SigCom LINCS: data and metadata search engine for a million gene expression signatures

• Published in: Nucleic acids research Vol. 50; no. W1; pp. W697 - W709
• Main Authors: Evangelista, John Erol, Clarke, Daniel J B, Xie, Zhuorui, Lachmann, Alexander, Jeon, Minji, Chen, Kerwin, Jagodnik, Kathleen M, Jenkins, Sherry L, Kuleshov, Maxim V, Wojciechowicz, Megan L, Schürer, Stephan C, Medvedovic, Mario, Ma’ayan, Avi
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 05.07.2022
• Subjects: Metadata; Search Engine; Transcriptome - genetics; Web Server Issue
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkac328

Abstract Millions of transcriptome samples were generated by the Library of Integrated Network-based Cellular Signatures (LINCS) program. When these data are processed into searchable signatures along with signatures extracted from Genotype-Tissue Expression (GTEx) and Gene Expression Omnibus (GEO), connections between drugs, genes, pathways and diseases can be illuminated. SigCom LINCS is a webserver that serves over a million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. SigCom LINCS is built with Signature Commons, a cloud-agnostic skeleton Data Commons with a focus on serving searchable signatures. SigCom LINCS provides a rapid signature similarity search for mimickers and reversers given sets of up and down genes, a gene set, a single gene, or any search term. Additionally, users of SigCom LINCS can perform a metadata search to find and analyze subsets of signatures and find information about genes and drugs. SigCom LINCS is findable, accessible, interoperable, and reusable (FAIR) with metadata linked to standard ontologies and vocabularies. In addition, all the data and signatures within SigCom LINCS are available via a well-documented API. In summary, SigCom LINCS, available at https://maayanlab.cloud/sigcom-lincs, is a rich webserver resource for accelerating drug and target discovery in systems pharmacology. Graphical Abstract Graphical Abstract SigCom LINCS user interface workflow map. SigCom LINCS has several entry points to query the database for mimicking and reversing signatures. Users can submit any search term. The search term can be converted to a gene set using the Geneshot or the Enrichr API or used to retrieve SigCom LINCS signatures. Users of SigCom LINCS can also start with a single human gene. The single human gene can be converted into up and down gene sets using co-expression data from ARCHS4 or submitted for reverse search using two Appyters. Users of SigCom LINCS can also submit a gene set or up and down gene sets for signature search.