Pulmonary fibrosis

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Unknown (8596)
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Models (1)

Organisms

Homo sapiens (632)
Mus musculus (505)
Rattus norvegicus (65)
Pseudomonas aeruginosa (41)
Burkholderia cenocepacia (17)
Burkholderia multivorans (6)
Pseudomonas aeruginosa PAO1 (6)
Arabidopsis thaliana (6)
Sus scrofa (5)
Mustela putorius furo (4)
Oryctolagus cuniculus (2)
Pseudomonas aeruginosa UCBPP-PA14 (2)
Viruses (2)
Canis lupus familiaris (2)
Veillonella parvula DSM 2008 (1)
Burkholderia cenocepacia H111 (1)
Burkholderia ambifaria (1)
Streptococcus anginosus (1)
Salmonella enterica (1)
Dictyostelium discoideum (1)
Burkholderia pseudomallei (1)
Escherichia coli ETEC H10407 (1)
Malus domestica (1)
Mus musculus domesticus (1)
unidentified (1)
Burkholderia contaminans (1)
Bordetella bronchiseptica (1)
Aspergillus fumigatus (1)
Burkholderia cepacia (1)
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (1)

Organisms

Homo sapiens (460)
Mus musculus (343)
Rattus norvegicus (39)
human lung metagenome (9)
Mycobacteroides abscessus (4)
mouse gut metagenome (4)
Mustela putorius furo (3)
Rasamsonia piperina (2)
lung metagenome (2)
Canis lupus familiaris (2)
Pseudomonas aeruginosa (2)
unidentified (2)
Pseudomonas sp. LG1E9 (1)
Mycolicibacter arupensis (1)
Mycobacterium simiae (1)
Burkholderia dolosa (1)
Physeter macrocephalus (1)
Achromobacter xylosoxidans (1)
Viruses (1)
Mycobacterium (1)
Ovis aries (1)
Sus scrofa (1)
Staphylococcus aureus (1)

Repository

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pride (98)
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ExpressionAtlas (2)
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GNPS (2)
GPMDB (2)
MetabolomicsWorkbench (2)
BioModels (1)

Tissue

Lung (47)
Fibroblast (12)
Epithelial cell (11)
Cell culture (10)
Blood plasma (6)
Bronchoalveolar lavage (5)
Macrophage (3)
Blood serum (3)
Type II pneumocyte (2)
Cell suspension culture (2)
Blood (2)
Breath (1)
Sputum (1)
Alveolar macrophage (1)
Gastric juice (1)
Lung epithelium (1)
MRC-5 cell (1)
Colonic mucosa (1)
Lung endothelial cell (1)
Bronchial epithelial cell (1)
Epithelial cell of lung (1)
Breast cancer cell (1)
Tissue (1)
Peripheral blood mononuclear cell (1)
Fibroblast of lung (1)
Sputum (1)
Bone marrow (1)
Cardiac muscle cell (1)
Heart (1)
Prokaryotic cell (1)

Disease

Idiopathic pulmonary fibrosis (19)
Pulmonary fibrosis (10)
Cystic fibrosis (7)
Normal (5)
Chronic obstructive pulmonary disease (5)
Porphyria NOS (2)
Fibrosis (2)
Not Available (2)
Cystic fibrosis (2)
Pulmonary hypertension (2)
Severe acute respiratory syndrome (2)
FRD1234 (1)
Mild cystic fibrosis, pulmonary disease (1)
Mild asthma (1)
Triple negative breast cancer (1)
Non-CF (1)
Fibrosis (1)
Reference (1)
Adenocarcinoma (1)
Hypercholesterolaemia (1)
Congenital digestive tract atresia, gastrointestinal motility disorder, intestinal malrotation, congenital gastrointestinal malformation, Hirschsprung disease, anorectal malformation, neonatal gastrointestinal perforation, pancreaticobiliary maljunction, biliary atresia, portal hypertension, liver fibrosis, congenital airway disease, pulmonary cystic disease, diaphragmatic hernia, vascular or lymphatic malformation, tumor disease, abdominal wall dysplasia, renal urological malformation, malformation syndrome, etc (1)
Melanoma (1)
Interstitial lung disease (1)
Diffuse pulmonary fibrosis (1)
Idiopathic interstitial pneumonia (1)
Sarcoidosis (1)
Chronic bronchitis (1)
Paracoccidioidomycosis (1)
Cardiovascular system disease (1)
Influenza (1)

