Ontology - OmicsDI

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Unknown (22397)
Genomics (3848)
Transcriptomics (3571)
Proteomics (2298)
Methylation profiling (101)
Other (38)
Metabolomics (32)
Models (3)
Genomic (2)
Clinical (2)
Multiomics (2)

Organisms

Homo sapiens (1618)
Mus musculus (978)
Rattus norvegicus (264)
Danio rerio (97)
Bos taurus (94)
Sus scrofa (85)
Arabidopsis thaliana (64)
Gallus gallus (56)
Drosophila melanogaster (50)
Saccharomyces cerevisiae (44)
Oryza sativa (30)
Ovis aries (30)
Taeniopygia guttata (28)
Oryza sativa Japonica Group (26)
Oncorhynchus mykiss (22)
Caenorhabditis elegans (22)
Zea mays (19)
Triticum aestivum (19)
Glycine max (13)
Macaca mulatta (13)
Vitis vinifera (13)
Salmo salar (13)
Solanum lycopersicum (13)
Xenopus laevis (12)
Oryza sativa Indica Group (9)
Pimephales promelas (9)
Escherichia coli (8)
Apis mellifera (8)
Hordeum vulgare (7)
Brassica napus (6)

Organisms

Homo sapiens (1149)
Mus musculus (715)
Rattus norvegicus (189)
Danio rerio (64)
Sus scrofa (60)
Bos taurus (59)
Gallus gallus (38)
Drosophila melanogaster (35)
Arabidopsis thaliana (31)
Oncorhynchus mykiss (20)
Ovis aries (20)
Saccharomyces cerevisiae (18)
Oryza sativa (17)
Caenorhabditis elegans (14)
Equus caballus (12)
Gossypium hirsutum (10)
Taeniopygia guttata (9)
Triticum aestivum (9)
Zea mays (9)
Vitis vinifera (8)
Canis lupus familiaris (8)
Solanum lycopersicum (8)
Candida albicans (8)
Oryza sativa Japonica Group (8)
Macaca mulatta (7)
Xenopus laevis (7)
Salmo salar (6)
Glycine max (6)
Paramphistomum cervi (5)
Folsomia candida (5)

Repository

ENA (3533)
geo (2533)
pride (1997)
biostudies-arrayexpress (1479)
iProX (184)
MassIVE (63)
jPOST (28)
MetaboLights (28)
PAXDB (14)
EGA (10)
PeptideAtlas (7)
GPMDB (5)
GNPS (4)
BioModels (3)
NODE (3)
dbGaP (2)
PanoramaPublic (2)

Tissue

Cell culture (392)
Brain (155)
Epithelial cell (118)
Leaf (77)
Liver (70)
Blood plasma (64)
Plant cell (62)
Whole body (59)
Heart (52)
Lung (46)
Blood serum (44)
Fibroblast (44)
Blood (38)
Root (38)
Permanent cell line cell (37)
Stem cell (35)
Macrophage (34)
Kidney (33)
Colon (31)
Skin (30)
Blood cell (28)
Cell suspension culture (28)
T cell (23)
Hepatocyte (22)
Primary cell (22)
Testis (22)
Urine (18)
Bone marrow (17)
Pancreas (2)
Breast (1)

Disease

Breast cancer (54)
Amyotrophic lateral sclerosis (7)
Normal (6)
Rheumatoid arthritis (2)
Cervical carcinoma (2)
Temporal lobe epilepsy (2)
Benign prostatic hyperplasia (2)
Early onset preeclampsia (1)
Burn injury (1)
Mantle cell lymphoma (1)
Androgen-dependent prostate cancer (1)
Keratoconus (1)
Advanced atherosclerosis (1)
Pneumococcal meningitis (1)
Dystrophic (1)
TAC operated 5 hours after surgery (1)
Scrapie infected (1)
Cancer cell line pool (1)
Critical chronic obstructive pulmonary disease (1)
SS2-infected (1)
Pre-diabetic (1)
Unaffected (1)
Chronic myelogenous leukemia (1)
Reference (1)
Diabetes (1)
Prostate cancer (1)
Infected by E. lata strain NE85-1 (1)
Adenocarcinoma (1)
Control (1)
Cervical cancer (1)

