Thomas Andrew L AL

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Genomics (71)
Unknown (44)
Transcriptomics (23)
Proteomics (6)
Metabolomics (2)
Models (1)
Multiomics (1)

Organisms

Homo sapiens (82)
Mus musculus (11)
Arabidopsis (1)
Fundulus heteroclitus (1)
Arabidopsis thaliana (1)

Repository

EGA (66)
biostudies-arrayexpress (28)
MassIVE (3)
MetaboLights (2)
PeptideAtlas (2)
BioModels (1)
pride (1)

Tissue

Breast cancer cell (1)

Disease

Acute myeloid leukemia (3)
Breast cancer (1)

Technology Type

AB SOLiD 4 System, Illumina HiSeq 2500, Illumina HiSeq 2000, AB SOLiD System 3.0 (1)
Illumina Genome Analyzer II (1)
Illumina HiSeq 2000 (1)
Illumina OncoArray (1)
Mass spectrometry (1)
NMR spectroscopy (1)
Mass Spectrometry (1)
Shotgun proteomics (1)

Instrument Platform

Illumina HiSeq 2500 (3)
Illumina NovaSeq 6000 (2)
Illumina HiSeq 2000 (2)
LTQ Orbitrap Elite (1)
Orbitrap Exploris 480 (1)
Orbitrap Fusion (1)
Q Exactive HF-X (1)
Liquid Chromatography MS - negative (1)
Liquid Chromatography MS - positive (1)
Nuclear Magnetic Resonance (NMR) - (1)
LTQ Orbitrap (1)
LTQ Orbitrap Velos (1)

Publication Date

2014 (6)
2008 (5)
2012 (4)
2011 (4)
2025 (3)
2013 (3)
2018 (2)
2015 (2)
2024 (1)
2016 (1)
2010 (1)
2022 (1)
2020 (1)
2023 (1)
2019 (1)

UNIPROT ID/AC

Q9LQT8 (1)
Q9MAA7 (1)
A0A5E1 (1)
A0ELI5 (1)
A0EQY3 (1)
A0JLQ7 (1)
A0JNY3 (1)
A0JNY7 (1)
A0MNP4 (1)
A0PJD7 (1)
A0PJL0 (1)
A0PK78 (1)
A0PK81 (1)
A1A553 (1)
A1A557 (1)
A1A558 (1)
A1A596 (1)
A1A5B6 (1)
A1E5T5 (1)
A1ILG8 (1)
A1L013 (1)
A1L0U3 (1)
A1L0U6 (1)
A1L0V6 (1)
A1L317 (1)
A1L329 (1)
A1L341 (1)
A1L347 (1)
A1L353 (1)
A1L361 (1)

ENSEMBL ID

ENSMUSG00000021039 (1)
ENSMUSG00000027651 (1)
ENSMUSG00000098557 (1)
ENSMUSP00000069525 (1)
ENSMUSP00000140201 (1)
ENSMUSP00000141097 (1)
ENSMUSP00000141637 (1)

CHEBI ID

CHEBI:15354 (2)
CHEBI:16467 (2)
CHEBI:16761 (2)
CHEBI:17053 (2)
CHEBI:17066 (2)
CHEBI:17115 (2)
CHEBI:17489 (2)
CHEBI:18019 (2)
CHEBI:18132 (2)
CHEBI:18183 (2)
CHEBI:30746 (2)
CHEBI:30832 (2)
CHEBI:29590 (1)
CHEBI:29605 (1)
CHEBI:30088 (1)
CHEBI:32902 (1)
CHEBI:32906 (1)
CHEBI:10138 (1)
CHEBI:10565 (1)
CHEBI:116314 (1)
CHEBI:15344 (1)
CHEBI:15347 (1)
CHEBI:15365 (1)
CHEBI:15383 (1)
CHEBI:15422 (1)
CHEBI:15603 (1)
CHEBI:15611 (1)
CHEBI:15613 (1)
CHEBI:15698 (1)
CHEBI:15699 (1)

