miRFA: an automated pipeline for microRNA functional analysis with correlation support from TCGA and TCPA expression data in pancreatic cancer

Borgmästars, Emmy; Weerd, Hendrik A de; Lubovac-Pilav, Zelmina; Sund, Malin

doi:10.1186/s12859-019-2974-3

Cited by 17 publications

(10 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…MiRComb [ 13 ] conducts a miRNA-mRNA expression analysis followed by miRNA target prediction on the negatively correlated mRNA targets. miRFA [ 14 ] considers both the negatively and positively correlated using TCGA data. miTALOS [ 15 , 16 ] additionally provides a tissue-specific filtering of the targets.…”

Section: Introductionmentioning

confidence: 99%

NoRCE: non-coding RNA sets cis enrichment tool

2021

View full text Add to dashboard Cite

Background While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. Results We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. Conclusions NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users’ preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE.

show abstract

Section: Introductionmentioning

confidence: 99%

NoRCE: non-coding RNA sets cis enrichment tool

2021

View full text Add to dashboard Cite

show abstract

“…Subsequently, an analysis of the main components (PCA) was performed. Later, the target genes of the selected miRNAs were determined using the R miRFA pipeline [ 28 ], which is supported by data from the DIANA-TarBase v7, DIANA-microT-CDS and TargetScan v7.1 databases. Additionally, UniProt and Gene Ontology databases have been used to search for terms associated with the trabecular meshwork functions and the glaucoma pathology [ 29 ].…”

Section: Methodsmentioning

confidence: 99%

miRNAs and Genes Involved in the Interplay between Ocular Hypertension and Primary Open-Angle Glaucoma. Oxidative Stress, Inflammation, and Apoptosis Networks

Raga-Cervera

Bolarín

Millán

et al. 2021

JCM

View full text Add to dashboard Cite

Glaucoma has no cure and is a sight-threatening neurodegenerative disease affecting more than 100 million people worldwide, with primary open angle glaucoma (POAG) being the most globally prevalent glaucoma clinical type. Regulation of gene expression and gene networks, and its multifactorial pathways involved in glaucoma disease are landmarks for ophthalmic research. MicroRNAs (miRNAs/miRs) are small endogenous non-coding, single-stranded RNA molecules (18–22 nucleotides) that regulate gene expression. An analytical, observational, case-control study was performed in 42 patients of both sexes, aged 50 to 80 years, which were classified according to: (1) suffering from ocular hypertension (OHT) but no glaucomatous neurodegeneration (ND) such as the OHT group, or (2) have been diagnosed of POAG such as the POAG group. Participants were interviewed for obtaining sociodemographic and personal/familial records, clinically examined, and their tear samples were collected and frozen at 80 °C until processing for molecular-genetic assays. Tear RNA extraction, libraries construction, and next generation sequencing were performed. Here, we demonstrated, for the first time, the differential expression profiling of eight miRNAs when comparing tears from the OHT versus the POAG groups: the miR-26b-5p, miR-152-3p, miR-30e-5p, miR-125b-2-5p, miR-224-5p, miR-151a-3p, miR-1307-3p, and the miR-27a-3p. Gene information was set up from the DIANA-TarBase v7, DIANA-microT-CDS, and TargetScan v7.1 databases. To build a network of metabolic pathways, only genes appearing in at least four of the following databases: DisGeNet, GeneDistiller, MalaCards, OMIM PCAN, UniProt, and GO were considered. We propose miRNAs and their target genes/signaling pathways as candidates for a better understanding of the molecular-genetic bases of glaucoma and, in this way, to gain knowledge to achieve optimal diagnosis strategies for properly identifying HTO at higher risk of glaucoma ND. Further research is needed to validate these miRNAs to discern the potential role as biomarkers involved in oxidative stress, immune response, and apoptosis for the diagnosis and/or prognosis of OHT and the prevention of glaucoma ND.

show abstract

“…Apparently Apart from this, high-dose ATO (5 mg/kg), low-dose ATO (1 mg / kg) and saline were used as the control group for local injection of subcutaneous transplanted tumor [19]. For the reason that we put [24]. However, some studies have shown that increased levels of miRNA-885-5p in tissues or body fluids can be used as diagnostic markers for tumors and short survival period.…”

Section: Validation Of Prognostic Values Of Mir-885-5p and Mtpn In Ccamentioning

confidence: 99%

ATO /miRNA-885-5p/MTPN axis induced reversal of drug-resistance in cholangiocarcinoma

Wang

Zhang

Chen

et al. 2020

Preprint

View full text Add to dashboard Cite

Backgroud: In recent years, the incidence of cholangiocarcinoma (CCA) has increased, and it has become the second most malignant tumor of the hepatobiliary system. Chemotherapy has become the main treatment for cholangiocarcinoma due to its difficulty in diagnosis and rapid progress. Primary drug resistance is the main reason for the poor efficacy of chemotherapeutic drugs. Methods Western blot and quantitative real-time PCR assays were used to detect the expression levels of myotrophin (MTPN) and microRNA-885-5p(miR-885-5p) in CCA tissues and cells; Cell viabilities treated with arsenic trioxide (ATO), 5-fluorouracil (5-Fu) and cisplatin (CDDP) were analyzed by a CCK-8 kit. Luciferase reporter assay detected the relationship between miR-885-5p and MTPN. Kaplan-Meier analysis showed survival time curve. Results We found that ATO can reduce the resistance of CCA cells to 5-Fu and CDDP and promote the killing effect of 5-Fu and CDDP. Low-dose ATO played an anti-drug-resistance role through up-regulating the expression of miR-885-5p. Combined with sequencing results and database prediction, we found that MTPN was a direct target gene of miR-885-5p. The sensitivity of CCA cells to 5-Fu and CDDP was increased after MTPN was knocked out. After MTPN knockout, the sensitivity of cholangiocarcinoma cells to 5-FU and CDDP was increased. ATO can reverse chemotherapy resistance induced by overexpression of MTPN. Conclusions Our study suggests that the ATO/miR-885-5p/MTPN axis is a potential therapeutic strategy for improving the sensitivity of CCA to chemotherapy.

show abstract

miRFA: an automated pipeline for microRNA functional analysis with correlation support from TCGA and TCPA expression data in pancreatic cancer

Cited by 17 publications

References 52 publications

NoRCE: non-coding RNA sets cis enrichment tool

NoRCE: non-coding RNA sets cis enrichment tool

miRNAs and Genes Involved in the Interplay between Ocular Hypertension and Primary Open-Angle Glaucoma. Oxidative Stress, Inflammation, and Apoptosis Networks

ATO /miRNA-885-5p/MTPN axis induced reversal of drug-resistance in cholangiocarcinoma

Contact Info

Product

Resources

About