Abstract:
:Circular RNAs (circRNAs) are a new kind of endogenous non-coding RNAs, which have been discovered continuously. More and more studies have shown that circRNAs are related to the occurrence and development of human diseases. Identification of circRNAs associated with diseases can contribute to understand the pathogenesis, diagnosis and treatment of diseases. However, experimental methods of circRNA prediction remain expensive and time-consuming. Therefore, it is urgent to propose novel computational methods for the prediction of circRNA-disease associations. In this study, we develop a computational method called LLCDC that integrates the known circRNA-disease associations, circRNA semantic similarity network, disease semantic similarity network, reconstructed circRNA similarity network, and reconstructed disease similarity network to predict circRNAs related to human diseases. Specifically, the reconstructed similarity networks are obtained by using Locality-Constrained Linear Coding (LLC) on the known association matrix, cosine similarities of circRNAs and diseases. Then, the label propagation method is applied to the similarity networks, and four relevant score matrices are respectively obtained. Finally, we use 5-fold cross validation (5-fold CV) to evaluate the performance of LLCDC, and the AUC value of the method is 0.9177, indicating that our method performs better than the other three methods. In addition, case studies on gastric cancer, breast cancer and papillary thyroid carcinoma further verify the reliability of our method in predicting disease-associated circRNAs.
journal_name
Genomicsjournal_title
Genomicsauthors
Ge E,Yang Y,Gang M,Fan C,Zhao Qdoi
10.1016/j.ygeno.2019.08.001subject
Has Abstractpub_date
2020-03-01 00:00:00pages
1335-1342issue
2eissn
0888-7543issn
1089-8646pii
S0888-7543(19)30420-3journal_volume
112pub_type
杂志文章相关文献
GENOMICS文献大全abstract::A complete genetic linkage map of the soybean, in which sequence-based (SB) genetic markers are evenly distributed genomewide, was constructed from an F(12) population composed of 113 recombinant inbred lines derived from an interspecific cross involving Korean genotypes Hwangkeum and IT182932. Several approaches were...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2008.03.008
更新日期:2008-07-01 00:00:00
abstract:UNLABELLED:Next-generation sequencing data can be mapped to a reference genome to identify single-nucleotide polymorphisms/variations (SNPs/SNVs; called SNPs hereafter). In theory, SNPs can be compared across several samples and the differences can be used to create phylogenetic trees depicting relatedness among the sa...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2014.06.001
更新日期:2014-07-01 00:00:00
abstract::There is a high level of conservation between human chromosomes and bovine syntenic groups. One such comparison is between human chromosome 12 and bovine chromosome 5, where at least 16 loci have been shown to be conserved in an homologous segment. However, the degree of conservation of order of the loci on bovine chr...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/s0888-7543(05)80280-0
更新日期:1992-09-01 00:00:00
abstract::We isolated a mouse cDNA encoding APEX2 protein and demonstrated that APEX2 binds to PCNA. The level of Apex2 mRNA was high in the thymus, bone marrow, spleen, and kidney in adult mice. Apex2 consists of six exons and is flanked on the 3' end by Alas2 on X chromosome 63.0. Furthermore, Apex2 is flanked on the 5' end b...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/s0888-7543(02)00009-5
更新日期:2003-01-01 00:00:00
abstract::The transforming growth factor beta (TGF-beta) superfamily is a family of multifunctional cytokines that transduce signals via serine/threonine kinase receptors. Recent studies revealed that Mothers against dpp (Mad) in Drosophila and its homologs play important roles in the intracellular signal transduction of the se...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1997.5149
更新日期:1998-02-15 00:00:00
abstract::Bacterial artificial chromosomes (BACs) provide a well-characterized resource for studying the functional organization of genes and other large chromosomal domains. To facilitate functional studies in cell cultures, we have developed a simple approach for generating stable cell lines with variable copy numbers of any ...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/s0888-7543(03)00205-2
更新日期:2004-01-01 00:00:00
abstract::Imprinting is an epigenetic modification that is reprogrammed in the germ line and leads to the monoallelic expression of some genes. Imprinting involves DNA methylation. Maternal imprint is reset during oocyte growth and maturation. In vitro maturation (IVM) of oocytes may, therefore, interfere with imprint acquisiti...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2005.10.008
