Evidence map›Paper›PMID 25480373›Full record

ArticleBioinformatics (Oxford, England)2015

Graphical algorithm for integration of genetic and biological data: proof of principle using psoriasis as a model.

Lam C Tsoi, James T Elder, Goncalo R Abecasis

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed, 2 pooled it
0.9field-weighted citation impact, top 27% of its field
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

7 citing papers in PubMed, 2 syntheses or guidelines pooled it, 12 citations in OpenAlex.

  1. Pooled it
  2. Pooled it
  3. Article
  4. Psoriasis and Genetics.Acta dermato-venereologica · 2020
    Review
  5. Article
  6. Review
  7. 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

3 authors at 1 institution in 1 country.

Lam C TsoiDepartment of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA, Department of Dermatology, University of Michigan, Ann Arbor, MI, USA, and Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA.
James T ElderDepartment of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA, Department of Dermatology, University of Michigan, Ann Arbor, MI, USA, and Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA, Department of Dermatology, University of Michigan, Ann Arbor, MI, USA, and Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA.
Goncalo R AbecasisDepartment of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA, Department of Dermatology, University of Michigan, Ann Arbor, MI, USA, and Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA.
University of Michigan–Ann Arbor · US

Funding

Linkage analysis of familial psoriasis(Supplement)R01AR042742 · NIAMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ELDER, JAMES TILFORD · 1994 to 2021
$10.1M
Genetic and Genomic Dissection of Psoriatic ArthritisR01AR063611 · NIAMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ELDER, JAMES TILFORD, GLADMAN, DAFNA D · 2012 to 2023
$6.2M
More Complete Assessment of DNA Variation in Age-Related Macular DegenerationR01EY022005 · NEI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ABECASIS, GONCALO · 2011 to 2014
$4.7M
Identification of Psoriatic Arthritis Genes in the MHCR01AR050511 · NIAMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ELDER, JAMES TILFORD · 2004 to 2013
$4.2M
Combined Analysis of Gene Expression and DNA Variation in PsoriasisR01AR054966 · NIAMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ELDER, JAMES TILFORD · 2007 to 2011
$3.2M
Computational and statistical models for human geneticsR01HG007022 · NHGRI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ABECASIS, GONCALO · 2012 to 2016
$3.0M
Functional Genomics of PsoriasisR01AR065183 · NIAMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ELDER, JAMES TILFORD · 2013 to 2016
$1.7M
NEI NIH HHS R01EY022005NHGRI NIH HHS R01HG007022NIAMS NIH HHS R01 AR042742NIAMS NIH HHS R01 AR050511NIAMS NIH HHS R01 AR054966NIAMS NIH HHS R01 AR062382NIAMS NIH HHS R01 AR063611NIAMS NIH HHS R01 AR065183
6 · The paper itself

Abstract

motivationPathway analysis to reveal biological mechanisms for results from genetic association studies have great potential to better understand complex traits with major human disease impact. However, current approaches have not been optimized to maximize statistical power to identify enriched functions/pathways, especially when the genetic data derives from studies using platforms (e.g. Immunochip and Metabochip) customized to have pre-selected markers from previously identified top-rank loci. We present here a novel approach, called Minimum distance-based Enrichment Analysis for Genetic Association (MEAGA), with the potential to address both of these important concerns.

resultsMEAGA performs enrichment analysis using graphical algorithms to identify sub-graphs among genes and measure their closeness in interaction database. It also incorporates a statistic summarizing the numbers and total distances of the sub-graphs, depicting the overlap between observed genetic signals and defined function/pathway gene-sets. MEAGA uses sampling technique to approximate empirical and multiple testing-corrected P-values. We show in simulation studies that MEAGA is more powerful compared to count-based strategies in identifying disease-associated functions/pathways, and the increase in power is influenced by the shortest distances among associated genes in the interactome. We applied MEAGA to the results of a meta-analysis of psoriasis using Immunochip datasets, and showed that associated genes are significantly enriched in immune-related functions and closer with each other in the protein-protein interaction network. AVAILABILITY AND IMPLEMENTATION: http://genome.sph.umich.edu/wiki/MEAGA CONTACT: : tsoi.teen@gmail.com or goncalo@umich.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

AlgorithmsComputer GraphicsGene Regulatory NetworksProtein Interaction MapsComputer SimulationDatabases, FactualHumansMeta-Analysis as TopicPsoriasisSystems Biology

Identifiers

PMID25480373
PMCPMC4393514
OpenAlexW2122792094

What OpenQuestion holds

Textmetadata
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.