LncRNADisease: a database for long-non-coding RNA-associated diseases

Chen, Geng; Wang, Ziyun; Wang, Dongqing; Qiu, Chengxiang; Liu, Mingxi; Chen, Xing‐Xing; Zhang, Qipeng; Ge, Yan; Cui, Qinghua

doi:10.1093/nar/gks1099

Cited by 835 publications

(651 citation statements)

References 23 publications

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“…Therefore, in order to improve this situation, the identification of the genes and regulatory mechanisms involved in lymph node metastasis has become a research area of increasing interest. In recent years, a large number of lncRNAs have been identified in genetic studies, and have been found to be associated with various diseases (20).…”

Section: Discussionmentioning

confidence: 99%

Identification and functional characterization of long non-coding RNAs in human gastric cancer

Liang

Yao

et al. 2018

Oncol Lett

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Abstract. Abnormal regulation of long non-coding RNAs (lncRNAs) appears to be a primary feature of numerous types of human cancer. However, the association between the dysregulation of lncRNAs and functional alterations in gastric cancer (GC) remains unclear. In previous studies, we applied microarray and bioinformatics analyses to screen for key lncRNAs from the tumor tissues and matched adjacent non-tumor tissues of 10 patients with GC. There were seven key lncRNAs demonstrated to be significantly different between carcinoma tissues and adjacent non-tumor tissues. In the present study, the expression of these seven selected lncRNAs were validated in 82 patients with GC to further investigate the association between lncRNAs and GC clinical characterization. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) results demonstrated that RP5-919F19, MCPH1 antisense RNA 1 (CTD-2541M15) and urothelial carcinoma-associated 1 (UCA1) exhibited consistent upregulation in cancer compared with adjacent non-tumor tissues, whereas AP000459, LOC101928316, tumor suppressor candidate 8 (LINC01071) and maternally expressed 3 (MEG3) showed consistent downregulation. The results from the microarray and RT-qPCR experiments achieved 100% agreement. A correlation analysis indicated that RP5-919F19, LOC101928316 and MEG3 were significantly associated with tumor differentiation degree, RP5-919F19, UCA1 and MEG3 were significantly associated with lymph node metastasis, and RP5-919F19, CTD-2541M15 and UCA1 were significantly associated with tumor-node-metastasis stage (P<0.05). In addition, it was identified that the differential expression of LINC01071 and LOC101928316 significantly correlated with the age and gender of the GC patients, respectively (P<0.05). The results suggest that the lncRNAs RP5-919F19, LOC101928316, CTD-2541M15, UCA1 and MEG3 are closely associated with the invasion and metastasis of GC, which reveals these indicators as potential specificity biomarkers for the diagnosis, prognosis and classification of GC. Thus, these lncRNAs merit further study as novel candidate biomarkers for the clinical diagnosis of GC and as potential targets for therapy. IntroductionGastric cancer (GC) is one of the most lethal types of cancer and has been increasing in incidence and mortality over the last several decades. In China, it has been estimated that ~464,000 new cases were diagnosed in 2012, which accounts for over 40% of the total cases (~989,600) worldwide (1). According to evidence from clinical studies, the majority of patients with GC are diagnosed at an advanced stage and are thus not suitable for radical surgery (2). Previous studies have also reported that earlier diagnosis and treatment of GC could produce a 5-year survival rate of >90% (3).Recent developments in the field of digestive system endoscopy have been remarkable due to their association with decreased trauma, accelerated recovery and fewer complications (4,5). However, endoscopic biopsy and observation of pathological morphology are unable t...

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Section: Discussionmentioning

confidence: 99%

Identification and functional characterization of long non-coding RNAs in human gastric cancer

Liang

Yao

et al. 2018

Oncol Lett

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“…lncRNAs can be easily selected by size Functional RNA Database (fRNAdb), Kin et al (2007) http://www.ncrna.org/frnadb/ fRNAdb contains noncoding RNA annotations of ten species. It provides information on transcription factors, associated diseases, sequence ontology, and gene ontology for some lncRNAs Characterized lncRNA annotation Long noncoding RNA Database (lncRNAdb), Amaral et al (2011) http://www.lncrnadb.org/ This database provides expression, literature, and some other characterizations of 50 characterized lncRNAs in various species The lncRNA and Disease Database (LncRNADisease), Chen et al (2013) http://cmbi.bjmu.edu.cn/lncrnadisease This website provides both experimentally supported and predicted lncRNA-human disease relationships, based on hundreds of publications. It also shows relevant lncRNAprotein interaction, where applicable Function and interaction prediction Noncoding RNA Functional Annotation Server (ncFANs), Liao et al (2011) http://www.bioinfo.org/ncfans/ This tool provides a platform for obtaining lncRNA expression information from human and mouse microarray data.…”