更新日期:2006-03-01 00:00:00
abstract::The WD-repeat protein family consists of a large group of structurally related yet functionally diverse proteins found predominantly in eukaryotic cells. These factors contain several (4-16) copies of a recognizable amino-acid sequence motif (the WD unit) thought to be organized into a "propeller-like" structure invol...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.2001.6682
更新日期:2002-01-01 00:00:00
abstract::The rat diabetes susceptibility gene, Lyp or Lymphopenia, has been localized to RNO4. Proximal to Lyp are the genes caspase-2 (Casp2) and pancreatic trypsin 1 (Prss1), while neuropeptide Y (Npy) is the closest distally positioned gene. In human, the three genes are syntenic on HSA7, but they are not on a conserved seg...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.2000.6130
更新日期:2000-04-01 00:00:00
abstract::A new member of the insulin gene superfamily (INSL5) was identified by searching EST databases for the presence of the conserved insulin B-chain cysteine motif. Human and murine INSL5 are both polypeptides of 135 amino acids, matching the classical signature of the insulin superfamily. Through the B- and A-chain regio...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1999.5899
更新日期:1999-08-15 00:00:00
abstract::Neogenin was first identified in the chick embryo, and like a number of cell surface proteins of the immunoglobulin (Ig) superfamily, including N-CAM and L1 (generally called cell adhesion molecules or CAMs), it is expressed on growing nerve cells in the developing nervous system of vertebrate embryos. Neogenin is als...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1997.4688
更新日期:1997-05-01 00:00:00
abstract::We have hybridized all 28 chromosome-specific painting probes from the domestic sheep (Ovis aries, 2n = 54) onto metaphase chromosomes of the Indian muntjac deer (Muntiacus muntjak vaginalis, 2n = 6,7) and identified 35 conserved chromosomal segments. Results from this study show that most of the sheep acrocentric chr...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1997.4998
更新日期:1997-11-15 00:00:00
abstract::Large deletions in Xq21 often are associated with contiguous gene syndromes consisting of X-linked deafness type 3 (DFN3), mental retardation (MRX), and choroideremia (CHM). The identification of deletions associated with classic CHM or DFN3 facilitated the positional cloning of the underlying genes, REP-1 and POU3F4,...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1999.6004
更新日期:1999-12-15 00:00:00
abstract::The desmogleins, together with the desmocollins, both members of the cadherin superfamily, are the adhesive proteins of the desmosome type of cell junction, characteristically found in epithelial cells. Three different human desmoglein isoforms are encoded by separate genes (DSG1, DSG2, and DSG3) located on chromosome...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(95)80067-v
更新日期:1995-01-20 00:00:00
abstract::We conducted a comprehensive analysis of codon usage bias (CUB) based on the available non-redundant full-length cDNA (nrFLcDNA) and expressed sequence tags (ESTs) data of cultivar Micro-Tom and evaluated the associations of observed CUB and measurements of transcriptional and translational effectiveness. The analysis...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2013.02.008
更新日期:2013-05-01 00:00:00
abstract::Rippling muscle disease (RMD) is an autosomal dominant disorder characterized by electrically silent, percussion-induced muscular contractions. We previously reported the localization of a gene for RMD to 1q41-q42 by genome-wide linkage analysis in a large family from Oregon. This RMD gene was initially found to be co...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1998.5689
更新日期:1999-02-01 00:00:00
abstract::Denaturing high-performance liquid chromatography (DHPLC) is a novel high-capacity technique for detecting new mutations. We have evaluated the sensitivity and specificity of this method in a blind analysis of exon H of the factor IX gene and exon 16 of the neurofibromatosis type 1 gene. Under a single set of conditio...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1998.5411
更新日期:1998-08-15 00:00:00
abstract::Dynamins, microtubule-binding GTPases, are encoded by at least three genes in mammals. Two distinct gene-specific cDNAs were used to analyze the segregation of dynamin genes Dnm1 and Dnm2 in a mouse interspecies backcross. The nervous system-expressed gene Dnm1 was localized to Chr 2 between the genes for vimentin and...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1997.4634
更新日期:1997-04-15 00:00:00
abstract::We have established PCR assays for the genes coding for the major proteins of the desmosome type of cell junction, the desmosomal cadherins DGI (desmoglein) and DGII/III (desmocollins), and the plaque proteins DPI/II (desmoplakin) and DPIII (plakoglobin) and used them to test human-mouse and human-rat somatic cell hyb...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(91)90446-l
