title: LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.
abstract: For the Library of Integrated Network-based Cellular Signatures (LINCS) project many gene expression signatures using the L1000 technology have been produced. The L1000 technology is a cost-effective method to profile gene expression in large scale. LINCS Canvas Browser (LCB) is an interactive HTML5 web-based software application that facilitates querying, browsing and interrogating many of the currently available LINCS L1000 data. LCB implements two compacted layered canvases, one to visualize clustered L1000 expression data, and the other to display enrichment analysis results using 30 different gene set libraries. Clicking on an experimental condition highlights gene-sets enriched for the differentially expressed genes from the selected experiment. A search interface allows users to input gene lists and query them against over 100 000 conditions to find the top matching experiments. The tool integrates many resources for an unprecedented potential for new discoveries in systems biology and systems pharmacology. The LCB application is available at http://www.maayanlab.net/LINCS/LCB. Customized versions will be made part of the http://lincscloud.org and http://lincs.hms.harvard.edu websites.
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA.
authors.forename: Qiaonan
authors.initials: Q
authors.lastname: Duan
authors.affiliation: Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Corey
authors.initials: C
authors.lastname: Flynn
authors.affiliation: Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Mario
authors.initials: M
authors.lastname: Niepel
authors.affiliation: Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Hafner
authors.affiliation: Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Jeremy L
authors.initials: JL
authors.lastname: Muhlich
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA.
authors.forename: Nicolas F
authors.initials: NF
authors.lastname: Fernandez
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Rouillard
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Tan
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA.
authors.forename: Edward Y
authors.initials: EY
authors.lastname: Chen
authors.affiliation: Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Todd R
authors.initials: TR
authors.lastname: Golub
authors.affiliation: Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Peter K
authors.initials: PK
authors.lastname: Sorger
authors.affiliation: Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Aravind
authors.initials: A
authors.lastname: Subramanian
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA avi.maayan@mssm.edu.
authors.forename: Avi
authors.initials: A
authors.lastname: Ma'ayan
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology; D001943:Breast Neoplasms / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D007378:Interleukins / Q000494:pharmacology; D020407:Internet; D008264:Macrophages / Q000187:drug effects / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D000970:Antineoplastic Agents; D007378:Interleukins