Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis

LA Corchete, EA Rojas, D Alonso-López… - Scientific reports, 2020 - nature.com
… as qRT-PCR, both at absolute and relative gene expression measurement levels 7 . All these
facts have led to a great expansion of RNA-seq, becoming the first choice in transcriptomic …

Exaggerated false positives by popular differential expression methods when analyzing human population samples

Y Li, X Ge, F Peng, W Li, JJ Li - Genome biology, 2022 - Springer
… in all these genes’ measurements relative to the assumed … is the case with gene expression
counts measured by RNA-… GTEx data, we selected six pairs of tissues with sample sizes

Dream: powerful differential expression analysis for repeated measures designs

GE Hoffman, P Roussos - Bioinformatics, 2021 - academic.oup.com
… so that it decreases power for gene g. Increasing sample size does not overcome this issue.
… that this variation was driven by genetic regulation of gene expression. To test this, we use …

Prediction of Alzheimer's disease using blood gene expression data

T Lee, H Lee - Scientific reports, 2020 - nature.com
… to relatively low gene expression intensities… gene expression values in 100 or more samples,
as performed in the previous study 25 . If there were multiple probes annotated in one gene

Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols

S Zhao, Z Ye, R Stanton - Rna, 2020 - rnajournal.cshlp.org
… plots of gene expression profiles for four biological replicates of blood samples (raw data
RPKM and TPM represent relative abundance of a gene or transcript in a sample. The direct …

Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies

S Sun, J Zhu, X Zhou - Nature methods, 2020 - nature.com
… has enabled gene-expression profiling with spatial … Simulations were performed under
moderate sample size (n … interest is analyzing the relative gene-expression level. Other …

Evaluating DNA methylation, gene expression, somatic mutation, and their combinations in inferring tumor tissue-of-origin

H Liu, C Qiu, B Wang, P Bing, G Tian… - Frontiers in cell and …, 2021 - frontiersin.org
sample size of more than 100, while the largest sample size … algorithm, we achieved relatively
stable and reliable results … , we found that the gene expression profile data obtained the …

… gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles

MJ Umer, L Bin Safdar, H Gebremeskel… - Horticulture …, 2020 - academic.oup.com
… The relative expression of these genes also complemented the sugar content at … power
of our analysis was low due to the small sample size. Nevertheless, the expression profiling of …

Expression profile of immune checkpoint genes and their roles in predicting immunotherapy response

FF Hu, CJ Liu, LL Liu, Q Zhang… - Briefings in …, 2021 - academic.oup.com
… [23] level-3 gene expression data were used to assess the expression … the sample size. (B)
PFS difference between high and low groups as defined in (A), with all cancer tumor samples

ssGSEA score-based Ras dependency indexes derived from gene expression data reveal potential Ras addiction mechanisms with possible clinical implications

M Yi, DV Nissley, F McCormick, RM Stephens - Scientific reports, 2020 - nature.com
… genome-wide gene expression profiling to represent RDIs, … relatively weak correlation with
our in-house-derived siREN … to a much larger sample size for DEMETER data (460 shared …