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Unknown (47342)
Genomics (4171)
Transcriptomics (3309)
Proteomics (1463)
Metabolomics (475)
Other (112)
Methylation profiling (57)
Models (45)
Genomic (9)
Clinical (9)
Multiomics (7)

Organisms

Homo sapiens (2493)
Mus musculus (1221)
Pan troglodytes (241)
Drosophila melanogaster (133)
Macaca mulatta (104)
Rattus norvegicus (64)
Arabidopsis thaliana (56)
Danio rerio (49)
Saccharomyces cerevisiae (45)
Caenorhabditis elegans (35)
Gallus gallus (33)
Sus scrofa (23)
Escherichia coli (21)
Bos taurus (21)
Methanococcus maripaludis S2 (17)
Oryza sativa (17)
Schizosaccharomyces pombe (16)
Streptomyces coelicolor (15)
Oryza sativa Japonica Group (9)
Sinorhizobium meliloti (9)
Mycobacterium tuberculosis (9)
Hordeum vulgare (9)
cellular organisms (8)
Severe acute respiratory syndrome-related coronavirus (1)
Hepatitis B virus (1)
Methanothermobacter thermautotrophicus (1)
Methanothermobacter marburgensis str. Marburg (1)
Methanothermobacter thermautotrophicus str. Delta H (1)
Dehalococcoides (1)
Lutzia (1)

Organisms

Homo sapiens (741)
Mus musculus (344)
Sorghum bicolor (122)
Panicum hallii (87)
seawater metagenome (74)
Pan troglodytes (43)
Drosophila melanogaster (40)
Halobacterium salinarum NRC-1 (34)
Caenorhabditis elegans (24)
Kingella kingae 11220434 (23)
Acinetobacter baumannii (16)
Pan paniscus (13)
Rattus norvegicus (13)
salt pan metagenome (12)
Escherichia coli (11)
Pseudomonas aeruginosa (10)
Klebsiella pneumoniae (10)
Severe acute respiratory syndrome coronavirus 2 (9)
Arabidopsis thaliana (9)
Saccharomyces cerevisiae (9)
Mycoplasma mycoides subsp. mycoides (8)
Danio rerio (8)
Gallus gallus (8)
soil metagenome (8)
Vibrio alginolyticus (7)
unidentified (7)
Cenchrus americanus (6)
Gossypium hirsutum (6)
Sus scrofa (5)
Aggregatibacter actinomycetemcomitans (4)

Repository

ENA (3151)
biostudies-arrayexpress (2839)
geo (1332)
pride (832)
MetaboLights (468)
iProX (326)
EGA (254)
MassIVE (178)
EVA (67)
jPOST (41)
PeptideAtlas (40)
BioModels (33)
PAXDB (28)
PanoramaPublic (12)
PMR (11)
dbGaP (9)
NODE (9)
GNPS (7)
ExpressionAtlas (3)
Cell Collective (1)
GPMDB (1)

Tissue

Cell culture (211)
Epithelial cell (67)
Brain (50)
Liver (41)
B cell (39)
Blood (36)
Lung (33)
Kidney (23)
Blood plasma (23)
Permanent cell line cell (23)
Skin (19)
Others (10)
Uterine cervix (2)
Breast (2)
Esophagus (2)
Mouth mucosa (2)
Large intestine (2)
Stomach (2)
Pancreas (2)
Ovary (2)
Uterus (2)
Skeletal muscle tissue (2)
Urinary bladder (2)
Prostate gland (2)
Thyroid gland (2)
Prefrontal Cortex (2)
Cerebrospinal fluid (1)
SK-N-SH cell line (1)
Female Reproductive System (1)
Ovary (1)

