Literature DB >> 34390470

Comment on "Altered Expression of Long Non-coding RNAs in Peripheral Blood Mononuclear Cells of Patients with Alzheimer's Disease".

Yuqing Wang1, Heng Zhao1, Xiaoqiang Liu2, Lei Yan3,4.   

Abstract

We read with great interest the article by Kurt and colleagues. The authors, using microarray in clinical samples, found altered expression of lncRNAs in peripheral blood mononuclear cells (PBMCs) of patients with Alzheimer's disease (AD). The findings from this study may open a door to the understanding of AD pathogenesis targeted by lncRNAs. In our opinion, it is necessary to further clarify the data analysis strategy of this study. According to the authors' description, they seem to use unadjusted p values and fold change of expression values when defining significantly differentially expressed lncRNAs in PBMCs of subjects with probable AD and healthy control groups. However, due to the characteristics of lncRNA and high false positives caused by multiple comparisons, t-test is not suitable for high-level microarray analysis. It seems that a specialized high-level microarray analysis method is essential to reach a reliable result. Accurate analysis results will provide a convincing basis for subsequent experiments.
© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Bioinformatics; LncRNA; Microarray; Statistics

Mesh:

Substances:

Year:  2021        PMID: 34390470     DOI: 10.1007/s12035-021-02513-8

Source DB:  PubMed          Journal:  Mol Neurobiol        ISSN: 0893-7648            Impact factor:   5.590


  11 in total

1.  Altered Expression of Long Non-coding RNAs in Peripheral Blood Mononuclear Cells of Patients with Alzheimer's Disease.

Authors:  Serap Kurt; Ayse Gaye Tomatir; Pervin Elvan Tokgun; Cagatay Oncel
Journal:  Mol Neurobiol       Date:  2020-09-03       Impact factor: 5.590

2.  [The present status of colpocytology in Slovakia].

Authors:  T Vrobel
Journal:  Cesk Gynekol       Date:  1966-11

3.  An Immune-Related Six-lncRNA Signature to Improve Prognosis Prediction of Glioblastoma Multiforme.

Authors:  Meng Zhou; Zhaoyue Zhang; Hengqiang Zhao; Siqi Bao; Liang Cheng; Jie Sun
Journal:  Mol Neurobiol       Date:  2017-05-19       Impact factor: 5.590

4.  Regulation of tumor cell migration and invasion by the H19/let-7 axis is antagonized by metformin-induced DNA methylation.

Authors:  L Yan; J Zhou; Y Gao; S Ghazal; L Lu; S Bellone; Y Yang; N Liu; X Zhao; A D Santin; H Taylor; Y Huang
Journal:  Oncogene       Date:  2014-08-04       Impact factor: 9.867

5.  The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

Authors:  Thomas Derrien; Rory Johnson; Giovanni Bussotti; Andrea Tanzer; Sarah Djebali; Hagen Tilgner; Gregory Guernec; David Martin; Angelika Merkel; David G Knowles; Julien Lagarde; Lavanya Veeravalli; Xiaoan Ruan; Yijun Ruan; Timo Lassmann; Piero Carninci; James B Brown; Leonard Lipovich; Jose M Gonzalez; Mark Thomas; Carrie A Davis; Ramin Shiekhattar; Thomas R Gingeras; Tim J Hubbard; Cedric Notredame; Jennifer Harrow; Roderic Guigó
Journal:  Genome Res       Date:  2012-09       Impact factor: 9.043

6.  RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.

Authors:  Charity W Law; Monther Alhamdoosh; Shian Su; Gordon K Smyth; Matthew E Ritchie
Journal:  F1000Res       Date:  2016-06-17

7.  Inferential considerations for low-count RNA-seq transcripts: a case study on the dominant prairie grass Andropogon gerardii.

Authors:  Seth Raithel; Loretta Johnson; Matthew Galliart; Sue Brown; Jennifer Shelton; Nicolae Herndon; Nora M Bello
Journal:  BMC Genomics       Date:  2016-02-27       Impact factor: 3.969

8.  LNCipedia: a database for annotated human lncRNA transcript sequences and structures.

Authors:  Pieter-Jan Volders; Kenny Helsens; Xiaowei Wang; Björn Menten; Lennart Martens; Kris Gevaert; Jo Vandesompele; Pieter Mestdagh
Journal:  Nucleic Acids Res       Date:  2012-10-05       Impact factor: 16.971

9.  Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans.

Authors:  Aleksandra E Kornienko; Christoph P Dotter; Philipp M Guenzl; Heinz Gisslinger; Bettina Gisslinger; Ciara Cleary; Robert Kralovics; Florian M Pauler; Denise P Barlow
Journal:  Genome Biol       Date:  2016-01-29       Impact factor: 13.583

10.  Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data.

Authors:  Alemu Takele Assefa; Katrijn De Paepe; Celine Everaert; Pieter Mestdagh; Olivier Thas; Jo Vandesompele
Journal:  Genome Biol       Date:  2018-07-24       Impact factor: 13.583

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