Methotrexate - OmicsDI

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Organisms

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Organisms

Homo sapiens (133)
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Disease

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Technology Type

Mass spectrometry (36)
Mass spectrometry assay (28)
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EI (4)
ESI (4)
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Instrument Platform

Illumina NovaSeq 6000 (17)
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Chromium X instrument (10x Genomics); GEM-X Flex Sample Preparation v2 Kit (10x Genomics; 1000781); Human Gene Expression Probe Set v1.0.1 (10x Genomics) (1)
Countess 3 FL Automated Cell Counter (Thermo Fisher Scientific; AMQAF2000); GEM-X Flex Sample Preparation v2 Kit (10x Genomics; 1000781) (1)
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PCR machine; AMPure XP beads; TruSeq Stranded mRNA stranded prep. kit (1)
PCR machine; Superscript II polymerase Kit (Invitrogen); PCR machine; AMPure XP beads; TruSeq stranded mRNA sample prep kit.; TruSeq Stranded mRNA stranded prep. kit (1)
Centrifuge 5424R (Eppendorf); miRNeasy Mini Kit (Qiagen); TURBO^TM DNase (Ambion); Bioanalyser (Agilent) (1)
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PCR machine; MICROBExpress kit (Ambion); TruSeq Stranded mRNA stranded prep. kit (1)
PCR machine; AMPure XP beads; TruSeq stranded mRNA sample prep. kit. (1)
None (1)
Illumina Genome Analyzer IIx (1)
Ion Torrent PGM (1)

Publication Date

2025 (49)
2026 (46)
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2014 (26)
2022 (24)
2009 (24)
2008 (21)
2015 (20)
2017 (17)
2013 (16)
2010 (16)
2021 (15)
2023 (14)
2011 (14)
2020 (13)
2012 (12)
2019 (11)
2016 (11)
2007 (9)
2018 (8)
2006 (6)
2005 (4)
2003 (4)

UNIPROT ID/AC

P00374 (1)

CHEBI ID

CHEBI:17596 (11)
CHEBI:30769 (11)
CHEBI:16708 (10)
CHEBI:16750 (10)
CHEBI:17748 (10)
CHEBI:17568 (10)
CHEBI:18050 (9)
CHEBI:17230 (2)
CHEBI:15428 (2)
CHEBI:17622 (2)
CHEBI:18406 (2)
CHEBI:15637 (2)
CHEBI:15641 (2)
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CHEBI:16474 (2)
CHEBI:24367 (1)
CHEBI:17822 (1)
CHEBI:1989 (1)
CHEBI:15635 (1)
CHEBI:15638 (1)
CHEBI:18272 (1)
CHEBI:15740 (1)
CHEBI:17115 (1)
CHEBI:16842 (1)
CHEBI:15634 (1)
CHEBI:15636 (1)
CHEBI:20506 (1)
CHEBI:18009 (1)
CHEBI:15422 (1)
CHEBI:30751 (1)

Metabolite Name

Methotrexate (56)
Uridine (36)
Inosine (34)
Taurine (30)
Adenine (29)
Guanosine (29)
L-Tyrosine (28)
Xanthosine (27)
Biocytin (27)
Xanthine (27)
Porphobilinogen (26)
L-Phenylalanine (26)
Hypoxanthine (26)
Uracil (25)
L-Histidine (25)
Sebacic acid (24)
Adenosine (24)
Riboflavin (24)
Myristic acid (24)
Uric acid (24)
Thymidine (24)
Biotin (24)
Aspartame (23)
Indolelactic acid (23)
Tetradecanedioic acid (23)
Palmitic acid (23)
L-Tryptophan (23)
Dodecanedioic acid (23)
Deoxyinosine (23)
Heptadecanoic acid (22)

First Public Date

2014 (54)
2026 (32)
2024 (24)
2025 (17)
2023 (14)
2021 (14)
2022 (13)
2019 (12)
2017 (10)
2020 (8)
2018 (6)
2013 (6)
2016 (5)
2015 (3)

Modelling Approach

Ordinary differential equation model (3)

Study status

Completed (7)
Terminated (3)
Not provided (2)
Withdrawn (1)
Recruiting (1)