Technology Type

Mass Spectrometry (1997)
Shotgun proteomics (1171)
Bottom-up proteomics (432)
Data-dependent acquisition (212)
Data-independent acquisition (129)
Affinity purification coupled with mass spectrometry proteomics (109)
Gel-based experiment (89)
SWATH MS (75)
Top-down proteomics (59)
Mass spectrometry (19)
Chemical cross-linking coupled with mass spectrometry proteomics (18)
SRM/MRM (17)
DiaPASEF (12)
All-ion fragmentation (11)
Mass spectrometry imaging (10)
HDMSE (9)
Mass spectrometry assay (7)
Affinity proteomics (6)
MSE (5)
Proteogenomics (3)
NMR spectroscopy assay (2)
Immunopeptidomics (2)
Illumina HiSeq 2000 (1)
PAcIFIC (1)
RNA mass spectrometry (1)

Instrument Platform

Illumina NovaSeq 6000 (32)
Illumina HiSeq 2000 (21)
Illumina HiSeq 2500 (14)
NextSeq 500 (11)
Illumina HiSeq 4000 (10)
Dell PowerEdge R750; CPU: 2 × Intel Xeon Gold 6346 (32 Cores / 64 Threads); RAM: 188 GB (6)
NucleoSpin RNA/Protein kit lysis buffer (350 µL per tube; Macherey‑Nagel). (5)
Illumina Genome Analyzer IIx (5)
See manuscript (4)
NextSeq 550 (4)
FastPrep‑24 homogenizer (MP Biomedicals) (3)
Illumina Genome Analyzer II (3)
NextSeq 2000 (3)
FastPrep‑24 homogenizer (MP Biomedicals), operated at 5 m/s for 10 seconds. (2)
Scanning hardware (2)
Illumina NovaSeq X (2)
Nanodrop (1)
Agilent 2100 Bioanalyzer (Agilent Technologies); Qubit Fluorometer (Thermo Fisher Scientific); standard electrophoresis system (1)
NanoDrop spectrophotometer, Agilent 2100 Bioanalyzer (1)
Nanodrop 2000c spectrophotometer (1)
Illumina NovaSeq 6000 sequencing platform (Illumina) (1)
Thermal cycler, Agilent BioAnalyzer 2100 (1)
Microcentrifuge, vortex spinner, pipettes, -80C freezer (1)
Zeiss Stereomicroscope, standard lab plasticware (1)
VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme); manual library preparation (1)
Agilent 2200 TapeStation system; centrifuge; Trizol reagent (1)
Flow cytometer (for CD146+/- cell sorting) (1)
RapidPURE RNA Plant Kit (MP Biomedicals, Illkirch, France) (1)
FastPrep-24 homogeniser (1)
Computer (1)

Publication Date

2025 (569)
2022 (563)
2021 (484)
2026 (458)
2024 (449)
2023 (432)
2020 (384)
2019 (322)
2014 (314)
2015 (284)
2013 (269)
2018 (248)
2012 (244)
2016 (239)
2010 (231)
2011 (197)
2017 (193)
2008 (166)
2009 (119)
2007 (99)
2006 (36)
2005 (21)
2004 (6)
2003 (4)

UNIPROT ID/AC

35KD_MYCTU (3)
6PGL_MYCTU (3)
A85A_MYCTU (3)
A85B_MYCTU (3)
A85C_MYCTU (3)
ACCD_MYCTU (3)
ACDH_MYCTU (3)
ACDP_MYCTU (3)
ACEA_MYCTU (3)
ACG_MYCTU (3)
ACNA_MYCTU (3)
ACPM_MYCTU (3)
ACPS_MYCTU (3)
ACR_MYCTU (3)
ACYP_MYCTU (3)
ADD_MYCTU (3)
ADHB_MYCTU (3)
ADHC_MYCTU (3)
ADOK_MYCTU (3)
AHPC_MYCTU (3)
AHPD_MYCTU (3)
AHPE_MYCTU (3)
AK_MYCTU (3)
ALDH_MYCTU (3)
ALF_MYCTU (3)
ALR_MYCTU (3)
AMI4_MYCTU (3)
P03034 (1)
P04483 (1)
P03023 (1)

