ArticleMolecular & cellular proteomics : MCP2025
Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data.
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Article in Molecular & cellular proteomics : MCP, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 1 paper.
0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
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
1 citing paper in PubMed.
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Corrections and comments
- Erratum issued
Authors and funding
74 authors.
Dušica VidovićBD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, Florida, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA. Electronic address: dvidovic@med.miami.edu.
Behrouz ShamsaeiBD2K-LINCS DCIC, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, USA.
Stephan C SchürerBD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, Florida, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA; BD2K-LINCS DCIC, Frost Institute for Data Science & Computing, University of Miami, Miami, Florida, USA.
Phillip KoganBD2K-LINCS DCIC, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, USA.
Szymon ChojnackiBD2K-LINCS DCIC, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, USA.
Michal KourilBD2K-LINCS DCIC, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, USA.
Mario MedvedovicBD2K-LINCS DCIC, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, USA.
Wen NiuBD2K-LINCS DCIC, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, USA.
Evren U AzelogluDToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Marc R BirtwistleDToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Yibang ChenDToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Tong ChenDToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA; DToxS, Center for Advanced Proteomics Research, Rutgers University New Jersey Medical School, Newark, New Jersey, USA.
Jens HansenDToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Bin HuDToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Ravi IyengarDToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Gomathi JayaramanDToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Hong LiDToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA; DToxS, Center for Advanced Proteomics Research, Rutgers University New Jersey Medical School, Newark, New Jersey, USA.
Tong LiuDToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA; DToxS, Center for Advanced Proteomics Research, Rutgers University New Jersey Medical School, Newark, New Jersey, USA.
Eric A SobieDToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Yuguang XiongDToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Matthew J BerberichHMS LINCS Center, Harvard Medical School, Boston, Massachusetts, USA.
Gary BradshawHMS LINCS Center, Harvard Medical School, Boston, Massachusetts, USA.
Mirra ChungHMS LINCS Center, Harvard Medical School, Boston, Massachusetts, USA.
Robert A EverleyHMS LINCS Center, Harvard Medical School, Boston, Massachusetts, USA.
Ben GaudioHMS LINCS Center, Harvard Medical School, Boston, Massachusetts, USA.
Marc HafnerHMS LINCS Center, Harvard Medical School, Boston, Massachusetts, USA.
Marian KalocsayHMS LINCS Center, Harvard Medical School, Boston, Massachusetts, USA.
Caitlin E MillsHMS LINCS Center, Harvard Medical School, Boston, Massachusetts, USA.
Maulik K NariyaHMS LINCS Center, Harvard Medical School, Boston, Massachusetts, USA.
Peter K SorgerHMS LINCS Center, Harvard Medical School, Boston, Massachusetts, USA.
Kartik SubramanianHMS LINCS Center, Harvard Medical School, Boston, Massachusetts, USA.
Chiara VictorHMS LINCS Center, Harvard Medical School, Boston, Massachusetts, USA.
Maria BanuelosNeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, California, USA.
Victoria DardovNeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, California, USA.
Ronald HolewinskiNeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, California, USA.
Danica-Mae ManaloNeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, California, USA.
Berhan MandefroNeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, California, USA.
Andrea D MatlockNeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, California, USA.
Loren OrnelasNeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, California, USA.
Dhruv SareenNeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, California, USA.
Clive N SvendsenNeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, California, USA.
Vineet VaibhavNeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, California, USA.
Jennifer E Van EykNeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, California, USA.
Vidya VenkatramanNeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, California, USA.
Steve FinkbienerNeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, California, USA.
Ernest FraenkelNeuroLINCS, Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA.
Jeffrey RothsteinNeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland, USA.
Leslie ThompsonNeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, California, USA.