Disease

Lymphoma (15)
Melanoma (11)
Chronic lymphocytic leukemia (8)
Lung adenocarcinoma (7)
Hepatocellular carcinoma (6)
Cholangiocarcinoma (6)
Renal cell carcinoma (2)
Pancreatic adenocarcinoma (2)
Follicular thyroid carcinoma (2)
Cervical adenocarcinoma (2)
Glioblastoma multiforme (2)
Colorectal adenocarcinoma (2)
Chromophobe renal cell carcinoma (2)
Gastric adenocarcinoma (2)
Prostate adenocarcinoma (2)
Sarcoma (2)
Endometrial adenocarcinoma (2)
Bladder transitional cell carcinoma (2)
Invasive lobular carcinoma (2)
Glioma (2)
Head and neck squamous cell carcinoma (2)
Squamous cell lung carcinoma (2)
Cervical squamous cell carcinoma (2)
Ovarian adenocarcinoma (2)
Esophageal adenocarcinoma (2)
B-cell non-Hodgkin lymphoma (2)
Breast adenocarcinoma (2)
Normal - esophagus muscularis mucosa (GTEx) (1)
Normal - uterus (GTEx) (1)
Normal - adjacent to lung adenocarcinoma (1)

Technology Type

Mass Spectrometry (832)
Shotgun proteomics (436)
Mass spectrometry (255)
Mass spectrometry assay (207)
Bottom-up proteomics (142)
Affinity purification coupled with mass spectrometry proteomics (138)
Data-dependent acquisition (81)
SWATH MS (55)
Gel-based experiment (40)
Data-independent acquisition (22)
Top-down proteomics (14)
Immunopeptidomics (13)
NMR spectroscopy (10)
Illumina HiSeq 2000 (4)
Illumina HiSeq 2000, ILLUMINA (2)
Illumina MiSeq, NextSeq 500, ILLUMINA (1)
ILLUMINA, Illumina HiSeq 2500, HiSeq X Ten, Illumina HiSeq 2000 (1)
Patented mSMRT-qPCR miRNA assay (MIRXES), Affymetrix Human Gene 1.0 ST Array, Agilent 1200 LC system, Illumina 2.5M and Illumina Exome array (1)
Illumina Multi-EthnicGlobal_A1 (1)
OXFORD_NANOPORE, MinION (1)
ILLUMINA, Illumina HiSeq 4000, Illumina MiSeq (1)
Illumina HiSeq 2500, ILLUMINA (1)
Illumina HiSeq 2500 (ILLUMINA) (1)
ILLUMINA, RNAseq, Illumina HiSeq 2000, Illumina Human Methylation 450k BeadChip (1)
Illumina HiSeq 2000, NextSeq 500, ILLUMINA (1)
Illumina Genome Analyzer IIx, Illumina HiSeq 2000 (1)
Illumina HiSeq 2500 (1)
Illumina Genome Analyzer II, Illumina HiSeq 2000 (1)
Whole Genome Sequencing (1)
NMR spectroscopy assay (1)

Instrument Platform

Illumina NovaSeq 6000 (506)
NextSeq 500 (129)
Illumina NovaSeq X (122)
NextSeq 2000 (97)
Illumina HiSeq 2000 (86)
Illumina HiSeq 2500 (79)
Illumina HiSeq 4000 (72)
NextSeq 550 (68)
DNBSEQ-G400 (29)
Illumina MiSeq (27)
NA (22)
Element AVITI (14)
None (11)
Illumina HiSeq X (10)
BGISEQ-500 (10)
DNBSEQ-T7 (9)
Illumina HiSeq 3000 (9)
PromethION (8)
N/A (8)
Illumina HiSeq 1500 (8)
Dell PowerEdge R750; CPU: 2 × Intel Xeon Gold 6346 (32 Cores / 64 Threads); RAM: 188 GB (7)
Illumina Genome Analyzer II (7)
NextSeq 1000 (7)
NucleoSpin RNA/Protein kit lysis buffer (350 µL per tube; Macherey‑Nagel). (6)
Chromium 10x (6)
10x Genomics Chromium (6)
None (6)
HiSeq X Ten (6)
See manuscript (5)
Racham server on Uppmax, NAISS (5)

Publication Date

2025 (1004)
2026 (1001)
2024 (429)
2023 (379)
2022 (325)
2021 (304)
2016 (268)
2010 (239)
2015 (238)
2020 (234)
2014 (233)
2011 (231)
2013 (229)
2012 (218)
2019 (212)
2018 (141)
2008 (106)
2017 (87)
2009 (64)
2007 (38)
2006 (30)
2005 (19)
2004 (4)
2003 (2)
2027 (1)

