Evidence map›Paper›PMID 29915188›Full record

ArticleNature methods2018

GeNets: a unified web platform for network-based genomic analyses.

Taibo Li, April Kim, Joseph Rosenbluh, Heiko Horn, Liraz Greenfeld, David An, Andrew Zimmer, Arthur Liberzon, Jon Bistline, Ted Natoli and 15 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.

0numbers the graph read from it
0cells of the map it votes in
37citing papers in PubMed
–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

37 citing papers in PubMed.

  1. Article
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  6. Review
  7. Article
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  11. Article
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  13. TIGA: target illumination GWAS analytics.Bioinformatics (Oxford, England) · 2021
    Article
  14. Article
  15. De novo variation in bipolar disorder.Molecular psychiatry · 2021
    Article
  16. Article
  17. Article
  18. Article
  19. Review
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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

25 authors.

Taibo LiDepartment of Surgery, Massachusetts General Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0002-6624-9293
April KimDepartment of Surgery, Massachusetts General Hospital, Boston, MA, USA.
Joseph RosenbluhBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Heiko HornDepartment of Surgery, Massachusetts General Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0003-4898-0557
Liraz GreenfeldDepartment of Surgery, Massachusetts General Hospital, Boston, MA, USA.
David AnBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Andrew ZimmerBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Arthur LiberzonBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Jon BistlineBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Ted NatoliBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Yang LiBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Aviad TsherniakBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-3797-1877
Rajiv NarayanBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Aravind SubramanianBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Ted LiefeldBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Bang WongBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Dawn ThompsonBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Sarah CalvoBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Steve CarrBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-7203-4299
Jesse BoehmBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-6795-6336
Jake JaffeBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-9845-1210
Jill MesirovBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Nir HacohenBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Aviv RegevBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Kasper LageDepartment of Surgery, Massachusetts General Hospital, Boston, MA, USA. lage.kasper@mgh.harvard.edu.ORCID http://orcid.org/0000-0001-6827-6239

Funding

THE DROSOPHILA GENETICS AND RNAI CORE (THE FLY CORE)P01HD068250 · NICHD · MASSACHUSETTS GENERAL HOSPITAL · PI CHUNG, WENDY K, DONAHOE, PATRICIA K · 2011 to 2022
$17.1M
Proteo-genomic Discovery, Prioritization and Verification of Cancer BiomarkersU24CA160034 · NCI · BROAD INSTITUTE, INC. · PI CARR, STEVEN A, PAULOVICH, AMANDA G · 2011 to 2016
$16.2M
Supporting Integrative Genomic Analysis Users with GenePatternR01GM074024 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P. · 2005 to 2019
$6.6M
Rare Sequence Variation and Diabetes Quantitative TraitsU01DK078616 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI MEIGS, JAMES B · 2015 to 2019
$3.6M
Discovery & Application of Proteomics-Based Biomarkers of Early Myocardial InjuryR01HL096738 · NHLBI · MASSACHUSETTS GENERAL HOSPITAL · PI CARR, STEVEN A, GERSZTEN, ROBERT E · 2009 to 2012
$2.9M
2/3 Building Integrative CNS Networks for Genomic Analysis of AutismR01MH109903 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI HANSEN, KASPER LAGE · 2016 to 2020
$1.4M
NCI NIH HHS U24 CA160034NHLBI NIH HHS HHSN268201000033CNHLBI NIH HHS R01 HL096738NICHD NIH HHS P01 HD068250NIDDK NIH HHS U01 DK078616NIGMS NIH HHS R01 GM074024NIMH NIH HHS R01 MH109903
6 · The paper itself

Abstract

Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which to interpret a particular genetic dataset. We present GeNets, a platform in which users can train a machine-learning model (Quack) to carry out these comparisons and execute, store, and share analyses of genetic and RNA-sequencing datasets.

Indexed as

InternetMachine LearningDatabases, Nucleic AcidDNAGenomicsNucleic Acid Amplification TechniquesRNASoftwareDNARNA

Identifiers

PMID29915188
PMCPMC6450090

What OpenQuestion holds

Textmetadata
LicenceTDM
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.