FARNA: knowledgebase of inferred functions of non-coding RNA transcripts

Alam, Tanvir; Uludağ, Mahmut; Essack, Magbubah; Salhi, Adil; Ashoor, Haitham; Hanks, John B.; Kapfer, Craig A.; Mineta, Katsuhiko; Gojobori, Takashi; Bajic, Vladimir B.

doi:10.1093/nar/gkw973

Cited by 30 publications

(32 citation statements)

References 109 publications

(135 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…On the page "Enriched pairs," "Oxidative stress response" in column 1 is linked to a number of miRNAs (see column 2 when the "Human miRNAs" dictionary is selected), among which there is "MIR4639" (hsa-miR-4639). We checked the FARNA database [137] for hsa-miR-4639 and found that this miRNA is expressed in the heart [137]. Furthermore, FARNA suggests that hsa-miR-4639 is implicated in heart failure.…”

Section: Example 2: Hypotheses and Potentially New Insightsmentioning

confidence: 99%

Literature-Based Enrichment Insights into Redox Control of Vascular Biology

Essack

Salhi

Stanimirović

et al. 2019

Oxidative Medicine and Cellular Longevity

Self Cite

View full text Add to dashboard Cite

In cellular physiology and signaling, reactive oxygen species (ROS) play one of the most critical roles. ROS overproduction leads to cellular oxidative stress. This may lead to an irrecoverable imbalance of redox (oxidation-reduction reaction) function that deregulates redox homeostasis, which itself could lead to several diseases including neurodegenerative disease, cardiovascular disease, and cancers. In this study, we focus on the redox effects related to vascular systems in mammals. To support research in this domain, we developed an online knowledge base, DES-RedoxVasc, which enables exploration of information contained in the biomedical scientific literature. The DES-RedoxVasc system analyzed 233399 documents consisting of PubMed abstracts and PubMed Central full-text articles related to different aspects of redox biology in vascular systems. It allows researchers to explore enriched concepts from 28 curated thematic dictionaries, as well as literature-derived potential associations of pairs of such enriched concepts, where associations themselves are statistically enriched. For example, the system allows exploration of associations of pathways, diseases, mutations, genes/proteins, miRNAs, long ncRNAs, toxins, drugs, biological processes, molecular functions, etc. that allow for insights about different aspects of redox effects and control of processes related to the vascular system. Moreover, we deliver case studies about some existing or possibly novel knowledge regarding redox of vascular biology demonstrating the usefulness of DES-RedoxVasc. DES-RedoxVasc is the first compiled knowledge base using text mining for the exploration of this topic.

show abstract

Section: Example 2: Hypotheses and Potentially New Insightsmentioning

confidence: 99%

Literature-Based Enrichment Insights into Redox Control of Vascular Biology

Essack

Salhi

Stanimirović

et al. 2019

Oxidative Medicine and Cellular Longevity

Self Cite

View full text Add to dashboard Cite

show abstract

“…RNAs differ from lncRNAs in possessing significantly longer ORFs (21,24,25,28), it is possible that protein-coding RNAs and lncRNAs may present different 13 relationships between GC content and ORF length. Of course, ORF length, as one of the important features, has been widely used by the existing algorithms in coding potential prediction (20,21,24,25,28).…”

Section: Relationshipmentioning

confidence: 99%

“…Long non-coding RNAs (lncRNAs) are prevalently expressed in a large number of organisms (1)(2)(3)(4)(5). Evidence has accumulated that lncRNAs play vital roles in biological processes including transcriptional regulation, post-transcriptional interference, translational control (6)(7)(8)(9) and are implicated in the development of a variety of human diseases (10)(11)(12)(13)(14). Although the rapid advancement in DNA sequencing technologies has led to an exponential increase in the number of lncRNAs (11,15,16), lncRNAs are often tissue/cell-specific (13,17,18) and lineage/species-specific (18,19) and thus a large number of novel lncRNAs are yet to be discovered.…”

Section: Introductionmentioning

confidence: 99%

Characterization and identification of long non-coding RNAs based on feature relationship

