Evidence map›Paper›PMID 18466581›Full record

ArticleBMC proceedings2007

Linkage analysis using principal components of gene expression data.

Elizabeth J Atkinson, Brooke L Fridley, Ellen L Goode, Shannon K McDonnell, Wen Liu-Mares, Kari G Rabe, Zhifu Sun, Susan L Slager, Mariza de Andrade

Abstract read
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In one paragraph

Article in BMC proceedings, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

9 authors.

Elizabeth J AtkinsonDivision of Biostatistics, Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 1st Street SW, Rochester, Minnesota 55905, USA. atkinson@mayo.edu
Brooke L Fridley
Ellen L Goode
Shannon K McDonnell
Wen Liu-Mares
Kari G Rabe
Zhifu Sun
Susan L Slager
Mariza de Andrade

Funding

Mayo Cancer Genetic Epidemiology Training ProgramR25CA092049 · NCI · MAYO CLINIC ROCHESTER · PI PETERSEN, GLORIA M., VACHON, CELINE M · 2001 to 2018
$5.3M
Statistical Genetic Methods for Cancer Gene StudiesK07CA094919 · NCI · MAYO CLINIC ROCHESTER · PI SLAGER, SUSAN L · 2002 to 2006
$663k
Novel approaches in linkage analysis for complex traitsR01HL071917 · NHLBI · MAYO CLINIC COLL OF MEDICINE, ROCHESTER · PI DE ANDRADE, MARIZA · 2002 to 2003
$289k
NCI NIH HHS K07 CA094919NCI NIH HHS R25 CA092049NHLBI NIH HHS R01 HL071917
6 · The paper itself

Abstract

The goal of this paper is to investigate the effect of using principal components as a data reduction method for expression data in linkage analysis. We used 45 probes normalized using the Affymetrix Global Scaling that had evidence of high heritability to estimate the first 10 principal components (PC). A genome-wide linkage scan was performed on the 45 expression values and the 10 PCs using 2272 single-nucleotide polymorphisms. Our conclusions were: 1) PC analyses under-performed the single-probe analysis for known signals; 2) the PC that best reproduced the single-probe analysis was primarily composed of that probe; 3) no new signals were detected in the PC analysis; 4) no new pleiotropic effects were detected in the PC analysis.

Identifiers

PMID18466581
PMCPMC2367556

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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.