更新日期:1991-07-01 00:00:00
abstract::Eight genes located on the short arm of the human X chromosome (MAOA, SYN1, OAT, OTC, CYBB, DMD, ZFX, POLA) have been mapped in several marsupial species by cell hybrid analysis and/or in situ hybridization using probes derived from human cDNA. Seven appear to be autosomal in all marsupial species examined. The eighth...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(91)90141-z
更新日期:1991-10-01 00:00:00
abstract::To identify genetic determinants relevant to non-insulin-dependent diabetes mellitus (NIDDM), we performed a genome-wide analysis for quantitative trait loci (QTLs) using 359 backcross progeny of the Otsuka Long-Evans Tokushima Fatty (OLETF) rat. The OLETF strain is a well-studied animal model of obese NIDDM, with fea...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1999.5789
更新日期:1999-06-15 00:00:00
abstract::The Xist sequence has been proposed as a potential candidate for the X-inactivation center based both on its localization within the candidate region for the X-inactivation center in man and mouse and on its unique pattern of expression from the inactive X chromosome. We have cloned 550 kb of DNA surrounding the mouse...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1993.1108
更新日期:1993-03-01 00:00:00
abstract::A cluster of genes coding for proteins of the extracellular matrix (ECM) containing sequence motifs essential for integrin-receptor interactions is located on HSA4q21 and on BTA6, within the critical region of a quantitative trait locus (QTL) affecting milk protein production. Genes within this cluster are involved in...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2004.03.005
更新日期:2004-08-01 00:00:00
abstract::Non-coding RNA (ncRNA) is a kind of RNA, produced by genomic transcription and does not encode protein, but can regulate the function of genes, thus widely regulating pathological and physiological processes. The dynamic balance of the reticular structure between them is needed to regulate the homeostasis, the abnorma...
journal_title:Genomics
pub_type: 杂志文章,评审
doi:10.1016/j.ygeno.2019.10.006
更新日期:2020-03-01 00:00:00
abstract::We mapped a new X-linked recessive atrophic macular degeneration locus to Xp21.1-p11.4 and show allelic involvement of the gene RPGR, which normally causes severe peripheral retinal degeneration leading to global blindness. Ten affected males whom we examined had primarily macular atrophy causing progressive loss of v...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.2002.6815
更新日期:2002-08-01 00:00:00
abstract::We isolated the human homologue, SUPT5H, of the yeast transcription factor, SPT5. The human homologue is 1088 aa long compared to 1063 aa for the yeast gene. SUPT5H maps to 19q13, near the ryanodine receptor. Like its family member, SUPT6H, and like yeast SPT5, SUPT5H has a very acidic 5' domain. Like its family membe...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1996.0646
更新日期:1996-12-15 00:00:00
abstract::One hundred forty-nine chromosome 15 loci were mapped by PCR with respect to chromosome breakpoints in three somatic cell hybrids retaining total or part of chromosome 15 and to a 10-Mb YAC contig. This chromosome was subdivided into 5 regions, yielding an average resolution of more than 1 sequence tagged site per meg...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1994.1550
更新日期:1994-10-01 00:00:00
abstract::Fibrillin-1 is a large cysteine-rich glycoprotein of the 10-nm microfibrils in the extracellular matrix. A spectrum of mutations in the fibrillin-1 gene (FBN1) have been identified in patients with Marfan syndrome (MFS), and the majority of mutations resulting in the neonatal and often lethal form of MFS have been ide...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1996.0492
更新日期:1996-09-15 00:00:00
abstract::Lymphocytes of mouse strains BALB/cHeA (BALB/c) and STS/A (STS) differ in the IL-2-induced proliferative response, STS being a high and BALB/c a low responder in the range of concentrations 125-2000 IE/ml. We analyzed the genetic basis of this strain difference using the recombinant congenic (RC) strains of the BALB/c...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1997.4694
更新日期:1997-05-15 00:00:00
abstract::The gene mutated in chorea-acanthocytosis (CHAC; approved gene symbol VPS13A) encodes chorein, a protein similar to yeast Vps13p. We detected several similar putative human proteins by BLAST analysis of chorein. We characterized the structure of three new genes encoding these CHAC-similar proteins, located on chromoso...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2004.04.012
更新日期:2004-09-01 00:00:00