Metabolite Name

L-Phenylalanine (2)
(+)-Pyroglutamic acid (1)
(+/-)-Pipecolate (1)
(+/-)-Propionylcarnitine chloride (1)
(-)-Tetradecanoylcarnitine (1)
(10E)-12-Oxododecenoic acid (1)
(10E,12Z,15Z)-9-hydroxyoctadeca-10,12,15-trienoic acid (1)
(13S)-Hydroxyoctadecadienoate (1)
(1s,3z)-3-[(2e)-2-[(1r,3ar,7as)-7a-Methyl-1-[(2r)-6-Methylheptan-2-Yl]-2,3,3a,5,6,7-Hexahydro-1h-Inden-4-Ylidene]ethylidene]-4-Methylidene-Cyclohexan-1-Ol (1)
(2-hydroxy-3-stearoyloxy-propyl) 2-(trimethylammonio)ethyl phosphate (1)
(2E)-2-Phenyl-2-propenoic acid (1)
(2E)-3-(1H-imidazol-4-yl)prop-2-enoic acid (1)
(2R,3R,4S,5S,6R)-2-[[(2R,3S,4S,5R,6R)-6-[(2R,3R,4S,5R,6R)-6-[(2S,3S,4R,5S)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl]oxy-3,4,5-trihydroxy-oxan-2-yl]methoxy]-6-(hydroxymethyl)oxane-3,4,5-triol (1)
(2S)-1-[(2S)-2-azaniumyl-3-phenyl-propanoyl]pyrrolidine-2-carboxylate (1)
(2S)-1-[(2S)-5-amino-2-[[(2S)-2-amino-4-methyl-pentanoyl]amino]-5-keto-pentanoyl]proline (1)
(2S)-2-(methylamino)Pentanedioic acid (1)
(2S)-2-Amino-3-methylbutanoic acid (1)
(2S)-2-[[(4S)-4-amino-4-carboxy-butanoyl]amino]-4-methyl-pentanoic acid (1)
(2S)-2-amino-5-[[(1S)-1-carboxy-2-methyl-propyl]amino]-5-oxo-pentanoic acid (1)
(2S)-3-(5-mercapto-3-methyl-imidazol-4-yl)-2-(methylammonio)propionate (1)
(2S,3R)-(-)-Threonine (1)
(2S,3R)-2-[[[[9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)-2-oxolanyl]-6-purinyl]amino]-oxomethyl]amino]-3-hydroxybutanoic acid (1)
(2S,3S)-alpha-Amino-beta-merthyl-n-valerate (1)
(2S,3S,4R)-2-aminohexadecane-1,3,4-triol (1)
(3R)-3-[(Z)-octadec-9-enoyl]oxy-4-(trimethylazaniumyl)butanoate (1)
(3R,3'S)-3,3'-Dihydroxy-beta,beta-carotene-4,4'-dione (1)
(3S,6S)-3-Benzyl-6-(2-methylpropyl)piperazine-2,5-dione (1)
(4S)-4-amino-5-[[(1S)-1-carboxyethyl]amino]-5-keto-valeric acid (1)
(6R)-6-[(3R,5S,7R,8R,9S,10S,13R,14S,17R)-3,7-dihydroxy-10,13-dimethyl-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]-2-methylheptanoic acid (1)
(9Z)-octadec-9-enamide (1)

IsPrivate

False (1)

Modelling Approach

Ordinary differential equation model (1)

Study type

Transcription profiling by array (17)
ChIP-seq (2)
MicroRNA profiling by array (2)
DNA-seq (2)
Translation profiling (1)
ATAC-seq (1)
Hi-C (1)
Methylation profiling by high throughput sequencing (1)
RNA-seq of coding RNA (1)

Release Date

2021 (10)
2012 (7)
2022 (7)
2025 (6)
2014 (6)
2018 (5)
2011 (5)
2008 (5)
2015 (4)
2024 (3)
2023 (3)
2016 (2)
2013 (2)
2010 (2)
2026 (2)
2019 (2)
2020 (1)

Lab affiliation

Applied Bioinformatics of Cancer University of Edinburgh Cancer Research Centre Institute of Genetics and Molecular Medicine Edinburgh, United Kingdom (1)

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Metabolic profiling of rheumatoid arthritis neutrophils reveals altered energy metabolism that is not affected by JAK inhibition

Neutrophils play a key role in the pathophysiology of rheumatoid arthritis (RA) where release of ROS and proteases directly causes damage to joints and tissues. Neutrophil function is directly affected by Janus Kinase (JAK) inhibitor drugs, including tofacitinib and baricitinib, which are clinically...

