Evidence map›Paper›PMID 29140462›Full record

ArticleNucleic acids research2018

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data.

Amar Koleti, Raymond Terryn, Vasileios Stathias, Caty Chung, Daniel J Cooper, John P Turner, Dušica Vidovic, Michele Forlin, Tanya T Kelley, Alessandro D'Urso and 19 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
106citing papers in PubMed, 2 pooled it
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

106 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Pooled it
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  15. Advanced RPL19-TRAPNatural products and bioprospecting · 2025
    Article
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46 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

29 authors.

Amar KoletiCenter for Computational Science, University of Miami, FL, USA.
Raymond TerrynCenter for Computational Science, University of Miami, FL, USA.
Vasileios StathiasBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Caty ChungCenter for Computational Science, University of Miami, FL, USA.
Daniel J CooperBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
John P TurnerCenter for Computational Science, University of Miami, FL, USA.
Dušica VidovicCenter for Computational Science, University of Miami, FL, USA.
Michele ForlinCenter for Computational Science, University of Miami, FL, USA.
Tanya T KelleyBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Alessandro D'UrsoCenter for Computational Science, University of Miami, FL, USA.
Bryce K AllenCenter for Computational Science, University of Miami, FL, USA.
Denis TorreBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Kathleen M JagodnikBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Lily WangBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Sherry L JenkinsBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Christopher MaderCenter for Computational Science, University of Miami, FL, USA.
Wen NiuBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Mehdi FazelBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Naim MahiBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Marcin PilarczykBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Nicholas ClarkBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Behrouz ShamsaeiBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Jarek MellerBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Juozas VasiliauskasBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
John ReichardBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Mario MedvedovicBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Avi Ma'ayanBD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
Ajay PillaiDivision of Genome Sciences, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Stephan C SchürerCenter for Computational Science, University of Miami, FL, USA.

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
$23.5M
TRAINING PROGRAM IN MOLECULAR AND CELLULAR CARDIOLOGYT32HL007824 · NHLBI · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI GELB, BRUCE D · 1995 to 2022
$8.6M
NHLBI NIH HHS T32 HL007824NHLBI NIH HHS U54 HL127624
6 · The paper itself

Abstract

The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses. Integration of, and unified access to LINCS data has therefore been particularly challenging. The Big Data to Knowledge (BD2K) LINCS Data Coordination and Integration Center (DCIC) has developed data standards specifications, data processing pipelines, and a suite of end-user software tools to integrate and annotate LINCS-generated data, to make LINCS signatures searchable and usable for different types of users. Here, we describe the LINCS Data Portal (LDP) (http://lincsportal.ccs.miami.edu/), a unified web interface to access datasets generated by the LINCS DSGCs, and its underlying database, LINCS Data Registry (LDR). LINCS data served on the LDP contains extensive metadata and curated annotations. We highlight the features of the LDP user interface that is designed to enable search, browsing, exploration, download and analysis of LINCS data and related curated content.

Indexed as

Databases, FactualCell BiologyComputational BiologyDatabases, GeneticData CurationEpigenomicsHumansMetadataProteomicsSoftwareSystems BiologyUser-Computer Interface

Identifiers

PMID29140462
PMCPMC5753343

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

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.