ENSEMBL ID

ENSMUSG00000098557 (2)
ENSMUSP00000141097 (2)
ENSMUSP00000141542 (2)
ENSG00000147251 (1)
ENSG00000170477 (1)
ENSG00000229353 (1)

CHEBI ID

CHEBI:17620 (10)
CHEBI:30769 (9)
CHEBI:22660 (8)
CHEBI:6650 (8)
CHEBI:17992 (7)
CHEBI:17822 (7)
CHEBI:26271 (7)
CHEBI:16811 (7)
CHEBI:28044 (7)
CHEBI:15741 (7)
CHEBI:18012 (7)
CHEBI:22653 (7)
CHEBI:28300 (6)
CHEBI:16119 (6)
CHEBI:30763 (6)
CHEBI:16704 (6)
CHEBI:17533 (6)
CHEBI:18237 (6)
CHEBI:16856 (6)
CHEBI:27897 (6)
CHEBI:17596 (6)
CHEBI:18344 (6)
CHEBI:20386 (5)
CHEBI:28238 (5)
CHEBI:22470 (5)
CHEBI:30778 (5)
CHEBI:50202 (5)
CHEBI:36090 (5)
CHEBI:30816 (5)
CHEBI:33699 (1)

Metabolite Name

Methionine (6)
Serine (5)
Threonine (5)
Proline (5)
Phenylalanine (5)
Glutamine (5)
Cytidine (4)
Uracil (4)
Kynurenic acid (4)
Pantothenic acid (4)
Asparagine (4)
Tryptophan (4)
Trans-astringin (3)
Chlorogenic acid (3)
2,6-diaminopimelic acid (3)
Hydrocinnamic acid (3)
Resveratrol (3)
N-acetylputrescine (3)
Alpha-tocopherol (3)
Phenylacetaldehyde (3)
Leucine (3)
Glycine (3)
Uridine (3)
Taurine (3)
Proline (3)
N-acetylglutamate (3)
Guanosine (3)
Guanine (3)
Asparagine (3)
Glycerol (3)

First Public Date

2014 (603)
2025 (364)
2024 (351)
2021 (320)
2022 (275)
2023 (274)
2020 (266)
2026 (262)
2019 (210)
2018 (161)
2017 (143)
2015 (125)
2013 (89)
2016 (85)
2012 (3)
2011 (2)

Modelling Approach

Ordinary differential equation model (2)
Other (1)

Study status

Recruiting (2)

Lab affiliation

CRUK Scotland Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (6)
Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Republic of Korea (6)
First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (5)
Instituto de Investigaciones Sanitarias de Santiago de Compostela (5)
Professor (5)
State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China (5)
1 Department of Cardiac Surgery, Fujian Medical University Union Hospital, Fuzhou, China 2 Department of Toxicology, Fujian Center for Evaluation of New Drug, Fujian Medical University, Fuzhou, China (4)
1VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium 2Department of Biomolecular Medicine, Ghent University, 9052 Ghent, Belgium (4)
DEPARTMENT OF MEDICINE, ALL INDIA INSTITUTE OF MEDICAL SCIENCES, ANSARI NAGAR, NEW DELHI-110029 (4)
Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg im Breisgau, Germany (4)
Emmy-Noether Research Group Cellular Proteomics and Metabolic Signaling Institute for Diabetes and Obesity Helmholtz Diabetes Center Germany (4)
Key Lab of Integrated Crop Pest Management of Shandong, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China (4)
Nantong Key Laboratory of Environmental Toxicology, Department of Occupational Medicine and Environmental Toxicology, School of Public Health, Nantong University, Nantong, China (4)
Northwest University (4)
Shandong University (4)
Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China (4)
Agronomy College, Henan Agricultural University, China (3)
China Agricultural University (3)
College of Veterinary Medicine, Northwest A&F University (3)
Department of Cell Biology, Harvard Medical School, USA (3)
Department of Glycobiology, Institute of Chemistry, Slovak Academy of Sciences (3)
Department of Molecular & Clinical Cancer Medicine Institute of Systems, Molecular & Integrative Biology University of Liverpool (3)
Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea (3)
Functional proteomics group; Molecular Biomedicine department; CIB-CSIC (3)
Hadassah Hebrew-University Medical Center (3)
IRCCS Istituto G Gaslini (3)
IRCCS Istituto Giannina Gaslini (3)
Institute of Cellular Biology and Pathology (3)
Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (3)
National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, 5 Dong Dan San Tiao, Dongcheng District, Beijing 100005, China. (3)

