Pan C C - OmicsDI

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Unknown (18227)
Transcriptomics (2288)
Proteomics (1130)
Genomics (783)
Metabolomics (463)
Other (13)
Models (12)
Multiomics (5)
Genomic (4)
Methylation profiling (3)
Clinical (1)

Organisms

Homo sapiens (1781)
Mus musculus (875)
Drosophila melanogaster (99)
Pan troglodytes (58)
Arabidopsis thaliana (57)
Rattus norvegicus (57)
Saccharomyces cerevisiae (54)
Danio rerio (48)
Caenorhabditis elegans (34)
Gallus gallus (27)
Macaca mulatta (26)
Escherichia coli (24)
Oryza sativa (23)
Methanococcus maripaludis S2 (17)
Bos taurus (16)
Streptomyces coelicolor (15)
Schizosaccharomyces pombe (15)
Zea mays (15)
Sus scrofa (14)
Halobacterium salinarum (12)
Oryza sativa Japonica Group (9)
Mycobacterium tuberculosis (9)
Hordeum vulgare (8)
Canis lupus familiaris (8)
Brassica napus (7)
mixed sample (7)
Dehalococcoides (1)
Methanothermobacter marburgensis str. Marburg (1)
Methanothermobacter thermautotrophicus (1)
Methanothermobacter thermautotrophicus str. Delta H (1)

Organisms

Homo sapiens (71)
Mus musculus (41)
Halobacterium salinarum NRC-1 (33)
Caenorhabditis elegans (23)
Pan troglodytes (5)
Drosophila melanogaster (4)
Thermococcus kodakarensis (3)
Pyrococcus furiosus (2)
Candidozyma auris (2)
Planococcus halocryophilus (1)
Deformed wing virus (1)
Ceratocystis fimbriata (1)
Acetivibrio thermocellus (1)
Pyrodictium abyssi (1)
Sulfolobus acidocaldarius (1)
Haloferax volcanii (1)
Campylobacter jejuni subsp. jejuni (1)
Vigna radiata (1)
Bifidobacterium breve (1)
Ciona robusta (1)
Campylobacter (1)
Limosilactobacillus reuteri (1)
Medicago truncatula (1)
Oncorhynchus mykiss (1)
Salmonella enterica (1)
Saccharomyces cerevisiae (1)
Plasmodium falciparum (1)
Pseudomonas aeruginosa (1)
Sus scrofa (1)
Danio rerio (1)

Repository

biostudies-arrayexpress (2591)
pride (774)
MetaboLights (459)
ENA (268)
iProX (130)
geo (126)
MassIVE (88)
EGA (80)
jPOST (54)
PeptideAtlas (44)
PAXDB (25)
EVA (23)
PanoramaPublic (13)
BioModels (7)
dbGaP (4)
GNPS (4)
Cell Collective (3)
FAIRDOMHub (2)
GPMDB (1)
NODE (1)

Tissue

Cell culture (194)
Epithelial cell (62)
B cell (37)
Brain (37)
Blood (34)
Liver (28)
T cell (23)
Lung (22)
Heart (21)
Permanent cell line cell (21)
Blood plasma (20)
Kidney (17)
Leaf (17)
Primary cell (15)
Skin (15)
Colon (14)
Macrophage (14)
Monocyte (13)
Whole body (13)
Hepatocyte (12)
Cell suspension culture (11)
Fibroblast (11)
Plant cell (11)
Bone marrow (9)
Peripheral blood mononuclear cell (9)
Root (9)
Blood cell (8)
Dendritic cell (8)
Blood serum (7)
Prefrontal Cortex (1)

Disease

Colon cancer (23)
Disease free (20)
Breast cancer (16)
Brain cancer (13)
Lymphoma (13)
Acute leukemia (10)
Influenza (10)
Normal (8)
Cardiovascular system disease (8)
Alzheimer's disease (7)
Cervix carcinoma (7)
Chagas disease (6)
Chronic lymphocytic leukemia (6)
Lung cancer (6)
Melanoma (6)
Lung adenocarcinoma (5)
Pancreatic cancer (5)
Tuberculosis (5)
Type 2 diabetes mellitus (5)
Acute myeloid leukemia (4)
COVID-19 (4)
Hepatocellular carcinoma (4)
Ischemic (1)
Colon cancer Dukes C (1)
Pre-tumoral lesion in a mouse model of human adamantinomatous craniopharyngioma (ACP) (1)
N/A (culture-derived) (1)
Renal cancer (1)
Hepatitis C infected (1)
Metastatic colorectal cancer (1)
Not Available (1)