Technology Type

Mass Spectrometry (100)
Shotgun proteomics (55)
Bottom-up proteomics (23)
Data-independent acquisition (10)
Data-dependent acquisition (10)
Mass spectrometry (7)
SWATH MS (6)
Mass spectrometry assay (4)
HDMSE (4)
Gel-based experiment (3)
Top-down proteomics (3)
Affinity purification coupled with mass spectrometry proteomics (3)
ESI (2)
HiSeq X Ten (ILLUMINA) (1)
NMR spectroscopy (1)
DiaPASEF (1)
SRM/MRM (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (16)
Illumina HiSeq 2000 (6)
Illumina HiSeq 4000 (6)
NextSeq 500 (5)
NextSeq 550 (4)
Illumina MiSeq (3)
Manual (2)
10x Genomics Chromium (2)
Illumina NovaSeq X (2)
- (2)
NanoDrop 2000 Spectrophotometer, Agilent 2100 Bioanalyzer (1)
Mastercycler pro S Thermocyler (Eppendorf); 2100 Bioanalyzer (Agilent) (1)
2100 Bioanalyzer (Agilent); Axio Imager.Z2 (ZEISS) (1)
CryoStar NX70 Cryostat (Epredia) (1)
Microbeads (1)
GeneChip Instrument System (1)
Affymetrix mouse gene 1.0 ST arrays (1)
ATR03 reader (1)
Axon GenePix4000B (1)
Model 450 Fluidics Station/Affymetrix GeneChip Scanner 3000 TG System (1)
Agilent 2100 Bioanalyzer (1)
G2505A DNA microarray scanner [Agilent] (1)
G2565BA DNA microarray scanner [Agilent] (1)
Axon GenePix 4000B scanning hardware (1)
Illumina NovaSeq X Plus (1)
RNeasy Mini Kit (QIAGEN) (1)
None (1)
NA (1)
NextSeq 2000 (1)
Illumina HiSeq 1000 (1)

Publication Date

2026 (174)
2025 (151)
2024 (122)
2023 (101)
2021 (80)
2020 (76)
2022 (74)
2013 (70)
2012 (66)
2011 (65)
2019 (57)
2014 (57)
2015 (55)
2018 (52)
2010 (46)
2008 (37)
2017 (29)
2007 (24)
2016 (23)
2009 (23)
2006 (4)
2005 (4)
2004 (1)
2003 (1)

CHEBI ID

CHEBI:16856 (3)
CHEBI:16708 (3)
CHEBI:17053 (3)
CHEBI:16015 (3)
CHEBI:32805 (3)
CHEBI:17191 (3)
CHEBI:15603 (3)
CHEBI:17895 (3)
CHEBI:17295 (3)
CHEBI:17287 (2)
CHEBI:16040 (2)
CHEBI:16977 (2)
CHEBI:15824 (2)
CHEBI:16958 (2)
CHEBI:15741 (2)
CHEBI:15727 (2)
CHEBI:17115 (2)
CHEBI:16335 (2)
CHEBI:17568 (2)
CHEBI:7916 (2)
CHEBI:15891 (2)
CHEBI:18183 (2)
CHEBI:21547 (2)
CHEBI:18050 (2)
CHEBI:422 (2)
CHEBI:16704 (2)
CHEBI:16857 (2)
CHEBI:15996 (2)
CHEBI:15422 (2)
CHEBI:18012 (2)

Metabolite Name

Adenine (5)
Betaine (4)
Choline (4)
Adenosine (4)
Histamine (4)
Guanine (4)
Cytosine (4)
Guanosine (4)
Creatinine (4)
Creatine (4)
L-Leucine (4)
Butabarbital (3)
Phenylacetic acid (3)
Aniline (3)
L-Arginine (3)
N-Acetylornithine (3)
L-Histidine (3)
Methionine (3)
Taurine (3)
Citric acid (3)
Arginine (3)
Lysine (3)
Alanine (3)
Phenylalanine (3)
Cytidine (3)
Uridine (3)
L-Isoleucine (3)
L-Tyrosine (3)
L-Phenylalanine (3)
Hypoxanthine (3)

First Public Date

2026 (177)
2025 (172)
2024 (162)
2023 (100)
2014 (86)
2022 (79)
2020 (68)
2021 (67)
2019 (61)
2018 (48)
2017 (28)
2015 (25)
2013 (17)
2016 (8)

Modelling Approach

Constraint-based model (1)

Study status

Recruiting (2)
Completed (1)