Jacob AsieduPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Steven A CarrPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Karen E ChristiansonPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Desiree DavisonPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Deborah O Dele-OniPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Katherine C DeRuffPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Shawn B EgriPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Alvaro Sebastian Vaca JacomePCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Jacob D JaffePCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Daniel LamPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Lev LitichevskiyPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Xiaodong LuPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
James MullahooPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Adam OfficerPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Malvina PapanastasiouPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Ryan PecknerPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Caidin ToderPCCSE, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Joel BlanchardPCCSE, Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Michael BulaPCCSE, Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Tak KoPCCSE, Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Li-Huei TsaiPCCSE, Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Jennie Z YoungPCCSE, Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Vagisha SharmaPCCSE, Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
Ajay PillaiNIH, Bethesda, Maryland, USA.
Jarek MellerBD2K-LINCS DCIC, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, USA. Electronic address: maccoss@uw.edu.
Michael J MacCossPCCSE, Department of Genome Sciences, University of Washington, Seattle, Washington, USA. Electronic address: mellerj@ucmail.uc.edu.
Funding
Data Coordination and Integration Center for LINCS-BD2KU54HL127624 · NHLBI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI MA'AYAN, AVI, SCHURER, STEPHAN C · 2014 to 2019
$23.5MPharmaco Response Signatures and Disease MechanismU54HL127365 · NHLBI · HARVARD MEDICAL SCHOOL · PI SORGER, PETER KARL · 2014 to 2019
$13.1MDrug Combination Signatures for Prediction and Mitigation of ToxicityU54HG008098 · NHGRI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI BIRTWISTLE, MARC R., IYENGAR, SRINIVAS RAVI V · 2014 to 2019
$11.8MNeuron and Glial Cellular Signatures from Normal and Diseased iPS Cells-SupplementU54NS091046 · NINDS · UNIVERSITY OF CALIFORNIA-IRVINE · PI FINKBEINER, STEVEN M, FRAENKEL, ERNEST · 2014 to 2020
$11.7MThere and Back Again: Epigenetic Reinforcement of Cellular Signaling States - OverallU54HG008097 · NHGRI · BROAD INSTITUTE, INC. · PI JAFFE, JACOB DAVID · 2014 to 2019
$9.3MMorPhiC Data Resource and Administrative Coordinating CenterU24HG012674 · NHGRI · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI Helen Elizabeth Parkinson, Stephan C Schurer · 2022 to 2026
$6.9MResource Dissemination and Outreach Center for Illuminating the Druggable GenomeU24TR002278 · NCATS · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI SCHURER, STEPHAN C, SKLAR, LARRY A. · 2018 to 2023
$3.7MUnifying Templates, Ontologies and Tools to Achieve Effective Annotation of Bioassay ProtocolsU01LM012630 · NLM · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI BUNIN, BARRY A, MUSEN, MARK A · 2017 to 2020
$2.1MOrbitrap Fusion Lumos Tribrid MS System for Proteomics Research at Rutgers Newark CampusS10OD025047 · OD · RBHS-NEW JERSEY MEDICAL SCHOOL · PI LI, HONG · 2018 to 2018
$1.1MNCATS NIH HHS U24 TR002278NHGRI NIH HHS U24 HG012674NHGRI NIH HHS U54 HG008097NHGRI NIH HHS U54 HG008098NHLBI NIH HHS U54 HL127365NHLBI NIH HHS U54 HL127624NIH HHS S10 OD025047NINDS NIH HHS U54 NS091046NLM NIH HHS U01 LM012630
Abstract
The Library of Integrated Network-based Cellular Signatures (LINCS), an NIH Common Fund program, has cataloged and analyzed cellular function and molecular activity profiles in response to >80,000 perturbing agents that are potentially disruptive to cells. Because of the importance of proteins and their modifications to the response of specific cellular perturbations, four of the six LINCS centers have included significant proteomics efforts in the characterization of the resulting phenotype. This manuscript aims to describe this effort and the data harmonization and integration of the LINCS proteomics data discussed in recent LINCS papers.
Indexed as
Databases, ProteinInformation DisseminationInternetMetadataProteomicsHumansMultiomicsFAIRnessLINCS data portalLINCS proteomics metadatametadata harmonizationP100 datapiNET
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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.