ArticlePloS one2017
Comparative analysis of genes frequently regulated by drugs based on connectivity map transcriptome data.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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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.
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Who cites it
3 citing papers in PubMed, 10 citations in OpenAlex.
- The Advantages of Connectivity Map Applied in Traditional Chinese Medicine.Frontiers in pharmacology · 2021Review
- Universal Nature of Drug Treatment Responses in Drug-Tissue-Wide Model-Animal Experiments Using Tensor Decomposition-Based Unsupervised Feature Extraction.Frontiers in genetics · 2020Article
- Comparative Analysis of Human Genes Frequently and Occasionally Regulated by mGenomics, proteomics & bioinformatics · 2018Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression is perturbated by drugs to different extent. Analyzing genes whose expression is frequently regulated by drugs would be useful for the screening of candidate therapeutic targets and genes implicated in side effect. Here, we obtained the differential expression number (DEN) for genes profiled in Affymetrix microarrays from the Connectivity Map project, and conducted systemic comparative computational analysis between high DEN genes and other genes. Results indicated that genes with higher down-/up-regulation number (down_h/up_h) tended to be clustered in genome, and have lower homologous gene number, higher SNP density and more disease-related SNP. Down_h and up_h were significantly enriched in cancer related pathways, while genes with lower down-/up-regulation number (down_l/up_l) were mainly involved in the development of nervous system diseases. Besides, up_h had lower interaction network degree, later developmental stage to express, higher tissue expression specificity than up_l, while down_h showed reversed tendency in comparison with down_l. Together, our analysis suggests that genes frequently regulated by drugs are more likely to be associated with disease-related functions, but the extensive activation of conserved and widely expressed genes by drugs is disfavored.
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