2023-07-11 | MTBLS4766 | MetaboLights

Experimental and computational approaches for deep metabolome annotation with application to the ecotoxicological model organism Daphnia magna

Identifying metabolomes with greater coverage and confidence is a critical step towards interpreting the metabolic basis of human and environmental health. Yet for over two decades the field of metabolomics has been inhibited by limited metabolite identification. To address this, we developed the...

MTBLS2273 | MetaboLights

Multicenter Phase IB Trial of Carboxyamidotriazole Orotate and Temozolomide for Recurrent and Newly Diagnosed Glioblastoma and Other Anaplastic Gliomas.

Not available

S-EPMC5993168 | biostudies-literature

Sessile serrated adenomas and conventional adenomas of the colon

Sessile serrated adenomas are now recognized as precursor lesions of a substantial subset of colorectal cancers arising via a so-called “serrated pathway”. However, their biological markers remain to be defined. The aim of our study was to identify differentially expressed genes in sessile serrated ...

ORGANISM(S): Homo sapiens

2008-08-26 | E-GEOD-12514 | biostudies-arrayexpress

Overexpression of non-degradable SAS-6 KEN box mutant in RPE-1 cells

Stable clones of RPE-1 cells expressing tetracycline-inducible wild type SAS-6 or SAS-6ND were obtained via lentiviral gene transduction with the pLVX tet-on Advanced inducible gene expression system (Clontech). Stable expressors were derived by selection with 5 μg/mL puromycin (Sigma-Aldrich, UK). ...

ORGANISM(S): Homo sapiens

2025-01-27 | E-MTAB-13783 | biostudies-arrayexpress

Middleton2012_GibberellinSignalling

This model is from the article: Mathematical modeling elucidates the role of transcriptional feedback in gibberellin signaling. Middleton AM , Úbeda-Tomás S , Griffiths J , Holman T , Hedden P , Thomas SG , Phillips AL , Holdsworth MJ , Bennett MJ , K...

2024-09-02 | BIOMD0000000422 | BioModels

Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1

Whole genome sequencing (WGS) from snap-frozen oesophageal tumour tissue and germline nucleic acids isolated from peripheral blood mononuclear cells (PBMC) was performed as part of the International Cancer Genome Consortium project and OCCAMS consortium (1,2). Filtered read sequences were mapped to ...

ORGANISM(S): Homo sapiens

2016-09-09 | E-MTAB-4600 | biostudies-arrayexpress

Dasatinib Plus Intensive Chemotherapy in Children, Adolescents, and Young Adults With Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia: Results of Children's Oncology Group Trial AALL0622.

Not available

S-EPMC6067800 | biostudies-literature

Genome-Wide Association Study of Event-Free Survival in Diffuse Large B-Cell Lymphoma Treated With Immunochemotherapy.

Not available

S-EPMC4879713 | biostudies-literature

RNA-seq to investigate differentially expressed genes in KPC mouse PDAC treated with CSF-1R small molecule inhibitor AZD7507 and/or the CXCR2 small molecule inhibitor AZD5069

Recently, we defined four subtypes of pancreatic cancer that are associated with distinct histopathological characteristics and differential survival, namely, Squamous, Pancreatic Progenitor, Immunogenic, and ADEX (Bailey et al 2016, Nature). We also found that loss of CXCR2 was associated with a sw...

ORGANISM(S): Mus musculus

2018-05-01 | E-MTAB-6620 | biostudies-arrayexpress

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