Lab affiliation

Capital Institute of Pediatrics, Beijing (1)
Centre For Eye Research Australia(CERA) (1)
Charles Perkins Centre, School of Medical Sciences, University of Sydney, Sydney, Australia. (1)
Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México (1)
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden (1)
Department of Medical Biochemistry and Biophysics,Karolinska Institutetl, Stockholm, Sweden (1)
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands (1)
Department of Molecular Systems Pharmaceutics, Biomedical and Health Sciences, Hiroshima University (1)
Department of Molecular Systems Pharmaceutics, Graduate School of Biomedical and Health Sciences, Hiroshima University (1)
Department of Oncology-Pathology, Karolinska Institutet Stockholm, Sweden (1)
Division of Chemistry I, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Biomedicum A9, Solnavägen 9, SE-171 77 Stockholm, Sweden (1)
Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden (1)
Laboratorio C036, Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Ciudad de México, México (1)
Lipidomics Group Leibniz-Institute for analytical science – ISAS – e.V. Otto-Hahn-Straße 6b 44227 Dortmund, Germany (1)
National Center for Advancing Translational Sciences (NCATS) NIH (1)
ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, Belgium (1)
Professor Institutt for klinisk og molekylær medisin Norges teknisk-naturvitenskapelige universitet Erling Skjalgssons g 1, Laboratoriesenteret * 231.05.036 Trondheim 7030 Norway (1)
Roman A. Zubarev, PhD, professor Division of Chemistry I, Head Department of Medical Biochemistry & Biophysics Karolinska Institutet Scheelesväg 2, SE 17177 Stockholm, Sweden (1)
The Laboratory for Medical Mass Spectrometry Department of Health Science and Technology Aalborg University Denmark (1)
VIB Medical Biotechnology Center, VIB, A. Baertsoenkaai 3 B-9000 Ghent, Belgium (1)
Washington University in St Louis (1)

Keyword

Methotrexate (10)
Cyclophosphamide (4)
Small intestine lymphoma (3)
Stage IV adult T-cell leukemia/lymphoma (3)
Tacrolimus (2)
Cutaneous B-cell non-Hodgkin lymphoma (2)
Stage IV adult Burkitt lymphoma (2)
Stage IV adult diffuse large cell lymphoma (2)
Stage IV adult diffuse mixed cell lymphoma (2)
Stage IV adult diffuse small cleaved cell lymphoma (2)
Stage IV adult immunoblastic large cell lymphoma (2)
Stage IV adult lymphoblastic lymphoma (2)
Stage IV adult Hodgkin lymphoma (2)
Stage I adult T-cell leukemia/lymphoma (2)
Stage III adult T-cell leukemia/lymphoma (2)
Stage IV cutaneous T-cell non-Hodgkin lymphoma (2)
Stage IV grade 1 follicular lymphoma (2)
Stage IV grade 2 follicular lymphoma (2)
Stage IV grade 3 follicular lymphoma (2)
Stage IV mantle cell lymphoma (2)
Stage IV small lymphocytic lymphoma (2)
Stage IV marginal zone lymphoma (2)
Extranodal marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue (2)
Melphalan (2)
Cyclosporine (2)
Cyclosporins (2)
Etoposide (2)
Anaplastic large cell lymphoma (2)
Methylprednisolone (2)
Prednisolone (2)

IsPrivate

False (3)

Classification

protozoa (3)
bacteria (3)

Modification

-17.026549 (2)
15.994915 (2)
42.010565 (2)
-18.010565 (1)
57.021464 (1)

Study type

Transcription profiling by array (103)
RNA-seq of coding RNA from single cells (26)
RNA-seq of coding RNA (17)
Interventional (14)
ChIP-seq (4)
Unknown experiment type (3)
RNAi profiling by array (2)
Comparative genomic hybridization by array (2)
Other (2)
RNA-seq of non coding RNA (2)
Human - Methylation microarray (1)
ChIP-chip by tiling array (1)
Human - High-throughput sequencing (1)
Cell line - One-color microarray (1)
Cell line - High-throughput sequencing (1)
Spatial transcriptomics by high-throughput sequencing (1)
ScATAC-seq (1)
Single nucleus RNA sequencing (1)
DNA-seq (1)
Methylation profiling by array (1)

