Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circular RNAs and complex diseases: from experimental results to computational models.

ABSTRACT: Circular RNAs (circRNAs) are a class of single-stranded, covalently closed RNA molecules with a variety of biological functions. Studies have shown that circRNAs are involved in a variety of biological processes and play an important role in the development of various complex diseases, so the identification of circRNA-disease associations would contribute to the diagnosis and treatment of diseases. In this review, we summarize the discovery, classifications and functions of circRNAs and introduce four important diseases associated with circRNAs. Then, we list some significant and publicly accessible databases containing comprehensive annotation resources of circRNAs and experimentally validated circRNA-disease associations. Next, we introduce some state-of-the-art computational models for predicting novel circRNA-disease associations and divide them into two categories, namely network algorithm-based and machine learning-based models. Subsequently, several evaluation methods of prediction performance of these computational models are summarized. Finally, we analyze the advantages and disadvantages of different types of computational models and provide some suggestions to promote the development of circRNA-disease association identification from the perspective of the construction of new computational models and the accumulation of circRNA-related data.

SUBMITTER: Wang CC

PROVIDER: S-EPMC8575014 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Long non-coding RNAs and complex diseases: from experimental results to computational models.

Project description:LncRNAs have attracted lots of attentions from researchers worldwide in recent decades. With the rapid advances in both experimental technology and computational prediction algorithm, thousands of lncRNA have been identified in eukaryotic organisms ranging from nematodes to humans in the past few years. More and more research evidences have indicated that lncRNAs are involved in almost the whole life cycle of cells through different mechanisms and play important roles in many critical biological processes. Therefore, it is not surprising that the mutations and dysregulations of lncRNAs would contribute to the development of various human complex diseases. In this review, we first made a brief introduction about the functions of lncRNAs, five important lncRNA-related diseases, five critical disease-related lncRNAs and some important publicly available lncRNA-related databases about sequence, expression, function, etc. Nowadays, only a limited number of lncRNAs have been experimentally reported to be related to human diseases. Therefore, analyzing available lncRNA-disease associations and predicting potential human lncRNA-disease associations have become important tasks of bioinformatics, which would benefit human complex diseases mechanism understanding at lncRNA level, disease biomarker detection and disease diagnosis, treatment, prognosis and prevention. Furthermore, we introduced some state-of-the-art computational models, which could be effectively used to identify disease-related lncRNAs on a large scale and select the most promising disease-related lncRNAs for experimental validation. We also analyzed the limitations of these models and discussed the future directions of developing computational models for lncRNA research.

| S-EPMC5862301 | biostudies-other

Circular RNAs in rat models of cardiovascular and renal diseases.

Project description:Circular RNAs (circRNAs) have emerged as an important new class of genomic regulatory molecules contributing to the development of various diseases, but their relevance to the development and progression of hypertension remains largely unknown. A major impediment to begin studying circRNAs in rat models of inherited hypertension is that the rat as a valuable model of human diseases lags far behind the mouse and human in providing knowledge on circRNAs. In this study, a genome-wide circRNA profiling was performed from four rat strains that are widely used in hypertension research: the Dahl salt-sensitive rat (S), the Dahl salt-resistant rat (R), the spontaneously hypertensive rat (SHR), and the Wistar Kyoto rat (WKY). Combined hybridization data obtained from these four strains allowed for the identification of 12,846 circRNAs as being expressed in the rat kidneys. Out of these, 318 and 110 circRNAs were differentially expressed with a fold change > 1.5 (P < 0.05) in S vs. R and SHR vs. WKY, respectively. Among these circRNAs, circRNA/microRNA interaction was predicted since circRNAs are known as microRNA sponges to sequester microRNAs. Several circRNAs were further validated by quantitative real-time PCR. To our knowledge, our study is the primary report of profiling circRNAs in renal tissue and illustrates that circRNAs could be candidate genetic factors controlling blood pressure.

| S-EPMC5625271 | biostudies-literature

Circular RNAs in Rat Models of Cardiovascular and Renal diseases

Project description:The objective of this study was to profile circular RNAs (circRNAs) in rat genetic models of cardiovascular and renal disease. Renal profiles were obtained from the Dahl Salt-Sensitive rat (S), the Dahl Salt-Resistant rat (R), the Spontaneously Hypertensive Rat (SHR) and the Wistar Kyoto rat (WKY).