Lab affiliation

Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany (5)
Boehringer Ingelheim Pharma GmbH & Co. KG Drug Discovery Sciences (3)
Institute of Lung Biology and Disease and Comprehensive Pneumology Center, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, German (2)
Helmholtz Zentrum München, Institute of Lung Biology and Disease, Group Systems Medicine of Chronic Lung Disease, Member of the German Center for Lung Research (DZL), Munich, Germany (2)
Department of Biochemistry and Molecular Biology, Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA (2)
The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, UK (2)
Systems Biology Ireland, University College Dublin (2)
Nantes Université, CNRS, INSERM, l’institut du thorax, 44000 Nantes, France (1)
Lung Biology, Department of Experimental Medical Science, Lund University, Lund, Sweden. (1)
Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK. (1)
Molecular Proteomics Laboratory Institute for Molecular Medicine Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany (1)
Spanish National Cancer Research Centre (CNIO), Spain (1)
Universidade Federal do Mato Grosso do Sul- UFMS (1)
Proteome Dynamics, Max Delbruck Center for Molecular Medicine, Germany (1)
Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO 80045 (1)
Infection Medicine Proteomics BMC D13 Klinikgatan 28 22241 Lund Sweden (1)
Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA (1)
Meng Lab, Department of Basic Research, Guangzhou National Laboratory No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District Guangzhou, Guangdong, 510005, China (1)
Wayne State University Proteomics Facility Core Detroit, MI, USA (1)
Department of Pathology and Cell Biology Morsani College of Medicine University of South Florida (1)
Institute of Lung Health and Immunity, and Comprehensive Pneumology Center with the CPC-M bioArchive, Ludwig-Maximilians-Universität München and Helmholtz Zentrum München, Munich, Germany, Member of the German Center for Lung Research (DZL); 8Department of Pediatrics, and Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA (1)
University of Michigan Medical Center Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine 1150 West Medical Center Drive 6301 MSRB III Ann Arbor, MI 48109-5642 (1)
Siamwala Lab Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI Warren Alpert Medical School of Brown University, Providence VA Medical Center, Providence, RI (1)
1Department of Medicine, University of Minnesota, 420 Delaware Street, SE, Minneapolis, Minnesota 55455, USA (1)
Medical Mycology Unit, Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland. (1)
Transplantation laboratory, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland (1)
Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany. Berlin Institute of Health (BIH), Berlin, Germany. (1)
Professor of Microbiology and Animal Sciences University of Illinois at Urbana/Champaign (1)
Laboratorio de Biología Molecular Departamento de Fibrosis Pulmonar Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas" (INER). Ciudad de México (1)
University of Bern, Department of BioMedical Research (DBMR), Lung Precision Medicine (LPM) Program (1)

Keyword

Rapamune (1)
Neoral (1)
Prograf (1)
Diabete Mellitus (1)
Sickle Cell Disease (1)
Sjogren’s Syndrome (1)

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Classification

bacteria (6)
viruses (1)

Study type

Transcription profiling by array (321)
RNA-seq of coding RNA (39)
RNA-seq of coding RNA from single cells (8)
Comparative genomic hybridization by array (6)
DNA-seq (6)
Unknown experiment type (4)
Methylation profiling by array (4)
ChIP-chip by tiling array (3)
Other (3)
ChIP-seq (3)
High-throughput sequencing (2)
Cell line - High-throughput sequencing (2)
Genotyping by array (2)
Proteomic profiling by array (2)
RNA-seq of total RNA (2)
Observational (2)
Transcription profiling by SAGE (1)
Plant - High-throughput sequencing (1)
Whole chromosome random sequencing (1)
Animal - High-throughput sequencing (1)
Transcription profiling by RT-PCR (1)
Spatial transcriptomics by high-throughput sequencing (1)
ATAC-seq (1)
MicroRNA profiling by array (1)
RNA-seq of non coding RNA (1)
Interventional (1)

Release Date

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2018 (471)
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2014 (233)
2013 (192)
2012 (190)
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2011 (163)
2010 (98)
2009 (87)
2008 (85)
2007 (56)
2006 (30)
2005 (17)
2004 (10)
2003 (7)
2002 (4)
1999 (3)
2001 (2)
2000 (1)
1998 (1)

Location

United States (1)
United Kingdom (1)
Japan (1)

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Gene expression profiles based on Pulmonary Artery Pressures in Pulmonary Fibrosis

Pulmonary Hypertension (PH) is a frequent complication of Pulmonary Fibrosis (PF). PH can be seen in PF in the abscence of hypoxemia, irrespective of the degree of fibrosis. At the same time, a consistent number of patients with advanced PF never develop PH. The pathogenesis of PH secondary to PF re...

