miRTissue ce: extending miRTissue web service with the analysis of ceRNA-ceRNA interactions

Fiannaca, Antonino; Paglia, Laura La; Rosa, Massimo La; Rizzo, Riccardo; Urso, Alfonso

doi:10.1186/s12859-020-3520-z

Cited by 16 publications

(13 citation statements)

References 67 publications

(69 reference statements)

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“…The starBase includes miRNA-mRNA interactions predicted by probing 108 CLIP-seq datasets. As described above, a similar three-step approach has been previously followed by the miRTissue ce , a ceRNA-ceRNA web application tool [11]. In the first step, we used a hypergeometric test to identify lncRNA/pseudogene -mRNA pairs with a significant number of shared miRNAs.…”

Section: Competing Endogenous Rna Network Analysismentioning

confidence: 99%

“…Previous bioinformatics studies have identified ceRNA candidates as prognostic or predictive biomarkers for common cancer types such as colorectal, endometrial, prostate, and breast cancers [6][7][8][9][10]. Several web-based tools such as miRTissue ce , LncACTdb 2.0, and lnCeDB have been developed, supporting the search for ceRNA interaction networks in multiple tissues [11][12][13]. A recent colorectal cancer ceRNA study identified a network of nine hub genes, thirteen lncRNAs, and twenty-nine candidate miRNAs, integrating multiple genomic datasets [6].…”

Section: Introductionmentioning

confidence: 99%

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Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers

Jayarathna

Rentería

Sauret

et al. 2021

Biology

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The discovery of microRNAs (miRNAs) has fundamentally transformed our understanding of gene regulation. The competing endogenous RNA (ceRNA) hypothesis postulates that messenger RNAs and other RNA transcripts, such as long non-coding RNAs and pseudogenes, can act as natural miRNA sponges. These RNAs influence each other’s expression levels by competing for the same pool of miRNAs through miRNA response elements on their target transcripts, thereby modulating gene expression and protein activity. In recent years, these ceRNA regulatory networks have gained considerable attention in cancer research. Several studies have identified cancer-specific ceRNA networks. Nevertheless, prior bioinformatic analyses have focused on long-non-coding RNA-associated ceRNA networks. Here, we identify an extended ceRNA network (including both long non-coding RNAs and pseudogenes) shared across a group of five hormone-dependent (HD) cancers, i.e., prostate, breast, colon, rectal, and endometrial cancers, using data from The Cancer Genome Atlas (TCGA). We performed a functional enrichment analysis for differentially expressed genes in the shared ceRNA network of HD cancers, followed by a survival analysis to determine their prognostic ability. We identified two long non-coding RNAs, nine genes, and seventy-four miRNAs in the shared ceRNA network across five HD cancers. Among them, two genes and forty-one miRNAs were associated with at least one HD cancer survival. This study is the first to investigate pseudogene-associated ceRNAs across a group of related cancers and highlights the value of this approach to understanding the shared molecular pathogenesis in a group of related diseases.

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Section: Competing Endogenous Rna Network Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers

Jayarathna

Rentería

Sauret

et al. 2021

Biology

View full text Add to dashboard Cite

show abstract

“…The starBase includes miRNA-mRNA interactions predicted by probing 108 CLIP-seq datasets. As described above, a similar three-step approach has been previously followed by the miRTissuece, a ceRNA-ceRNA web application tool [11]. In the first step, we used the hypergeometric test to identify lncRNA/pseudogene-mRNA pairs with a significant number of shared miRNAs.…”

Section: Long Non-coding Rna/pseudogene-microrna-mrna Networkmentioning

confidence: 99%

“…Previous bioinformatics studies have identified ceRNA candidates as prognostic or predictive biomarkers for common cancer types such as colorectal, endometrial, prostate, and breast cancers [6][7][8][9][10]. Several web-based tools such as miRTissuece, LncACTdb 2.0, and lnCeDB have been developed, supporting the search for ceRNA interactions networks in multiple tissues [11][12][13]. A recent colorectal cancer ceRNA study identified a network of nine hub genes, thirteen lncRNAs, and twenty-nine candidate miRNAs integrating multiple genomic datasets [6].…”

