ArticleBMC genomics2012
A searchable cross-platform gene expression database reveals connections between drug treatments and disease.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Transcription-Driven Repurposing of Cardiotonic Steroids for Lithium Treatment of Severe Depression.Cells · 2025Article
- Pathological mechanisms and candidate therapeutic approaches in the hearing loss of mice carrying human MIR96 mutations.Genome medicine · 2024Article
- Genomic evidence for the suitability of Göttingen Minipigs with a rare seizure phenotype as a model for human epilepsy.Neurogenetics · 2024Article
- Prediction and analysis of genetic effect in idiopathic pulmonary fibrosis and gastroesophageal reflux disease.IET systems biology · 2023Article
- Navigating Transcriptomic Connectivity Mapping Workflows to Link Chemicals with Bioactivities.Chemical research in toxicology · 2022Review
- Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.Genome biology · 2022Article
- Drug connectivity mapping and functional analysis reveal therapeutic small molecules that differentially modulate myelination.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2022Article
- Drug repositioning and repurposing for Alzheimer disease.Nature reviews. Neurology · 2020Review
- Transcription-based drug repurposing for COVID-19.Virus research · 2020Article
- Whole transcriptome in silico screening implicates cardiovascular and infectious disease in the mechanism of action underlying atypical antipsychotic side effects.Alzheimer's & dementia (New York, N. Y.) · 2020Article
- No transcriptional evidence for active NaChannels (Austin, Tex.) · 2019Article
- Drug repurposing for Alzheimer's disease based on transcriptional profiling of human iPSC-derived cortical neurons.Translational psychiatry · 2019Article
- Astrocytes are direct cellular targets of lithium treatment: novel roles for lysyl oxidase and peroxisome-proliferator activated receptor-γ as astroglial targets of lithium.Translational psychiatry · 2019Article
- Targeted repositioning identifies drugs that increase fibroblast growth factor 20 production and protect against 6-hydroxydopamine-induced nigral cell loss in rats.Scientific reports · 2019Article
- From gene networks to drugs: systems pharmacology approaches for AUD.Psychopharmacology · 2018Review
- A question of fate.PLoS biology · 2017Article
- Pharmacogenomic identification of small molecules for lineage specific manipulation of subventricular zone germinal activity.PLoS biology · 2017Article
- Quantitative Identification of Compound-Dependent On-Modules and Differential Allosteric Modules From Homologous Ischemic Networks.CPT: pharmacometrics & systems pharmacology · 2016Article
- Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.Nature communications · 2016Article
- Database of Gene Co-Regulation (dGCR): A Web Tool for Analysing Patterns of Gene Co-regulation across Publicly Available Expression Data.Journal of genomics · 2015Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTranscriptional data covering multiple platforms and species is collected and processed into a searchable platform independent expression database (SPIED). SPIED consists of over 100,000 expression fold profiles defined independently of control/treatment assignment and mapped to non-redundant gene lists. The database is thus searchable with query profiles defined over genes alone. The motivation behind SPIED is that transcriptional profiles can be quantitatively compared and ranked and thus serve as effective surrogates for comparing the underlying biological states across multiple experiments.
resultsDrug perturbation, cancer and neurodegenerative disease derived transcriptional profiles are shown to be effective descriptors of the underlying biology as they return related drugs and pathologies from SPIED. In the case of Alzheimer's disease there is high transcriptional overlap with other neurodegenerative conditions and rodent models of neurodegeneration and nerve injury. Combining the query signature with correlating profiles allows for the definition of a tight neurodegeneration signature that successfully highlights many neuroprotective drugs in the Broad connectivity map.
conclusionsQuantitative querying of expression data from across the totality of deposited experiments is an effective way of discovering connections between different biological systems and in particular that between drug action and biological disease state. Examples in cancer and neurodegenerative conditions validate the utility of SPIED.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.