UNIPROT ID/AC

1433B_HUMAN (12)
1433E_HUMAN (12)
1433F_HUMAN (12)
1433G_HUMAN (12)
1433S_HUMAN (12)
1433T_HUMAN (12)
1433Z_HUMAN (12)
2AAA_HUMAN (12)
3HIDH_HUMAN (12)
4F2_HUMAN (12)
5NTD_HUMAN (12)
9606.ENSP00000291295 (12)
9606.ENSP00000330842 (12)
9606.ENSP00000347168 (12)
9606.ENSP00000348924 (12)
9606.ENSP00000349467 (12)
9606.ENSP00000352119 (12)
9606.ENSP00000352627 (12)
9606.ENSP00000355778 (12)
9606.ENSP00000358154 (12)
9606.ENSP00000358160 (12)
9606.ENSP00000364802 (12)
9606.ENSP00000366679 (12)
9606.ENSP00000366956 (12)
9606.ENSP00000366962 (12)
9606.ENSP00000366974 (12)
9606.ENSP00000366999 (12)
P10276 (1)
P0A6P1 (1)
P0CE47 (1)

ENSEMBL ID

ENSPTRG00000006370.4 (1)
ENSPTRG00000002585.5 (1)
ENSPTRG00000000202.3 (1)
ENSPTRG00000011379.2 (1)
ENSPTRG00000007314.4 (1)
ENSPTRG00000005135.4 (1)
ENSPTRG00000001888.4 (1)
ENSPTRG00000023766.2 (1)
ENSPTRG00000007287.5 (1)
ENSPTRG00000002829.4 (1)
ENSPTRG00000008466.4 (1)
ENSPTRG00000003451.4 (1)
ENSPTRG00000024082.4 (1)
ENSPTRG00000002599.3 (1)
ENSPTRG00000021736.4 (1)
ENSPTRG00000022287.4 (1)
ENSPTRG00000011025.4 (1)
ENSPTRG00000018372.4 (1)
ENSPTRG00000001003.3 (1)
ENSPTRG00000008789.1 (1)
ENSPTRG00000007616.2 (1)
ENSPTRG00000014174.3 (1)
ENSPTRG00000014450.5 (1)
ENSPTRG00000034370.1 (1)
ENSPTRG00000015718.4 (1)
ENSPTRG00000008919.5 (1)
ENSPTRG00000014468.4 (1)
ENSPTRG00000017776.5 (1)
ENSPTRG00000005364.3 (1)
ENSPTRG00000009395.3 (1)

CHEBI ID

CHEBI:58201 (17)
CHEBI:50606 (17)
CHEBI:16659 (17)
CHEBI:57692 (17)
CHEBI:57986 (17)
CHEBI:57451 (17)
CHEBI:58433 (17)
CHEBI:58762 (17)
CHEBI:58443 (17)
CHEBI:57328 (17)
CHEBI:58525 (17)
CHEBI:57597 (17)
CHEBI:57502 (17)
CHEBI:58228 (17)
CHEBI:58115 (17)
CHEBI:57967 (17)
CHEBI:37563 (17)
CHEBI:58069 (17)
CHEBI:57623 (17)
CHEBI:58057 (17)
CHEBI:58435 (17)
CHEBI:57936 (17)
CHEBI:57845 (17)
CHEBI:128769 (17)
CHEBI:58421 (17)
CHEBI:57472 (17)
CHEBI:58085 (17)
CHEBI:57499 (17)
CHEBI:58245 (17)
CHEBI:57705 (17)

Metabolite Name

Hypoxanthine (103)
Creatine (96)
Uridine (94)
Adenosine (93)
Adenine (92)
Choline (89)
Guanosine (89)
Uracil (87)
Taurine (84)
Inosine (84)
Guanine (81)
Xanthine (79)
Cytidine (76)
Betaine (75)
Creatinine (75)
L-Tyrosine (73)
L-Histidine (71)
Cytosine (71)
Azelaic acid (71)
L-Phenylalanine (71)
L-Tryptophan (70)
Oleamide (67)
Riboflavin (67)
Indole (66)
Xanthosine (65)
Thymidine (65)
Thymine (63)
Pantothenic acid (63)
Citric acid (62)
Histamine (61)

First Public Date

2025 (401)
2026 (371)
2024 (352)
2023 (293)
2013 (282)
2018 (251)
2022 (227)
2020 (217)
2019 (205)
2014 (201)
2021 (185)
2017 (68)
2016 (45)
2015 (42)
2012 (7)
2011 (4)