Technology Type

Mass Spectrometry (774)
Shotgun proteomics (380)
Mass spectrometry (245)
Mass spectrometry assay (208)
Bottom-up proteomics (147)
Affinity purification coupled with mass spectrometry proteomics (130)
Data-dependent acquisition (95)
SWATH MS (44)
Gel-based experiment (40)
Data-independent acquisition (23)
Immunopeptidomics (17)
Chemical cross-linking coupled with mass spectrometry proteomics (11)
Top-down proteomics (11)
NMR spectroscopy (10)
SRM/MRM (10)
Proteogenomics (7)
All-ion fragmentation (5)
Illumina HiSeq 2000 (3)
Affinity proteomics (3)
DiaPASEF (3)
MSE (3)
Illumina HiSeq 2000, ILLUMINA (2)
Metaproteomics (2)
Illumina Genome Analyzer II, Illumina HiSeq 2000 (1)
Illumina Genome Analyzer IIx, Illumina HiSeq 2000 (1)
Illumina HiSeq 2000, NextSeq 500, ILLUMINA (1)
Illumina HiSeq 2500 (1)
Illumina HiSeq 2500, ILLUMINA (1)
OXFORD_NANOPORE, MinION (1)
NMR spectroscopy assay (1)

Instrument Platform

Illumina NovaSeq 6000 (488)
Illumina NovaSeq X (129)
NextSeq 500 (116)
NextSeq 2000 (96)
Illumina HiSeq 2500 (74)
NextSeq 550 (67)
Illumina HiSeq 4000 (65)
Illumina HiSeq 2000 (64)
DNBSEQ-G400 (29)
Illumina MiSeq (27)
NA (24)
N/A (15)
Element AVITI (14)
None (11)
Illumina HiSeq 3000 (10)
Illumina HiSeq X (9)
DNBSEQ-T7 (9)
BGISEQ-500 (9)
PromethION (8)
Maxwell RSC Instrument (7)
Dell PowerEdge R750; CPU: 2 × Intel Xeon Gold 6346 (32 Cores / 64 Threads); RAM: 188 GB (7)
NextSeq 1000 (7)
HiSeq X Ten (7)
NucleoSpin RNA/Protein kit lysis buffer (350 µL per tube; Macherey‑Nagel). (6)
Chromium 10x (6)
None (6)
Illumina Genome Analyzer II (6)
See manuscript (5)
Illumina Genome Analyzer IIx (5)
Racham server on Uppmax, NAISS (5)

Publication Date

2026 (889)
2025 (748)
2024 (219)
2023 (211)
2022 (202)
2010 (198)
2013 (196)
2014 (194)
2015 (183)
2021 (179)
2011 (178)
2016 (167)
2012 (166)
2019 (137)
2020 (125)
2008 (100)
2018 (72)
2009 (49)
2017 (47)
2006 (29)
2007 (23)
2005 (12)
2004 (4)
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)
9606.ENSP00000367034 (12)
9606.ENSP00000382982 (12)
9606.ENSP00000385479 (12)