Section: Introductionmentioning

confidence: 99%

Identifying Complex lncRNA/Pseudogene-miRNA-mRNA Crosstalk in Hormone-Dependent Cancers

Jayarathna¹,

Rentería²,

Sauret³

et al. 2021

Preprint

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The discovery of microRNAs (miRNAs) has fundamentally transformed our understanding of gene regulation. The competing endogenous RNA (ceRNA) hypothesis postulates that not only messenger RNAs but also other RNA transcripts, such as long non-coding RNAs and pseudogenes, can act as natural miRNA sponges. These RNAs influence each other’s expression levels by competing for the same pool of miRNAs through miRNA response elements on their target transcripts, thereby modulating gene expression and protein activity. In recent years, these ceRNA regulatory networks have gained considerable attention in cancer research. Several studies have identified cancer-specific ceRNA networks. Nevertheless, prior bioinformatic analyses have focused on long non-coding RNAs-associated ceRNA networks. Here, we identify an extended-ceRNA network (including both long non-coding RNAs and pseudogenes) shared across a group of four hormone-dependent (HD) cancers, i.e., prostate, breast, colorectal, and endometrial cancers, using data from The Cancer Genome Atlas (TCGA). We performed a functional enrichment analysis for differentially expressed genes in the shared ceRNA network of HD cancers, followed by a survival analysis to determine their prognostic ability. We identified two long non-coding RNAs, nine genes, and seventy-four miRNAs in the shared ceRNA network across four HD cancers. Among them, two genes and forty-one miRNAs were associated with at least one HD cancer survival. This study is the first to investigate pseudogene associated ceRNAs across a group of related cancers and highlights the value of this approach to understanding shared molecular pathogenesis in a group of related diseases.

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“…A number of resources have been proposed for studying ceRNAs, including miRTissue ce ( 13 ), LnCeVar ( 14 ), Pan-ceRNADB ( 15 ), miRTarBase ( 16 ), ceRDB ( 17 ), lnCeDB ( 18 ), miRSponge ( 19 ), LncACTdb ( 20 ), miRcode ( 21 ), and starBase v2.0 ( 22 ) (see Supplementary Section S7 and Tables S1–3 for a systematic comparison). Only a few of these databases are dedicated to ceRNA networks.…”

Section: Introductionmentioning

confidence: 99%

SPONGEdb: a pan-cancer resource for competing endogenous RNA interactions

et al. 2021

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microRNAs (miRNAs) are post-transcriptional regulators involved in many biological processes and human diseases, including cancer. The majority of transcripts compete over a limited pool of miRNAs, giving rise to a complex network of competing endogenous RNA (ceRNA) interactions. Currently, gene-regulatory networks focus mostly on transcription factor-mediated regulation, and dedicated efforts for charting ceRNA regulatory networks are scarce. Recently, it became possible to infer ceRNA interactions genome-wide from matched gene and miRNA expression data. Here, we inferred ceRNA regulatory networks for 22 cancer types and a pan-cancer ceRNA network based on data from The Cancer Genome Atlas. To make these networks accessible to the biomedical community, we present SPONGEdb, a database offering a user-friendly web interface to browse and visualize ceRNA interactions and an application programming interface accessible by accompanying R and Python packages. SPONGEdb allows researchers to identify potent ceRNA regulators via network centrality measures and to assess their potential as cancer biomarkers through survival, cancer hallmark and gene set enrichment analysis. In summary, SPONGEdb is a feature-rich web resource supporting the community in studying ceRNA regulation within and across cancer types.

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miRTissue ce: extending miRTissue web service with the analysis of ceRNA-ceRNA interactions

Cited by 16 publications

References 67 publications

Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers

Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers

Identifying Complex lncRNA/Pseudogene-miRNA-mRNA Crosstalk in Hormone-Dependent Cancers

SPONGEdb: a pan-cancer resource for competing endogenous RNA interactions

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