Release Date

2022 (430)
2023 (378)
2021 (377)
2025 (341)
2020 (321)
2024 (293)
2019 (242)
2018 (202)
2016 (179)
2017 (178)
2015 (145)
2014 (130)
2013 (88)
2012 (63)
2011 (61)
2026 (58)
2009 (51)
2010 (46)
2008 (30)
2006 (19)
2007 (16)
2005 (6)
2003 (4)
1998 (4)
2004 (3)
2002 (2)
2000 (1)
1999 (1)
1996 (1)
1993 (1)

Location

United States (5)
United Kingdom (3)
Israel (2)
Norway (1)
Singapore (1)
Turkey (1)
France (1)

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Metabolomic Markers of Methotrexate Response, In Vitro

Not available

ORGANISM(S): Homo sapiens

ST001211 | MetabolomicsWorkbench

Transcription profiling of methotrexate-treated human colon cancer C85 cells

The experiment was aimed at identification of genes whose expression is upregulated in human colon cancer C85 cells during the process of establishment of methotrexate-induced senescence.

ORGANISM(S): Homo sapiens

2011-08-23 | E-MEXP-3018 | biostudies-arrayexpress

Genome position and gene amplification - expressional profiling of methotrexate resistant colonies

We investigated the influence of genome position on propensity to amplify. First, we integrated a mutant form of DHFR into different positions in the human genome, challenged cells with methotrexate and then studied the genomic alterations arising in drug resistant cells. We observed site specific d...

ORGANISM(S): Homo sapiens

2007-10-08 | E-GEOD-6361 | biostudies-arrayexpress

Time-resolved immune dynamics in rheumatoid arthritis under methotrexate therapy

Methotrexate (MTX) serves as the primary treatment for rheumatoid arthritis (RA), though its mechanism of action is not yet fully understood. The goal of this study was to map the cellular and molecular changes triggered by MTX across different points in time. Using a prospective longitudinal design...

ORGANISM(S): Homo sapiens

2026-07-01 | E-MTAB-17153 | biostudies-arrayexpress

methotrexate treatment-dynamics of Arabidopsis transcriptome during folate depletion

cea06-02_folate - methotrexate treatment - global analysis of the folate metabolism in Arabidopsis - Treatment of cells of Arabidopsis by methotrexate which is an inhibitor of the synthesis of the folate. Consequently, the pool of folates presents a strong reduction. The goal of this project is to l...

ORGANISM(S): Arabidopsis thaliana

2008-12-18 | E-GEOD-10675 | biostudies-arrayexpress

Methotrexate resistant Leishmania strains

This SuperSeries is composed of the following subset Series: GSE9947: Transcriptional analysis of Leishmania infantum methotrexate resistant strains using full-genome DNA microarrays GSE9948: Transcriptional analysis of Leishmania major methotrexate resistant strains using full-genome DNA microarray...

ORGANISM(S): Leishmania infantum

2010-05-25 | E-GEOD-9949 | biostudies-arrayexpress

Metabolic Markers of Methotrexate Response in Juvenile Idiopathic Arthritis

Not available

ORGANISM(S): Homo sapiens

ST001815 | MetabolomicsWorkbench

Effects of methotrexate on S3 Drosophila cells and Drosophila ovaries

Comparison of transcript abundance between control (untreated) and methotrexate treated S3 Drosophila cells and ovaries disected from female flies. S3 cells were exposed to 0 or 5.2 X 10^-8 M MTX for 4 days then harvested. Flies were exposed to 0 or 5 ppm MTX for 5 days then ovaries were dissected....

ORGANISM(S): Drosophila melanogaster

2010-06-30 | E-GEOD-3495 | biostudies-arrayexpress

Transcription profiling of human cancer cell lines resistant to methotrexate

This SuperSeries is composed of the following subset Series:; GSE11440: Role of Caveolin 1, E-Cadherin, Enolase 2 and PKCa on resistance to methotrexate in human HT29 colon cancer cells; GSE16066: Networking of differentially expressed genes in CaCo2 human colon cancer cells resistant to methotrexat...

ORGANISM(S): Homo sapiens

2009-09-11 | E-GEOD-16648 | biostudies-arrayexpress

Networking of differentially expressed genes in human MCF7 breast cancer cells resistant to methotrexate

A summary of the work associated to these microarrays is the following: The need for an integrated view of all data obtained from high-throughput technologies gave rise to network analyses. These are especially useful to rationalize phenomena in terms of how external perturbations propagate through...

ORGANISM(S): Homo sapiens

2009-09-08 | E-GEOD-16070 | biostudies-arrayexpress

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