Abstract:
:MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate mRNAs through a sequence-specific mechanism. By virtue of their structure and mechanism of action, computational methods have been devised to investigate the encoding of miRNA genes and the targets of miRNA action. A variety of assumptions have predicated the implementation of these various computational solutions. Evolutionary sequence conservation, secondary structure, and folding energetics are some of the assumptions that have been used. The success of these different computational solutions has been evaluated for both elucidation of new miRNAs and deducing targets of miRNA action. While the focus is on search techniques for new miRNAs, we have compared the programs miRseeker, miRScan, PalGrade, ProMiR, and miRAlign as examples of implementation of these techniques. For these programs, a benchmark comparison between theoretical estimation and actual identification is possible. We have also compared the target prediction programs TargetScanS, PicTar, DIANA-microT, miRanda, and RNAhybrid. However, it is difficult to rigorously assess the benchmark performance of these programs due to the difficulty in confirming their theoretical predictions.
journal_name
DNA Cell Bioljournal_title
DNA and cell biologyauthors
Doran J,Strauss WMdoi
10.1089/dna.2006.0546subject
Has Abstractpub_date
2007-05-01 00:00:00pages
353-60issue
5eissn
1044-5498issn
1557-7430journal_volume
26pub_type
杂志文章abstract::The present study was to explore whether the polymorphisms of FAM167 A-BLK region are associated with the susceptibility to autoimmune thyroid disease (AITD). The second sequencing technology was undertaken for seven tag loci mapping of the FAM167 A-BLK region, namely, rs11250144, rs2618431, rs4840568, rs13277113, rs2...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2018.4344
更新日期:2018-11-01 00:00:00
abstract::Our previous study showed that the mutation hotspots of the K-ras proto-oncogene in human functional adrenocortical tumors are in codons 15, 16, 18, and 31, thus differing from the sites in other tumors. In addition, analyzing the K-Ras protein by a recombinant DNA technique showed that the activity of endogenic GTPas...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/104454901750219116
更新日期:2001-04-01 00:00:00
abstract::Sterol regulatory element-binding proteins (SREBPs) are transcription factors governing transcription of genes related to cholesterol and fatty acid metabolism. To become active, SREBPs must undergo a proteolytic cleavage to allow an active NH(2)-terminal segment to translocate into the nucleus. SKI-1/S1P is the first...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2007.0624
更新日期:2007-11-01 00:00:00
abstract::Apelin, an endogenous ligand for apelin receptor (APJ), is reported to be involved in cardiomyocyte hypertrophy. In this study, we explored the mechanism of cardiomyocyte hypertrophy induced by apelin-13/APJ system. Left ventricular hypertrophy (LVH) rat model was established by constricting the abdominal aorta. Weste...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2016.3574
更新日期:2017-08-01 00:00:00
abstract::Metallothioneins (MT) are expressed during early development in species of several groups. To understand MT function in developmental processes, we studied the MT system of Xenopus laevis, a model vertebrate species in experimental embryology. We first purified and sequenced the liver MT from copper-treated animals. T...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.1993.12.341
更新日期:1993-05-01 00:00:00
abstract::Studies of the epigenome have attracted little interest in nephrology, especially in uremia. Several lines of evidence have suggested that there are links between genomic DNA hypomethylation and cardiovascular complications in uremia patients. However, to date, our knowledge about the alterations in histone methylatio...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2010.1076
更新日期:2011-03-01 00:00:00
abstract::Xenotransplantation from pigs to human beings is viewed as a potential solution for the acute organ shortage. However, consequent xenorejection induced by Gal alpha 1,3 Gal (a Gal, Gal antigen) prevents xenotransplantation from clinical application. Thus, the most attracting attempt to prevent xenorejection is the eli...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2005.24.235
更新日期:2005-04-01 00:00:00
abstract::Endothelin-converting enzyme-1 (ECE1) plays a key role in the development of a subset of neural crest lineages such as cardiogenesis. Genetic variants of ECE1 C338A (rs213045) and T839G (rs213046) have been shown to alter ECE1 expression. This observation led us to hypothesize that two polymorphisms might influence th...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2012.1626
更新日期:2012-08-01 00:00:00
