Modular network inference between miRNA–mRNA expression profiles using weighted co-expression network analysis

Wani, Nisar Ahmad; Barh, Debmalya; Raza, Khalid

doi:10.1515/jib-2021-0029

Cited by 7 publications

(2 citation statements)

References 36 publications

(39 reference statements)

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“…The functional annotation of identified miRNAs was performed using co-expression analysis [ 35 ]. Pearson’s correlation coefficients between mRNAs and miRNAs were calculated based on the mRNAs FPKM values, and the putative target mRNA should have a value >0.99 or <−0.99.…”

Section: Methodsmentioning

confidence: 99%

Reprogramming of Fundamental miRNA and Gene Expression during the Barley-Piriformospora indica Interaction

Guo

Zhang

et al. 2022

JoF

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The interactions between plants and microorganisms, which are widely present in the microbial-dominated rhizosphere, have been studied. This association is highly beneficial to the organisms involved, as plants benefit soil microorganisms by providing them with metabolites, while microorganisms promote plant growth and development by promoting nutrient uptake and/or protecting the plant from biotic and abiotic stresses. Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of a wide range of host plants and establishes various benefits for the plants. In this work, an interaction between barley and the P. indica was established to elucidate microRNA (miRNA)-based regulatory changes in miRNA profiles and gene expression that occurred during the symbiosis. Growth promotion and vigorous root development were confirmed in barley colonized by P. indica. The genome-wide expression profile analysis of miRNAs in barley root showed that 7,798,928, 6,418,039 and 7,136,192 clean reads were obtained from the libraries of mock, 3 dai and 7 dai roots, respectively. Sequencing of the barley genome yielded in 81 novel miRNA and 450 differently expressed genes (DEGs). Additionally, 11, 24, 6 differentially expressed microRNAs (DEMs) in barley were found in the three comparison groups, including 3 dai vs. mock, 7 dai vs. mock and 7 dai vs. 3 dai, respectively. The predicted target genes of these miRNAs are mainly involved in transcription, cell division, auxin signal perception and transduction, photosynthesis and hormone stimulus. Transcriptome analysis of P. indica identified 667 and 594 differentially expressed genes (DEG) at 3 dai and 7 dai. Annotation and GO (Gene Ontology) analysis indicated that the DEGs with the greatest changes were concentrated in oxidoreductase activity, ion transmembrane transporter activity. It implies that reprogramming of fundamental miRNA and gene expression occurs both in barley and P. indica. Analysis of global changes in miRNA profiles of barley colonized with P. indica revealed that several putative endogenous barley miRNAs expressed upon colonization belonging to known micro RNA families involved in growth and developmental regulation.

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Section: Methodsmentioning

confidence: 99%

Reprogramming of Fundamental miRNA and Gene Expression during the Barley-Piriformospora indica Interaction

Guo

Zhang

et al. 2022

JoF

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“…While the DESeq2 workflow for analysis of bulk RNA sequencing data focuses on differentially expressed genes, the Weighted Gene Co-expression Network Analysis (WGCNA, version 1.71) algorithm identifies clusters of genes with similar expression patterns and reveals related biological functions [ 14 ]. To date, WGCNA has been employed for identifying gene co-expression networks in physiological processes such as lactation [ 14 ], in various cancers to determine therapeutic targets and biomarkers [ 15 – 18 ], and for investigating transcriptional regulators including micro and long non-coding RNAs [ 19 , 20 ]. To gain more insights into the processes orchestrating EVT maturation, we employed WGCNA with our recent RNA-Seq data, where we compared isolated EVTs from first-trimester placental tissue (pEVTs) to EVTs derived from trophoblast organoids (TO-EVTs) from the same donors [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

Gene-network based analysis of human placental trophoblast subtypes identifies critical genes as potential targets of therapeutic drugs

Lackner,

Pollheimer,

Latos

et al. 2023

Journal of Integrative Bioinformatics

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During early pregnancy, extravillous trophoblasts (EVTs) play a crucial role in modifying the maternal uterine environment. Failures in EVT lineage formation and differentiation can lead to pregnancy complications such as preeclampsia, fetal growth restriction, and pregnancy loss. Despite recent advances, our knowledge on molecular and external factors that control and affect EVT development remains incomplete. Using trophoblast organoid in vitro models, we recently discovered that coordinated manipulation of the transforming growth factor beta (TGFβ) signaling is essential for EVT development. To further investigate gene networks involved in EVT function and development, we performed weighted gene co-expression network analysis (WGCNA) on our RNA-Seq data. We identified 10 modules with a median module membership of over 0.8 and sizes ranging from 1005 (M1) to 72 (M27) network genes associated with TGFβ activation status or in vitro culturing, the latter being indicative for yet undiscovered factors that shape the EVT phenotypes. Lastly, we hypothesized that certain therapeutic drugs might unintentionally interfere with placentation by affecting EVT-specific gene expression. We used the STRING database to map correlations and the Drug-Gene Interaction database to identify drug targets. Our comprehensive dataset of drug-gene interactions provides insights into potential risks associated with certain drugs in early gestation.

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Computational Intelligence-Based Gene Expression Analysis in Colorectal Cancer: A Review

Srivastava

Rai

Singh

et al. 2022

Computational Intelligence in Oncology

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Modular network inference between miRNA–mRNA expression profiles using weighted co-expression network analysis

Cited by 7 publications

References 36 publications

Reprogramming of Fundamental miRNA and Gene Expression during the Barley-Piriformospora indica Interaction

Reprogramming of Fundamental miRNA and Gene Expression during the Barley-Piriformospora indica Interaction

Gene-network based analysis of human placental trophoblast subtypes identifies critical genes as potential targets of therapeutic drugs

Computational Intelligence-Based Gene Expression Analysis in Colorectal Cancer: A Review

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