IsPrivate

False (3)

Classification

bacteria (29)
fungi (18)
protozoa (12)
helminths (3)

Modification

2x(15)N labeled L-lysine (3)
4x(15)N labeled L-arginine (3)
4-tetrahydrothiazine-3-carboxylic acid (2)
N6 (2)
N6-dimethyl-L-lysine (2)
15.99491 (1)
3'' (1)
4x(2)H labeled dimethylated residue (1)
57.02146 (1)

Study type

Transcription profiling by array (1053)
RNA-seq of coding RNA (232)
Unknown experiment type (34)
Methylation profiling by array (34)
ChIP-seq (30)
RNA-seq of non coding RNA (21)
Transcription profiling by SAGE (10)
RNA-seq of coding RNA from single cells (9)
Methylation profiling by high throughput sequencing (9)
ChIP-chip by tiling array (7)
Comparative genomic hybridization by array (7)
RNA-seq of total RNA (7)
Animal - High-throughput sequencing (4)
Animal - One-color microarray (2)
Cell line - One-color microarray (2)
Human - One-color microarray (2)
Transcription profiling by tiling array (2)
Transcription profiling by RT-PCR (2)
MicroRNA profiling by high throughput sequencing (2)
Other (2)
Interventional (2)
Animal - Two-color microarray (1)
Cell line - Two-color microarray (1)
Cell line - High-throughput sequencing (1)
ChIP-chip by array (1)
Bisulfite-seq (1)
MicroRNA profiling by array (1)

Release Date

2022 (3215)
2021 (2578)
2023 (2486)
2020 (2127)
2025 (1931)
2024 (1863)
2019 (1547)
2018 (1181)
2017 (945)
2016 (945)
2015 (915)
2014 (732)
2013 (697)
2012 (554)
2010 (458)
2011 (431)
2008 (312)
2009 (303)
2026 (209)
2007 (203)
2006 (114)
2005 (75)
2004 (32)
2003 (16)
2002 (5)
2001 (1)
2000 (1)

Location

Japan (2)

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The ontology of the gene ontology.

Not available

S-EPMC1480173 | biostudies-literature

The Gene Ontology project in 2008.

Not available

S-EPMC2238979 | biostudies-literature

The Gene Ontology Resource: 20 years and still GOing strong.

Not available

S-EPMC6323945 | biostudies-literature

Creating the gene ontology resource: design and implementation.

Not available

S-EPMC311077 | biostudies-literature

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Not available

S-EPMC4932724 | biostudies-literature

The Gene Ontology of eukaryotic cilia and flagella.

Not available

S-EPMC5688719 | biostudies-literature

Evaluating and Extending the Informed Consent Ontology for Representing Permissions from the Clinical Domain.

Not available

S-EPMC9616177 | biostudies-literature

Annotation of gene product function from high-throughput studies using the Gene Ontology.

Not available

S-EPMC6355445 | biostudies-literature

Transcriptomic and gene ontology profiling of the human corneal cell types

PRJNA499078 | ENA

Gene expression and gene ontology analysis of the transcriptional changes occurring in spinal cord from the G93A SOD1 gene mutant rat

We have investigated the process of disease-induced functional perturbation and the related transcriptional changes occurring in thoraco-lumbar spinal cord extracted from Sprague-Dawley rats heterozygous for the G93A SOD1 gene mutation (Emerging Model 2148 Het Male, Taconic USA; Wyeth and Amyotrophi...

ORGANISM(S): Rattus norvegicus

2010-06-23 | E-GEOD-20894 | biostudies-arrayexpress

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