ORGANISM(S): Homo sapiens

2011-06-01 | E-GEOD-24988 | biostudies-arrayexpress

Combined Mesenchymal Stem Cells and Metformin Therapy Modulates Key Macromolecular Pathways in Pulmonary Fibrosis: Evidence from Untargeted Metabolomics

Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal interstitial lung disease. Current treatment options remain limited, driving interest in novel therapeutic approaches. Mesenchymal stem cells (MSCs) possess immunomodulatory and regenerative properties, while metformin, traditionally ...

2025-08-25 | MTBLS12893 | MetaboLights

Development and Preclinical Efficacy of Novel Transforming Growth Factor-β1 (TGFβ1) siRNAs for Pulmonary Fibrosis

Idiopathic pulmonary fibrosis is a chronic devastating disease of unknown etiology. No therapy is currently available. A growing body of evidence supports the role of TGFβ1 as the major player in the pathogenesis of the disease. This study designed novel human- and mouse-specific siRNAs and siRNA/DN...

ORGANISM(S): Mus musculus

2011-11-22 | E-GEOD-28122 | biostudies-arrayexpress

Multi-omics Analysis Reveals New Insights into Yak Lung Fibrosis Mechanisms Under High-Altitude Adaptation

The lung of yak is an important adaptive organ in the cold and low oxygen environment. Hypoxia can induce the pathological manifestations of pulmonary fibrosis in yak, but there was no study on hypoxia induced pulmonary fibrosis in yak. In this study full target metabolomics were used to conduct ...

2025-07-07 | MTBLS11648 | MetaboLights

Bleomycin induces molecular changes directly relevant to idiopathic pulmonary fibrosis: A model for “active” disease

Genomic profiling of RNA from cultured human fibroblasts of donor samples in the 10-14th passage was carried out to determine expression changes in the fibroblasts of individual with different degrees of pulmonary fibrosis. Donors consisted of individuals with rapid progressing pulmonary fibrosis, s...

ORGANISM(S): Homo sapiens

2013-04-10 | E-GEOD-44723 | biostudies-arrayexpress

Spatial transcriptomics (Visium, 10x Genomics) data for human Idiopathic Pulmonary Fibrosis (IPF) and control lung tissue

Visium (10x Genomics) spatially resolved transcriptomics data generated from normal and Idiopathic Pulmonary Fibrosis (IPF) lung parenchyma tissues collected from human donors. The fresh-frozen tissues that were analyzed were from four healthy control (HC) subjects and from four IPF patients. For ea...

ORGANISM(S): Homo sapiens

2024-05-28 | E-MTAB-14121 | biostudies-arrayexpress

Early Detection of Cystic Fibrosis Acute Pulmonary Exacerbations in Adult and Pediatric Patients by Exhaled Breath Condensate Metabolomics.

Not available

ORGANISM(S): Homo sapiens

ST001164 | MetabolomicsWorkbench

miRNA expression data in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is an untreatable fibrotic lung disease characterized by fibroblast proliferation and epithelial mesenchymal transition. The expression and role of microRNAs (miRNA) has not been studied in IPF. Using miRNA expression microarrays we identified 46 differentially ex...

ORGANISM(S): Homo sapiens

2010-04-23 | E-GEOD-13316 | biostudies-arrayexpress

Human Epididymis Protein 4 Promotes Aberrant Epithelial-Fibroblast Crosstalk in Pulmonary Fibrosis

Invasive lung myofibroblasts are the main cause of tissue remodeling in idiopathic pulmonary fibrosis (IPF). A key mechanism contributing to this important feature is aberrant crosstalk between the abnormal/injured lung epithelium and pulmonary fibroblasts. Here, we demonstrated that lungs from pati...

ORGANISM(S): Homo Sapiens

2024-12-17 | PXD058959 |

MicroRNA expression data in Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is an untreatable fibrotic lung disease characterized by fibroblast proliferation and epithelial mesenchymal transition. Using miRNA expression microarrays we identified 96 differentially expressed miRNA in IPF lungs which included let-7d, miR-30 family, miR-29 fa...

ORGANISM(S): Homo sapiens

2013-01-04 | E-GEOD-27430 | biostudies-arrayexpress

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