ENSEMBL ID

ENSPTRG00000000012.3 (1)
ENSPTRG00000000038.4 (1)
ENSPTRG00000000051.4 (1)
ENSPTRG00000000052.3 (1)
ENSPTRG00000000109.3 (1)
ENSPTRG00000000124.3 (1)
ENSPTRG00000000138.3 (1)
ENSPTRG00000000153.3 (1)
ENSPTRG00000000158.5 (1)
ENSPTRG00000000197.5 (1)
ENSPTRG00000000202.3 (1)
ENSPTRG00000000217.5 (1)
ENSPTRG00000000242.4 (1)
ENSPTRG00000000255.5 (1)
ENSPTRG00000000263.4 (1)
ENSPTRG00000000264.2 (1)
ENSPTRG00000000265.2 (1)
ENSPTRG00000000276.1 (1)
ENSPTRG00000000277.2 (1)
ENSPTRG00000000278.3 (1)
ENSPTRG00000000279.3 (1)
ENSPTRG00000000280.2 (1)
ENSPTRG00000000290.3 (1)
ENSPTRG00000000302.3 (1)
ENSPTRG00000000338.4 (1)
ENSPTRG00000000339.4 (1)
ENSPTRG00000000340.3 (1)
ENSPTRG00000000363.4 (1)
ENSPTRG00000000370.5 (1)
ENSPTRG00000000371.4 (1)

CHEBI ID

CHEBI:10049 (3)
CHEBI:10066 (3)
CHEBI:10067 (3)
CHEBI:10246 (3)
CHEBI:10261 (3)
CHEBI:10489 (3)
CHEBI:10491 (3)
CHEBI:10492 (3)
CHEBI:10493 (3)
CHEBI:10494 (3)
CHEBI:10495 (3)
CHEBI:10497 (3)
CHEBI:10499 (3)
CHEBI:10500 (3)
CHEBI:10529 (3)
CHEBI:10530 (3)
CHEBI:10531 (3)
CHEBI:10532 (3)
CHEBI:10533 (3)
CHEBI:10745 (3)
CHEBI:10866 (3)
CHEBI:10888 (3)
CHEBI:10925 (3)
CHEBI:10966 (3)
CHEBI:10986 (3)
CHEBI:11033 (3)
CHEBI:11063 (3)
CHEBI:11186 (3)
CHEBI:11192 (3)
CHEBI:11195 (3)

Metabolite Name

Hypoxanthine (100)
Creatine (92)
Uridine (92)
Adenine (89)
Adenosine (88)
Guanosine (87)
Choline (85)
Uracil (82)
Inosine (81)
Taurine (79)
Guanine (75)
L-Phenylalanine (75)
L-Histidine (74)
L-Tyrosine (73)
Xanthine (73)
Cytidine (72)
L-Tryptophan (72)
Betaine (69)
Creatinine (69)
Azelaic acid (67)
Cytosine (67)
Indole (67)
Oleamide (66)
Riboflavin (63)
Xanthosine (63)
Thymidine (62)
L-Glutamine (61)
Thymine (60)
Citric acid (57)
L-Valine (57)

First Public Date

2014 (56)
2025 (49)
2024 (27)
2026 (24)
2023 (24)
2020 (21)
2022 (16)
2021 (11)
2018 (11)
2016 (8)
2019 (7)
2017 (6)
2015 (4)
2013 (4)

Modelling Approach

Constraint-based model (4)
Ordinary differential equation model (1)

Study status

Completed (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, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany (4)
Icahn School of Medicine at Mount Sinai (4)
Oak Ridge National Lab (4)
Department of Chemical & Systems Biology, Stanford University, USA (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, 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)
Institute for Systems Biology, Seattle, WA, USA (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)
Shanghai Institute of Materia Medica (3)
The University of Sydney (3)
University of Tübingen Interfaculty Institute for Cell Biology Department of Immunology Auf der Morgenstelle 15 72076 Tuebingen Germany (3)
(1) Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; (2) VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium. (2)
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)
Biobank of Nanjing Women and Children's Healthcare Hospital, Women's Hospital of Nanjing Medical University( Nanjing Women and Children's Healthcare Hospital), Nanjing 210004, China (2)
CEA-Marcoule, ProGénoMIX platform, DRF-Li2D, 30207 Bagnols-sur-Cèze, France (2)

Keyword

Vectibix (1)

IsPrivate

False (7)

Model Flag

Non Kinetic (3)

Submitter Keywords

FROG (3)

Classification

bacteria (4)
fungi (2)
protozoa (1)
viruses (1)

Modification

2x(15)N labeled L-lysine (4)
4x(15)N labeled L-arginine (4)
N6 (2)
Not available (2)
15.994915 (1)
42.010565 (1)
57.021464 (1)
N6-dimethyl-L-lysine (1)

