<i>cat</i>RAPID <i>omics</i>: a web server for large-scale prediction of protein–RNA interactions

Federico, Antonella; Zanzoni, Andreas; Klus, Petr; Marchese, Domenica; Cirillo, Davide; Tartaglia, Gian Gaetano

doi:10.1093/bioinformatics/btt495

Cited by 257 publications

(260 citation statements)

References 24 publications

Supporting

Mentioning

257

Contrasting

Order By: Relevance

“…Furthermore, experimental-data-constrained RNA secondary structures are not available for RBP binding sites in any current database. Finally, it is often desirable to know whether RBPs can interact with RNA molecules, especially novel lncRNAs; however, only a few online tools (21,22) are available for predicting RBP binding sites on given RNA sequences.…”

Section: Introductionmentioning

confidence: 99%

POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins

et al. 2016

View full text Add to dashboard Cite

We present POSTAR (http://POSTAR.ncrnalab.org), a resource of POST-trAnscriptional Regulation coordinated by RNA-binding proteins (RBPs). Precise characterization of post-transcriptional regulatory maps has accelerated dramatically in the past few years. Based on new studies and resources, POSTAR supplies the largest collection of experimentally probed (∼23 million) and computationally predicted (approximately 117 million) RBP binding sites in the human and mouse transcriptomes. POSTAR annotates every transcript and its RBP binding sites using extensive information regarding various molecular regulatory events (e.g., splicing, editing, and modification), RNA secondary structures, disease-associated variants, and gene expression and function. Moreover, POSTAR provides a friendly, multi-mode, integrated search interface, which helps users to connect multiple RBP binding sites with post-transcriptional regulatory events, phenotypes, and diseases. Based on our platform, we were able to obtain novel insights into post-transcriptional regulation, such as the putative association between CPSF6 binding, RNA structural domains, and Li-Fraumeni syndrome SNPs. In summary, POSTAR represents an early effort to systematically annotate post-transcriptional regulatory maps and explore the putative roles of RBPs in human diseases.

show abstract

Section: Introductionmentioning

confidence: 99%

POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Finally, Tartaglia and colleagues developed catRAPID, the first computational method capable of predicting RNA–protein interactions in a large scale [168]. The algorithm evaluates the interaction propensities of polypeptide and nucleotide chains based on physicochemical properties such as secondary structure information, hydrogen bonding and Van der Waals forces.…”

Section: Methodsmentioning

confidence: 99%

Ribonomic approaches to study the RNA‐binding proteome

Faoro

Ataide

2014

FEBS Letters

View full text Add to dashboard Cite

a b s t r a c tGene expression is controlled through a complex interplay among mRNAs, non-coding RNAs and RNA-binding proteins (RBPs), which all assemble along with other RNA-associated factors in dynamic and functional ribonucleoprotein complexes (RNPs). To date, our understanding of RBPs is largely limited to proteins with known or predicted RNA-binding domains. However, various methods have been recently developed to capture an RNA of interest and comprehensively identify its associated RBPs. In this review, we discuss the RNA-affinity purification methods followed by mass spectrometry analysis (AP-MS); RBP screening within protein libraries and computational methods that can be used to study the RNA-binding proteome (RBPome).

show abstract

“…9 From the results, the star rating system can provide a comprehensive score for each interaction pair, which was based on multiple criteria. These sequences were used as the input to predict the interactions between RBPs and target RNAs in catRAPID omics.…”

Section: Detection Of Putative Rnas Regulated By Apobec3g Eef1a2mentioning

confidence: 99%

Integrative analysis of significant RNA‐binding proteins in colorectal cancer metastasis

Zhou

Guo

2018

J of Cellular Biochemistry

View full text Add to dashboard Cite

The aberrant expression of RNA-binding proteins (RBPs) plays a crucial role in the occurrence and progression of human cancer. However, the key functions of RBPs in the metastasis of colorectal cancer have not yet been fully elucidated. Here, we integrated multi-omics data and identified four differentially expressed RBPs (APOBEC3G, EEF1A2, EIF5AL1 and CELF3) in patients with colorectal cancer metastasis. To clarify the underlying molecular mechanisms, we systematically analyzed the genomic features and downstream regulatory relationships of the four RBPs. In a genomic level, the copy number variations of APOBEC3G, EEF1A2, and CELF3 demonstrated significantly differential distributions between metastatic and nonmetastatic patients. Besides that, combining sequence and expression information, we identified 436 putative RNA targets regulated by the four RBPs through strict multistep bioinformatics screening. For the downstream analysis, the evidence from functional enrichment analysis and public literature indicated the roles of these target genes in the carcinogenesis and progression of colorectal cancer. Furthermore, through the machine learning algorithm and statistical analysis, we obtained two gene candidates that had obvious effects on the metastasis and overall survival status of patients with colorectal cancer. In summary, our study comprehensively explored the influence of APOBEC3G, EEF1A2, EIF5AL1, and CELF3 in colorectal cancer metastasis, which may offer favorable perspectives for clinical diagnosis and therapy.

show abstract

catRAPID omics: a web server for large-scale prediction of protein–RNA interactions

Cited by 257 publications

References 24 publications

POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins

POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins

Ribonomic approaches to study the RNA‐binding proteome

Integrative analysis of significant RNA‐binding proteins in colorectal cancer metastasis

Contact Info

Product

Resources

About