TFmiR2: constructing and analyzing disease-, tissue- and process-specific transcription factor and microRNA co-regulatory networks

Nazarieh, Maryam; Hamed, Mohamed; Spaniol, Christian; Will, Thorsten; Helms, Volkhard

doi:10.1093/bioinformatics/btz871

Cited by 5 publications

(2 citation statements)

References 16 publications

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“…DIANA‐mirExTra uncovers the co‐regulation with the differential expression analysis (DEA) (Vlachos et al, 2016). TFmiR is able to construct tissue‐ and biological process‐specific miRNA‐TF co‐regulatory networks and perform downstream network‐centric analysis, which can identify key driver genes (Nazarieh et al, 2020). In the miRNA‐TF co‐regulatory networks, there are recurring patterns of interactions noted as network motifs, including feedback loops and feedforward loops.…”

Section: Methodologies Of Ncrna Medical Analysismentioning

confidence: 99%

A comprehensive checklist of computational resources and methodologies for noncoding RNAs in systems medicine

Li,

Zhao,

Wang

et al. 2024

WIREs RNA

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Noncoding RNAs (ncRNAs), previously referred to as “dark matter” and now recognized as “bright star,” fulfill a variety of biological functions and are also emerging as potential biomarkers and therapies in oncology‐focused clinical trials. Systems medicine has become a holist paradigm to study the human body, which organically integrates data from basic research and clinical practice to improve our understanding and treatment of complex diseases. It is an interdisciplinary approach that brings systems biology and bioinformatics closer to clinical medicine. The development of high‐throughput techniques and the increasing adoption of computational methods across healthcare domains have accelerated and aided the tangible clinical applications of ncRNAs. Various resources and methodologies for ncRNAs enable a comprehensive analysis of heterogeneous and interlinked data, thereby providing new insights into systems medicine. In this review, we summarize the resources and models for ncRNA medical research, aiming to provide a technical manual for personalized and precision medicine at the system level.This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico

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Section: Methodologies Of Ncrna Medical Analysismentioning

confidence: 99%

A comprehensive checklist of computational resources and methodologies for noncoding RNAs in systems medicine

Li,

Zhao,

Wang

et al. 2024

WIREs RNA

View full text Add to dashboard Cite

show abstract

“…The TFmiR2 is a webserver for the analysis and the construction of transcription factor (TF) and miRNA co-regulatory networks [33]. The TFmiR2 was utilized to get the corresponding miRNA set for the extended gene set in response to melanoma disease for further analysis.…”

Section: Corresponding Microrna and Disease-enrichment Analysismentioning

confidence: 99%

Transcriptome-Wide Association Study Reveals New Molecular Interactions Associated with Melanoma

Saad

Hamed

2023

Preprint

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The journey of discovering melanoma biomarkers is never ending. Under that assumption, this study is attempted to partially fill in a gap in that journey by identifying biomarkers related to melanoma. A transcriptome-wide association study (TWAS) was conducted on genome-wide association study (GWAS) summary statistics of malignant melanoma of skin (UK biobank dataset) and The Cancer Genome Atlas-Skin Cutaneous Melanoma (TCGA-SKCM) gene expression weights. Afterwards, a gene enrichment analysis was applied on the TWAS significant associations. The melanoma’s gene-microRNA (miRNA) regulatory network was constructed from the TWAS genes and their corresponding miRNAs. At last, a disease enrichment analysis was conducted on the corresponding miRNAs. The TWAS detected 27 genes associated with melanoma having P-value less than 0.05, namely, AMIGO1, GSTM3, MDM4, COPA, DENND4B, RAB13, IL1A, ANAPC13, CRIPAK, LOC389458, LOC441204, MTERFD1, CBWD1, B3GAT1, HOXC10, DDX11, PROZ, DHRS1, SPATA5L1, C16orf73, EIF3CL, FANCA, SCRN2, ALDH16A1, UPK1A, EDEM2, and TEF. After Joint/Conditional test, one gene (AMIGO1) was dropped out, resulting in 26 significant genes. The gene ontology (GO) biological process ended with the association of the extended gene set (76 genes) with protein K11-linked ubiquitination, and regulation of cell cycle phase transition. K11-linked ubiquitin chains regulates cell division. Interestingly, the extended gene set was related to different skin cancer subtypes. Moreover, the enriched pathways were nsp1 from SARS-CoV-2 inhibits translation initiation in the host cell, cell cycle, translation factors, and DNA repair pathways Full Network. The gene-miRNA regulatory network identified 10 hotspot genes: TP53, BRCA1, FANCA, BLM, USP7, MDM2, MDM4, IL1A, EIF3F, and ANAPC16; and 4 hotspot miRNAs: mir-16, mir-15a, mir-125b, and mir-146a. Melanoma was one of the top ten diseases associated with the corresponding (106) miRNAs. Our results shed light on melanoma pathogenesis and biologically significant molecular interactions. Besides, our study gives a comprehensive pipeline for the TWASs generally.

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miRNome profiling in Duchenne muscular dystrophy; identification of asymptomatic and manifesting female carriers

et al. 2021

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Duchenne muscular dystrophy (DMD) is a fatal neuromuscular disorder that occurs due to inactivating mutations in DMD gene, leading to muscular dystrophy. Prediction of pathological complications of DMD and the identification of female carriers are important research points that aim to reduce disease burden. Herein, we describe a case of a late DMD patient and his immediate female family members, who all carry same DMD mutation and exhibited varied degrees of symptoms. In our study, we sequenced the whole miRNome in leukocytes and plasma of the family members and results were validated using Real-Time PCR. Our results highlighted the role of miR-409-3p, miR-424-5p, miR-144-3p as microRNAs that show correlation with the extent of severity of muscular weakness and can be used for detection of asymptomatic carriers. Cellular and circulating levels of miR-494-3p had showed significant increase in symptomatic carriers, which may indicate significant roles played by this miRNA in the onset of muscular weakness. Interestingly, circulating levels of miR-206 and miR-410-3p were significantly increased only in the severely symptomatic carrier. In conclusion, our study highlighted several miRNA species, which could be used in predicting the onset of muscle and/or neurological complications in DMD carriers.

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TFmiR2: constructing and analyzing disease-, tissue- and process-specific transcription factor and microRNA co-regulatory networks

Cited by 5 publications

References 16 publications

A comprehensive checklist of computational resources and methodologies for noncoding RNAs in systems medicine

A comprehensive checklist of computational resources and methodologies for noncoding RNAs in systems medicine

Transcriptome-Wide Association Study Reveals New Molecular Interactions Associated with Melanoma

miRNome profiling in Duchenne muscular dystrophy; identification of asymptomatic and manifesting female carriers

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