Study type

RNA-seq of coding RNA (709)
Transcription profiling by array (662)
ChIP-seq (299)
RNA-seq of coding RNA from single cells (165)
RNA-seq of total RNA (101)
DNA-seq (62)
ChIP-chip by tiling array (54)
Methylation profiling by array (54)
Other (48)
Unknown experiment type (44)
Methylation profiling by high throughput sequencing (40)
Comparative genomic hybridization by array (39)
Transcription profiling by tiling array (29)
ATAC-seq (26)
Single nucleus RNA sequencing (25)
RNA-seq of non coding RNA (22)
Genotyping by high throughput sequencing (21)
ChIP-chip by array (20)
CUT&RUN (20)
Spatial transcriptomics by high-throughput sequencing (17)
Hi-C (12)
ScATAC-seq (12)
Genotyping by array (10)
Transcription profiling by RT-PCR (10)
RIP-seq (10)
Cell line - High-throughput sequencing (9)
Animal - High-throughput sequencing (8)
MicroRNA profiling by high throughput sequencing (8)
Bisulfite-seq (8)
Ribo-seq (7)

Release Date

2025 (3079)
2022 (2537)
2023 (2336)
2024 (2220)
2021 (1891)
2020 (1381)
2019 (1052)
2026 (992)
2018 (876)
2017 (715)
2016 (680)
2015 (634)
2014 (579)
2013 (434)
2012 (373)
2010 (312)
2011 (295)
2008 (140)
2009 (132)
2007 (60)
2006 (34)
2005 (20)
2004 (17)
2003 (8)
2000 (7)
2002 (5)
1999 (4)
1998 (3)
2001 (2)

Location

Germany (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

Transcription profiling of liver from Pan troglodytes with chronic hepatitis C virus infection following therapeutic silencing of microRNA-122 using SPC3649

Chimpanzees with chronic Hepatitis C infection treated with LNA-antimiR-122.

ORGANISM(S): Pan troglodytes

2010-10-01 | E-MEXP-2375 | biostudies-arrayexpress

Pan-neuronal ribotagging in fasted C. elegans

PRJNA825582 | ENA

Pathogenesis of hepatitis E and hepatitis C in chimpanzees: Similarities and differences

The chimpanzee is the only model other than man for investigating the pathogenesis of viral hepatitis types A through E. Studies of the host response, including microarray analyses, have relied on the close relationship between these two primate species: chimpanzee samples are commonly tested with h...

ORGANISM(S): Pan troglodytes

2010-09-21 | E-GEOD-22160 | biostudies-arrayexpress

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

Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture.

Topological domains are key architectural building blocks of chromosomes in complex genomes. Their functional importance and evolutionary dynamics are however not well defined. Here we performed comparative Hi-C in liver cells from four mammalian species, and characterized the conservation and dive...

ORGANISM(S): Canis lupus familiaris

2015-02-26 | E-GEOD-65126 | biostudies-arrayexpress

Global gene expression change in the cerebellum of Niemann-Pick disease type C mice with deletion of Ccl3 or Purkinje neuron-specific NPC1 rescue

Macrophage inflammatory protein 1alpha/CCL3 protein is a known pro-inflammatory cytokine that can mediate chemotaxis of monocytes and promote cell degranulation. Ccl3 gene expression is elevated in the CNS and visceral tissue of many lysosomal storage disorders. The deletion of Ccl3 in a mouse model...

ORGANISM(S): Mus musculus

2012-04-16 | E-GEOD-36119 | biostudies-arrayexpress

Widespread N6-methyladenosine-dependent RNA Structural Switches Regulate RNA-Protein Interactions

We show that N6-methyladenosine (m6A), the most abundant internal modification in mRNA/lncRNA with still poorly characterized function, alters RNA structure to facilitate the access of RBM for heterogeneous nuclear ribonucleoprotein C (hnRNP C). We term this mechanism m6A-switch. Through combining P...

ORGANISM(S): Homo sapiens

2015-02-27 | E-GEOD-56010 | biostudies-arrayexpress

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