Wang

Yin

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

The significance of long non-coding RNAs (lncRNAs) in many biological processes and diseases has gained intense interests over the past several years. However, computational identification of lncRNAs in a wide range of species remains challenging; it requires prior knowledge of well-established sequences and annotations or species-specific training data, but the reality is that only a limited number of species have high-quality sequences and annotations. Here we first characterize lncRNAs by contrast to protein-coding RNAs based on feature relationship and find that the feature relationship between ORF (open reading frame) length and GC content presents universally substantial divergence in lncRNAs and protein-coding RNAs, as observed in a broad variety of species. Based on the feature relationship, accordingly, we further present LGC, a novel algorithm for identifying lncRNAs that is able to accurately distinguish lncRNAs from protein-coding RNAs in a cross-species manner without any prior knowledge. As validated on large-scale empirical datasets, comparative results show that LGC outperforms existing algorithms by achieving higher accuracy, well-balanced sensitivity and specificity, and is robustly effective (>90% accuracy) in discriminating lncRNAs from protein-coding RNAs across diverse species that range from plants to mammals. To our knowledge, this study, for the first time, differentially characterizes lncRNAs and protein-coding RNAs based on feature relationship, which is further applied in . CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/327882 doi: bioRxiv preprint first posted online May. 23, 2018; 4 computational identification of lncRNAs. Taken together, our study represents a significant advance in characterization and identification of lncRNAs and LGC thus bears broad potential utility for computational analysis of lncRNAs in a wide range of species.

show abstract

“…Several computational methods have been proposed for the functional analysis of lncRNAs [7,8,9,10,11]. Most of the computational methods rely on an analysis of mR-NAs that are co-expressed with the lncRNA(s) in question.…”

Section: Introductionmentioning

confidence: 99%

“…Linc2GO generates functional annotation for long intergenic non-coding RNAs (lincRNAs) based on the competing endogenous RNA hypothesis [7]. Unlike the previous methods, FARNA infers a transcript's function from the transcription factors and co-factors whose genes are co-expressed with the transcript controlled by this TFs and TcoFs [11].…”

Section: Introductionmentioning

confidence: 99%

Functional Enrichment Analysis of Deregulated Long Non-Coding RNAs in Cancer Based on their Genomic Neighbors

Olgun

Taştan

2020

Preprint

View full text Add to dashboard Cite

The dysregulation of long non-coding RNAs' (lncRNAs) expressions has been implicated in cancer. Since most of the lncRNAs' are not functionally characterized well, investigating the set of perturbed lncRNAs are is challenging. Existing methods that inspect lncRNAs functionally rely on the co-expressed coding genes, which are far better characterized functionally. LncRNAs can be known to act as transcriptional regulators; they may activate or repress the neighborhood's coding genes on the genome. Based on this, in this work, we aim to analyze the deregulated lncRNAs in cancer by taking into account their ability to regulate nearby loci on the genome. We perform functional analysis on differentially expressed lncRNAs for 28 different cancers considering their adjacent coding genes. We identify that some deregulated lncRNAs are cancer-specific, but a substantial number of lncRNAs are shared across cancers. Next, we assess the similarities of the cancer types based on the functional enrichment of the deregulated lncRNA sets. We find some cancers are very similar in the functions and biological processes related to the deregulated lncRNAs. We observe that some of the cancers for which we find similarity can be linked through primary, metastatic site relations. We investigate the similarity of enriched functional terms for the deregulated lncRNAs and the mRNAs. We further assess the enriched functions' similarity to the functions and processes that the known cancer driver genes take place. We believe that our methodology help to understand the impact of the lncRNAs in cancer functionally.

show abstract

FARNA: knowledgebase of inferred functions of non-coding RNA transcripts

Cited by 30 publications

References 109 publications

Literature-Based Enrichment Insights into Redox Control of Vascular Biology

Literature-Based Enrichment Insights into Redox Control of Vascular Biology

Characterization and identification of long non-coding RNAs based on feature relationship

Functional Enrichment Analysis of Deregulated Long Non-Coding RNAs in Cancer Based on their Genomic Neighbors

Contact Info

Product

Resources

About