Evidence map›Paper›PMID 33896739›Full record

ReviewJournal of genetics and genomics = Yi chuan xue bao2021

Pathway analysis for genome-wide genetic variation data: Analytic principles, latest developments, and new opportunities.

Micah Silberstein, Nicholas Nesbit, Jacquelyn Cai, Phil H Lee

Abstract readReview
In one paragraph

Review in Journal of genetics and genomics = Yi chuan xue bao, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed, 1 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

10 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Article
  3. Circulating miR-10b-5p as a candidate biomarker of atrial fibrillation recurrence after catheter ablation: a two-phase translational study.Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology · 2026
    Article
  4. Article
  5. Review
  6. Polymorphism of IL-12/IL-23 axis is associated with coronary heart disease.Journal of cellular and molecular medicine · 2024
    Article
  7. SPP2 plays a role in the tumorigenesis of hepatocellular carcinoma: A bioinformatic based analysis.Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences · 2023
    Article
  8. Article
  9. Article
  10. Article
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

4 authors.

Micah SilbersteinCenter for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
Nicholas NesbitCenter for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
Jacquelyn CaiCenter for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
Phil H LeeCenter for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: PLEE0@mgh.harvard.edu.

Funding

Comprehensive analysis of genetic pleiotropy in eleven neuropsychiatric disordersR01MH119243 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI LEE, PHIL H. · 2020 to 2024
$2.3M
Neuroimaging genetics to study social cognitive deficits in ASD and schizophreniaR00MH101367 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI LEE, PHIL H. · 2017 to 2019
$747k
NIMH NIH HHS R00 MH101367NIMH NIH HHS R01 MH119243
6 · The paper itself

Abstract

Pathway analysis, also known as gene-set enrichment analysis, is a multilocus analytic strategy that integrates a priori, biological knowledge into the statistical analysis of high-throughput genetics data. Originally developed for the studies of gene expression data, it has become a powerful analytic procedure for in-depth mining of genome-wide genetic variation data. Astonishing discoveries were made in the past years, uncovering genes and biological mechanisms underlying common and complex disorders. However, as massive amounts of diverse functional genomics data accrue, there is a pressing need for newer generations of pathway analysis methods that can utilize multiple layers of high-throughput genomics data. In this review, we provide an intellectual foundation of this powerful analytic strategy, as well as an update of the state-of-the-art in recent method developments. The goal of this review is threefold: (1) introduce the motivation and basic steps of pathway analysis for genome-wide genetic variation data; (2) review the merits and the shortcomings of classic and newly emerging integrative pathway analysis tools; and (3) discuss remaining challenges and future directions for further method developments.

Indexed as

Genetic VariationGenome-Wide Association StudyGenomicsHumansGene-set enrichment analysisGenome-wide association studyMultilocus association analysisPathway analysisSet-based association analysis

Identifiers

PMID33896739
PMCPMC8286309

What Socratic 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 Socratic graph.