2017-07-27 | GSE92669 | GEO

Long Noncoding RNAs and Circular RNAs in Autoimmune Diseases.

Project description:Immune responses are essential for the clearance of pathogens and the repair of injured tissues; however, if these responses are not properly controlled, autoimmune diseases can occur. Autoimmune diseases (ADs) are a family of disorders characterized by the body's immune response being directed against its own tissues, with consequent chronic inflammation and tissue damage. Despite enormous efforts to identify new drug targets and develop new therapies to prevent and ameliorate AD symptoms, no definitive solutions are available today. Additionally, while substantial progress has been made in drug development for some ADs, most treatments only ameliorate symptoms and, in general, ADs are still incurable. Hundreds of genetic loci have been identified and associated with ADs by genome-wide association studies. However, the whole list of molecular factors that contribute to AD pathogenesis is still unknown. Noncoding (nc)RNAs, such as microRNAs, circular (circ)RNAs, and long noncoding (lnc)RNAs, regulate gene expression at different levels in various diseases, including ADs, and serve as potential drug targets as well as biomarkers for disease progression and response to therapy. In this review, we will focus on the potential roles and genetic regulation of ncRNA in four autoimmune diseases-systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, and type 1 diabetes mellitus.

| S-EPMC7407480 | biostudies-literature

Detecting circular RNAs: bioinformatic and experimental challenges.

Project description:The pervasive expression of circular RNAs (circRNAs) is a recently discovered feature of gene expression in highly diverged eukaryotes. Numerous algorithms that are used to detect genome-wide circRNA expression from RNA sequencing (RNA-seq) data have been developed in the past few years, but there is little overlap in their predictions and no clear gold-standard method to assess the accuracy of these algorithms. We review sources of experimental and bioinformatic biases that complicate the accurate discovery of circRNAs and discuss statistical approaches to address these biases. We conclude with a discussion of the current experimental progress on the topic.

| S-EPMC5565156 | biostudies-other

Circular RNAs: Promising Biomarkers for Human Diseases.

Project description:Circular RNA (circRNA) is a group of endogenous noncoding RNA characterized by a covalently closed cyclic structure lacking poly-adenylated tails. Recent studies have suggested that circRNAs play a crucial role in regulating gene expression by acting as a microRNA sponge, RNA binding protein sponge and translational regulator. CircRNAs have become a research hotspot because of their close association with the development of diseases. Some circRNAs are reportedly expressed in a tissue- and development stage-specific manner. Furthermore, due to other features of circRNAs including stability, conservation and high abundance in body fluids, circRNAs are believed to be potential biomarkers for various diseases. In the present review, we provide the current understanding of biogenesis and gene regulatory mechanisms of circRNAs, summarize the recent studies on circRNAs as potential diagnostic and prognostic biomarkers, and highlight the major advantages and limitations of circRNAs as novel biomarkers based on existing knowledge.

| S-EPMC6116471 | biostudies-literature

Circular RNAs in immune responses and immune diseases.

Project description:Circular RNAs (circRNAs) are novel clusters of endogenous noncoding RNAs (ncRNAs) that are widely expressed in eukaryotic cells. In contrast to the generation of linear RNA transcripts, circRNAs undergo a "back-splicing" process to form a continuous, covalently closed, stable loop structure without 5' or 3' polarities and poly (A) tails during posttranscriptional modification. Due to the widespread availability of several technologies, especially high-throughput RNA sequencing, numerous circRNAs have been discovered not only in mammals but also in plants and insects. Notably, due to their abilities to serve as microRNA (miRNA) "sponges", miRNA "reservoirs", regulate gene expression and encode proteins, circRNAs participate in the development and progression of different immune responses and immune diseases by enriching various forms of epigenetic modification. CircRNAs have been demonstrated to be expressed in a tissue-specific and pathogenesis-related manner during the occurrence of multiple immune diseases. Additionally, because of their circular configurations, expression in blood and peripheral tissues and coexistence with exosomes, circRNAs show inherent conservation along with environmental resistance stability and may be regarded as potential biomarkers or therapeutic targets for some immune diseases. In this review, we summarize the characteristics, functions and mechanisms of circRNAs and their involvement in immune responses and diseases. Although our knowledge of circRNAs remains preliminary, this field is worthy of deeper exploration and greater research efforts.

