ArticleNucleic acids research2008
Gene expression module-based chemical function similarity search.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- Reconciling multiple connectivity-based systems biology methods for drug repurposing.Briefings in bioinformatics · 2025Review
- A review of connectivity map and computational approaches in pharmacogenomics.Briefings in bioinformatics · 2018Review
- Identification association of drug-disease by using functional gene module for breast cancer.BMC medical genomics · 2015Article
- Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain.Frontiers in plant science · 2015Article
- Predicting response to preoperative chemotherapy agents by identifying drug action on modeled microRNA regulation networks.PloS one · 2014Article
- Integrated analysis identifies interaction patterns between small molecules and pathways.BioMed research international · 2014Article
- A cross-species analysis method to analyze animal models' similarity to human's disease state.BMC systems biology · 2012Article
- Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses.Scientific reports · 2012Article
- Combining ZHENG Theory and High-Throughput Expression Data to Predict New Effects of Chinese Herbal Formulae.Evidence-based complementary and alternative medicine : eCAM · 2012Article
- Expression-based in silico screening of candidate therapeutic compounds for lung adenocarcinoma.PloS one · 2011Article
- Generalized random set framework for functional enrichment analysis using primary genomics datasets.Bioinformatics (Oxford, England) · 2011Article
- Association of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues.BMC bioinformatics · 2010Article
- Small Molecule Subgraph Detector (SMSD) toolkit.Journal of cheminformatics · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Investigation of biological processes using selective chemical interventions is generally applied in biomedical research and drug discovery. Many studies of this kind make use of gene expression experiments to explore cellular responses to chemical interventions. Recently, some research groups constructed libraries of chemical related expression profiles, and introduced similarity comparison into chemical induced transcriptome analysis. Resembling sequence similarity alignment, expression pattern comparison among chemical intervention related expression profiles provides a new way for chemical function prediction and chemical-gene relation investigation. However, existing methods place more emphasis on comparing profile patterns globally, which ignore noises and marginal effects. At the same time, though the whole information of expression profiles has been used, it is difficult to uncover the underlying mechanisms that lead to the functional similarity between two molecules. Here a new approach is presented to perform biological effects similarity comparison within small biologically meaningful gene categories. Regarding gene categories as units, a reduced similarity matrix is generated for measuring the biological distances between query and profiles in library and pointing out in which modules do chemical pairs resemble. Through the modularization of expression patterns, this method reduces experimental noises and marginal effects and directly correlates chemical molecules with gene function modules.
Indexed as
Identifiers
What OpenQuestion holds
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.