Modelling Approach

Constraint-based model (20)
Machine learning (3)
Ordinary differential equation model (3)
Computational model (2)
Steady-state model (1)

Study status

Recruiting (4)
Completed (3)
Withdrawn (1)
Not yet recruiting (1)

Lab affiliation

Molecular Biosciences and the Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA (9)
Instituto de Biotecnología, Grupo de Bioquímica y Parasitología Molecular, Departamento de Parasitología, Universidad de Granada, Granada, Spain. (6)
Molecular Biosciences and the Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX USA (6)
School of Computer Science Department of Microbiology and Plant Biology University of Oklahoma, Norman, OK (5)
University of Oxford (5)
Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany (4)
Oak Ridge National Lab (4)
Shanghai Institute of Materia Medica (4)
University of Tübingen Interfaculty Institute for Cell Biology Department of Immunology Auf der Morgenstelle 15 72076 Tuebingen Germany (4)
Department of Chemical & Systems Biology, Stanford University, USA (3)
Department of Clinical Laboratory, Shanghai Tenth People’s Hospital of Tongji University, Shanghai, 200072, China (3)
Department of Convergence Medicine, Convergence Medicine Research Center/Biomedical Research Center, Asan Medical Center, Asan Institute for Life Sciences, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Republic of Korea. (3)
Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, China. (3)
Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany (3)
Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne Office B25A/04/94 Rue du Bugnon 25a, CH-1005 Lausanne (3)
Division of Cell Matrix Biology & Regenerative Medicine (L5) / Division of Cell Matrix Biology & Regenerative Medicine, University of Manchester (3)
ETHZ IMSB (3)
Head of the Curie Institute Mass Spectrometry Platform (3)
Massachusetts Institute of Technology (3)
Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany (3)
Oak Ridge National Laboratory (3)
Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center (3)
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China (3)
The University of Sydney (3)
Zhejiang University (3)
Acupuncture and Tuina School/Third Teaching Hospital, Chengdu University of Traditional Chinese Medicine (2)
Ben May Department for Cancer Research, The University of Chicago (2)
Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Biophysical Chemistry Department of Clinical Chemistry, University Medical Center Goettingen (2)
CEA-Marcoule, ProGénoMIX platform, DRF-Li2D, 30207 Bagnols-sur-Cèze, France (2)
Cell Biology, Faculty of Science, Utrecht University, TheNetherlands (2)

Keyword

Guaiac fecal occult blood test (1)
Helicobacter pylori stool antigen test (1)
Bidirectional endoscopy (1)
HER2 Mutation (1)
HER2 Amplification (1)
Colorectal (CRC) (1)
Biliary Tract Cancer (BTC) (1)
Other Solid Tumors (1)
MFOLFOXIRI + Panitumumab (1)
RAS and BRAF wt (1)
Vectibix (1)
Fecal immunochemical test (1)
Nimotuzumab (1)
Squamous cell carcinoma of the head and neck (1)
Mass screening (1)
EGFR (1)
Liver cancer (1)
Stomach cancer (1)
Panitumumab (1)
Irinotecan (1)
Leucovorin (1)
Fluorouracil (1)
Levoleucovorin (1)
Oxaliplatin (1)

IsPrivate

False (33)

Model Flag

Non Kinetic (3)

Submitter Keywords

FROG (6)
Ersilia (5)
Machine Learning Model (5)
FAIR-AIML (3)

Classification

bacteria (264)
viruses (24)
fungi (6)
protozoa (6)

Modification

2x(15)N labeled L-lysine (4)
4x(15)N labeled L-arginine (4)
Not available (4)
N6 (2)
N6-dimethyl-L-lysine (2)
+3amu) (1)
15.994915 (1)
4-tetrahydrothiazine-3-carboxylic acid (1)
42.010565 (1)
57.021464 (1)

