Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks

Scientific Reports
Franziska LieseckeThomas Dugé de Bernonville

Abstract

Co-expression networks are essential tools to infer biological associations between gene products and predict gene annotation. Global networks can be analyzed at the transcriptome-wide scale or after querying them with a set of guide genes to capture the transcriptional landscape of a given pathway in a process named Pathway Level Coexpression (PLC). A critical step in network construction remains the definition of gene co-expression. In the present work, we compared how Pearson Correlation Coefficient (PCC), Spearman Correlation Coefficient (SCC), their respective ranked values (Highest Reciprocal Rank (HRR)), Mutual Information (MI) and Partial Correlations (PC) performed on global networks and PLCs. This evaluation was conducted on the model plant Arabidopsis thaliana using microarray and differently pre-processed RNA-seq datasets. We particularly evaluated how dataset × distance measurement combinations performed in 5 PLCs corresponding to 4 well described plant metabolic pathways (phenylpropanoid, carbohydrate, fatty acid and terpene metabolisms) and the cytokinin signaling pathway. Our present work highlights how PCC ranked with HRR is better suited for global network construction and PLC with microarray and RNA-seq data ...Continue Reading

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Citations

Aug 23, 2019·Acta Biochimica Et Biophysica Sinica·Xiaolan Rao, Richard A Dixon
Apr 30, 2019·Frontiers in Genetics·Abhijeet R SonawaneAmitabh Sharma
Jun 28, 2019·Plant Direct·Sonalisa Pandey, Debashis Sahoo
Oct 9, 2019·Scientific Reports·Franziska LieseckeThomas Dugé de Bernonville
Sep 13, 2020·Molecular Biology and Evolution·Emmelien VancaesterKlaas Vandepoele
Oct 10, 2020·Computational and Structural Biotechnology Journal·Mohammad Mazharul IslamRajib Saha
Jan 26, 2021·Cellular Oncology (Dordrecht)·Axel BengtssonDaniel Ansari
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Sep 26, 2021·The Plant Journal : for Cell and Molecular Biology·Thomas Depuydt, Klaas Vandepoele

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Datasets Mentioned

BETA
M00087
GPL198

Methods Mentioned

BETA
RNA-seq

Software Mentioned

R package ‘ corpcor
AUROC
Fastq
PCC
ArrayExpress
HRR
corpcor
Salmon
Trimmomatic
EGAD R package

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