)
Cell line - High-throughput sequencing (14)
Comparative genomic hybridization by array (14)
Human - High-throughput sequencing (11)
High-throughput sequencing (8)
Methylation profiling by high throughput sequencing (8)
DNA-seq (7)
RIP-seq (6)
Unknown experiment type (5)
MicroRNA profiling by high throughput sequencing (5)
ATAC-seq (5)
Ribo-seq (5)
CLIP-seq (4)
Methylation profiling by array (3)
Cell line - Single-cell sequencing (2)
Baseline (2)
Animal - Single-cell sequencing (2)
Genotyping by array (2)
Spatial transcriptomics by high-throughput sequencing (2)
Single nucleus RNA sequencing (2)
Genotyping by high throughput sequencing (2)
Null (1)
Transcription profiling by SAGE (1)

Release Date

2015 (271)
2014 (216)
2016 (206)
2013 (167)
2023 (163)
2022 (137)
2024 (127)
2025 (115)
2021 (110)
2019 (104)
2026 (99)
2012 (95)
2020 (91)
2018 (85)
2011 (80)
2017 (69)
2010 (58)
2009 (25)
2008 (21)
2007 (14)
2006 (10)
2005 (9)
2004 (9)
2002 (4)
2003 (3)
2001 (1)

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Triticeae resources in Ensembl Plants.

Not available

S-EPMC4301745 | biostudies-literature

prj_GCA_052040795.2-Ensembl-2026-09

Annotation evidence project for GCA_052040795.2, GCA_052040795.2-Ensembl-2026-09

PRJEB128123 | ENA

Generation of ENSEMBL-based proteogenomics databases boost the identification of novel peptides

A novel bioinformatics tool pypgatk and the pgdb workflow is presented in study to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, an...

ORGANISM(S): Homo sapiens (Human)

2021-10-26 | PXD029360 | Pride

Ensembl Reanalysis Proteogenomics

The Ensembl REST API: Ensembl Data for Any Language.

Not available

S-EPMC4271150 | biostudies-literature

Not available

S-EPMC7778975 | biostudies-literature

Not available

S-EPMC8728283 | biostudies-literature

Not available

S-EPMC6323964 | biostudies-literature

Not available

S-EPMC4383879 | biostudies-literature

Not available

S-EPMC9825606 | biostudies-literature

Not available

S-EPMC7145704 | biostudies-literature

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OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

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