| S-EPMC6376182 | biostudies-literature

Circular RNAs: typical biomarkers for bone-related diseases.

Project description:Bone is a connective tissue that has important functions in the human body. Cells and the extracellular matrix (ECM) are key components of bone and are closely related to bone-related diseases. However, the outcomes of conventional treatments for bone-related diseases are not promising, and hence it is necessary to elucidate the exact regulatory mechanisms of bone-related diseases and identify novel biomarkers for diagnosis and therapy. Circular RNAs (circRNAs) are single-stranded RNAs that form closed circular structures without a 5' cap or 3' tail and polycyclic adenylate tails. Due to their high stability, circRNAs have the potential to be typical biomarkers. Accumulating evidence suggests that circRNAs are involved in bone-related diseases, including osteoarthritis, osteoporosis, osteosarcoma, multiple myeloma, intervertebral disc degeneration, and rheumatoid arthritis. Herein, we summarize the recent research progress on the characteristics and functions of circRNAs, and highlight the regulatory mechanism of circRNAs in bone-related diseases.

| S-EPMC9758716 | biostudies-literature

Disease-Associated Circular RNAs: From Biology to Computational Identification.

Project description:Circular RNAs (circRNAs) are endogenous RNAs with a covalently closed continuous loop, generated through various backsplicing events of pre-mRNA. An accumulating number of studies have shown that circRNAs are potential biomarkers for major human diseases such as cancer and Alzheimer's disease. Thus, identification and prediction of human disease-associated circRNAs are of significant importance. To this end, a computational analysis-assisted strategy is indispensable to detect, verify, and quantify circRNAs for downstream applications. In this review, we briefly introduce the biology of circRNAs, including the biogenesis, characteristics, and biological functions. In addition, we outline about 30 recent bioinformatic analysis tools that are publicly available for circRNA study. Principles for applying these computational strategies and considerations will be briefly discussed. Lastly, we give a complete survey on more than 20 key computational databases that are frequently used. To our knowledge, this is the most complete and updated summary on publicly available circRNA resources. In conclusion, this review summarizes key aspects of circRNA biology and outlines key computational strategies that will facilitate the genome-wide identification and prediction of circRNAs.

| S-EPMC7450300 | biostudies-literature

The Role of Circular RNAs in Immune-Related Diseases.

Project description:Circular RNAs (circRNAs) are a novel class of RNAs with a covalently closed loop structure without a 3' polyadenylation [poly-(A)] tail or a 5' cap. They used to be considered as the occasional and useless products of RNA splicing errors because they could not be detected by traditional RNA sequencing technology. Benefiting from the development of specific biochemical and computational approaches, researchers showed that circRNAs are universally expressed and functional. Further studies have revealed their important functions regarding regulating gene expression at the transcriptional and post-transcriptional levels. These functions include acting as microRNA (miRNA) sponges, binding to RNA-binding proteins (RBPs), acting as transcriptional regulatory factors, and serving as translation templates. The advances in circRNA research has opened researchers' eyes to a new area of research on the roles of circRNAs in the pathogenesis of various diseases, especially at the immune level because of the close relationship between circRNAs and the immune response. Emerging research indicates that circRNAs could act as potential biomarkers related to diagnosis, therapeutic effects, and prognosis, and they may be effective therapeutic targets in immunological disorders, including certain diseases that are currently difficult to treat.

| S-EPMC7142234 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data