Study type

Transcription profiling by array (723)
RNA-seq of coding RNA (719)
ChIP-seq (329)
RNA-seq of coding RNA from single cells (183)
RNA-seq of total RNA (100)
DNA-seq (70)
Methylation profiling by high throughput sequencing (67)
Methylation profiling by array (63)
RNA-seq of non coding RNA (60)
ChIP-chip by tiling array (58)
Other (57)
Unknown experiment type (53)
Comparative genomic hybridization by array (44)
ATAC-seq (29)
Transcription profiling by tiling array (28)
Single nucleus RNA sequencing (27)
Genotyping by high throughput sequencing (21)
ChIP-chip by array (20)
CUT&RUN (20)
Spatial transcriptomics by high-throughput sequencing (18)
Cell line - High-throughput sequencing (15)
Genotyping by array (12)
Hi-C (12)
ScATAC-seq (11)
Transcription profiling by RT-PCR (10)
MicroRNA profiling by high throughput sequencing (10)
RIP-seq (10)
Ribo-seq (10)
Animal - High-throughput sequencing (9)
Bisulfite-seq (9)

Release Date

2025 (7195)
2022 (6465)
2023 (5888)
2024 (5538)
2021 (5044)
2020 (3681)
2019 (2689)
2018 (2289)
2017 (1931)
2016 (1670)
2026 (1488)
2015 (1448)
2014 (1263)
2013 (851)
2012 (728)
2011 (557)
2010 (516)
2009 (296)
2008 (223)
2007 (128)
2006 (82)
2005 (72)
2004 (30)
2003 (28)
2002 (22)
2000 (17)
2001 (16)
1999 (11)
1998 (6)
1997 (3)

Location

China (3)
Netherlands (2)
Taiwan (1)
Germany (1)
Italy (1)
United States (1)

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Metabolomics dataset of PPAR-pan treated rat liver (eicosanoid assay)

This article contains mass spectrometry (MS) data investigating small molecule changes as an effect of a triple peroxisome proliferator-activated receptor (PPAR-pan) agonist GW625019 in the liver as described in the manuscript “PPAR-pan Activation Induces Hepatic Oxidative Stress and Lipidomic Re...

2016-05-13 | MTBLS278 | MetaboLights

Metabolomics dataset of PPAR-pan treated rat liver (acyl-carnitine and aqueous metabolite assays)

2016-05-13 | MTBLS303 | MetaboLights

The International Cancer Genome project: Pan-Cancer Analysis of Whole Genomes (PCAWG)

The Pan-Cancer Analysis of Whole Genomes (PCAWG) study is an international collaboration to identify common patterns of mutation in more than 2,800 cancer whole genomes from the International Cancer Genome Consortium. Building upon previous work which examined cancer coding regions, this project is ...

ORGANISM(S): Homo sapiens

2020-02-05 | E-MTAB-5200 | biostudies-arrayexpress

The International Cancer Genome project: Pan-Cancer Analysis of Whole Genomes (PCAWG)- Alternative view by individual

ORGANISM(S): Homo sapiens

2020-02-05 | E-MTAB-5423 | biostudies-arrayexpress

Probing the pan genome of a foodborne bacterial pathogen Listeria monocytogenes

Full title: Probing the pan genome of a foodborne bacterial pathogen Listeria monocytogenes: Implications for its niche adaptation, pathogenesis, and evolution Listeria monocytogenes is a foodborne bacterial pathogen well known for adaptability to diverse environmental and host niches, and a high f...

ORGANISM(S): Listeria monocytogenes EGD-e

2010-04-06 | E-GEOD-20367 | biostudies-arrayexpress

Pan-analysis of Single Amino-acid Polymorphism

Uncovering dark mass in population proteomics: Pan-analysis of Single Amino-acid Polymorphism (Pan-SAP) revealed quantitative relevance with cognition and aging

ORGANISM(S): Homo Sapiens

2024-12-31 | PXD059327 |

The pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii

The human gut microbiota harbors methanogens represented by the dominant archaeon, Methanobrevibacter smithii, a polyphyletic group of acetogens, and sulfate-reducing bacteria. Defining their roles in the H2-economy of the gut has potential therapeutic importance for modulating the efficiency of fe...

ORGANISM(S): Methanobrevibacter smithii

2011-03-30 | E-GEOD-25408 | biostudies-arrayexpress

Pan paniscus

Pan paniscus alternate pseudohaplotype genome sequencing

PRJNA941362 | ENA

Pan troglodytes

Pan troglodytes alternate pseudohaplotype genome sequencing

PRJNA941354 | ENA

Pan troglodytes

Pan troglodytes principal pseudohaplotype genome sequencing

PRJNA941355 | ENA