Section: Lncrnas In Mammalian Spermatogenesismentioning

confidence: 99%

Long noncoding RNAs in spermatogenesis: insights from recent high-throughput transcriptome studies

Luk¹,

Chan²,

Rennert³

et al. 2014

Reproduction

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Spermatogenesis is a complex developmental process in which undifferentiated spermatogonia are differentiated into spermatocytes and spermatids through two rounds of meiotic division and finally giving rise to mature spermatozoa (sperm). These processes involve many testis-or male germ cell-specific gene products that undergo strict developmental regulations. As a result, identifying critical, regulatory genes controlling spermatogenesis provide the clues not only to the regulatory mechanism of spermatogenesis at the molecular level, but also to the identification of candidate genes for infertility or contraceptives development. Despite the biological importance in male germ cell development, the underlying mechanisms of stage-specific gene regulation and cellular transition during spermatogenesis remain largely elusive. Previous genomic studies on transcriptome profiling were largely limited to protein-coding genes. Importantly, protein-coding genes only account for a small percentage of transcriptome; the majority are noncoding transcripts that do not translate into proteins. Although small noncoding RNAs (ncRNAs) such as microRNAs, siRNAs, and Piwi-interacting RNAs are extensively investigated in male germ cell development, the role of long ncRNAs (lncRNAs), commonly defined as ncRNAs longer than 200 bp, is relatively unexplored. Herein, we summarize recent transcriptome studies on spermatogenesis and show examples that a subset of noncoding transcript population, known as lncRNAs, constitutes a novel regulatory target in spermatogenesis.

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“…They are linked to common disease states including, most prominently, cancer and nervous system disorders, as well as immunological, metabolic, vascular, and other pathologies [75]. These include, but are not limited to, susceptibility to viral and bacterial pathogens; human immunodeficiency virus replication; type 2 diabetes; hemolysis, elevated liver enzymes, and low platelets syndrome; brachydactyly and other developmental defects; and cancer risk, progression, and metastasis.…”

Section: Establishing Paradigms For Lncrna-related Pathologymentioning

confidence: 99%

Long Non-coding RNAs: Novel Targets for Nervous System Disease Diagnosis and Therapy

2013

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The human genome encodes tens of thousands of long non-coding RNAs (lncRNAs), a novel and important class of genes. Our knowledge of lncRNAs has grown exponentially since their discovery within the last decade. lncRNAs are expressed in a highly cell-and tissue-specific manner, and are particularly abundant within the nervous system. lncRNAs are subject to post-transcriptional processing and inter-and intra-cellular transport. lncRNAs act via a spectrum of molecular mechanisms leveraging their ability to engage in both sequence-specific and conformational interactions with diverse partners (DNA, RNA, and proteins). Because of their size, lncRNAs act in a modular fashion, bringing different macromolecules together within the three-dimensional context of the cell. lncRNAs thus coordinate the execution of transcriptional, post-transcriptional, and epigenetic processes and critical biological programs (growth and development, establishment of cell identity, and deployment of stress responses). Emerging data reveal that lncRNAs play vital roles in mediating the developmental complexity, cellular diversity, and activitydependent plasticity that are hallmarks of brain. Corresponding studies implicate these factors in brain aging and the pathophysiology of brain disorders, through evolving paradigms including the following: (i) genetic variation in lncRNA genes causes disease and influences susceptibility; (ii) epigenetic deregulation of lncRNAs genes is associated with disease; (iii) genomic context links lncRNA genes to disease genes and pathways; and (iv) lncRNAs are otherwise interconnected with known pathogenic mechanisms. Hence, Electronic supplementary material The online version of this article

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LncRNADisease: a database for long-non-coding RNA-associated diseases

Cited by 835 publications

References 23 publications

Identification and functional characterization of long non-coding RNAs in human gastric cancer

Identification and functional characterization of long non-coding RNAs in human gastric cancer

Long noncoding RNAs in spermatogenesis: insights from recent high-throughput transcriptome studies

Long Non-coding RNAs: Novel Targets for Nervous System Disease Diagnosis and Therapy

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