abstract::Long noncoding RNAs (lncRNAs) may serve as potential molecular diagnostic markers to improve the capacity of earlier and more accurate diagnosis of dilated cardiomyopathy (DCM). We integrated five independent transcriptomic datasets (n = 504) from Gene Expression Omnibus for systematic identification of lncRNA-based d...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2020.5670
更新日期:2020-11-03 00:00:00
abstract::Alzheimer's disease (AD) is a neurodegenerative disorder characterized by overproduction of beta-amyloid (Abeta), which is formed from amyloid precursor protein (APP), with the subsequent pathologic deposition of Abeta in regions of the brain important for memory and cognition. Recently, vaccination of murine models o...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/10445490152717587
更新日期:2001-11-01 00:00:00
abstract::Interstitial lung disease (ILD) is the main reason of death in patients with systemic sclerosis (SSc). The potential microRNA (miRNA)-messenger RNA (mRNA) interaction networks of SSc-ILD from a systematic biological perspective are unclear. To characterize differentially expressed miRNAs (DE-miRNAs) and differentially...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2019.4780
更新日期:2019-09-01 00:00:00
abstract::Immune dysregulation has been implicated in myelodysplastic syndrome (MDS) pathogenesis. Refractory anemia with ringed sideroblasts (RARS) is a low-risk subtype of MDS. Our previous study has reported an abnormal γδ T cell receptor (TCR) repertoire in patients with intermediate or high-risk MDS. To characterize the st...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2015.2925
更新日期:2015-09-01 00:00:00
abstract::Hearing loss in Ménière's disease (MD) is associated with loss of spiral ganglion neurons and hair cells. In a guinea pig model of endolymphatic hydrops, nitric oxide synthases (NOS) and oxidative stress mediate loss of spiral ganglion neurons. To test the hypothesis that functional variants of NOS1 and NOS2A are asso...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2011.1259
更新日期:2011-09-01 00:00:00
abstract::At supramolecular resolution, DNA synthesis begins at preferred replication origins in the chromosomes of metazoan cells. To characterize one of these origins in detail, the initiation of replication was examined in the HeLa c-myc origin. Polymerase chain reaction (PCR) amplification of size-fractionated nascent chrom...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.1998.17.885
更新日期:1998-10-01 00:00:00
abstract::Osteosarcoma (OS) is a bone malignancy with high incidence. The underlying molecular mechanisms that are associated with the development of OS need further investigation. In this study, we showed that SLC34A2, a member of the solute carrier gene family, was significantly downregulated in OS patients and cell lines. Ov...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2017.3750
更新日期:2017-09-01 00:00:00
abstract::Protein homeostasis in the endoplasmic reticulum (ER) in eukaryotic cells is maintained by a conserved quality control system named ER-associated degradation (ERAD). The ERAD system retains misfolded or unassembled polypeptides in the ER, retrotranslocates them into the cytosol for degradation by the ubiquitin proteas...
journal_title:DNA and cell biology
pub_type: 杂志文章,评审
doi:10.1089/dna.2014.2452
更新日期:2014-08-01 00:00:00
abstract::The role of p53 in mediating nitric oxide (NO)-induced cell death remains uncertain. The exogenous NO donor S-nitrosoglutathione (GSNO) produced a concentration-dependent reduction in cell viability in embryonic chick cardiomyocytes in culture. Western blotting and immunocytochemistry for p53 showed that p53 was incre...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2007.0576
更新日期:2007-07-01 00:00:00
abstract::Defective T cell receptor (TCR) signaling resulting in lower T cell function plays a crucial role in the pathogenesis of T cell immunodeficiency in leukemia. Previous studies have indicated that lower TCRζ levels are a common characteristic of patients with leukemia, and upregulating TCRζ could partially recover T cel...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2015.2810
更新日期:2015-07-01 00:00:00
abstract::The aim of this article is to review our current understanding of the role of cytokines, chemokines, T cells, Langerhans cells, and neutrophils (PMN) and their interactions in vivo in the host response to Pseudomonas aeruginosa ocular challenge. The cellular/cytokine network in vivo has begun to be unraveled, and the ...
journal_title:DNA and cell biology
pub_type: 杂志文章,评审
doi:10.1089/10445490260099665
更新日期:2002-05-01 00:00:00
abstract::Matrix metalloproteinase-7 (MMP-7) is a small secreted proteolytic enzyme with broad substrate specificity. Its expression is associated with tumor invasion, metastasis, and survival for a number of cancers. However, data from published studies with individually low statistical power are conflicting. Here, we performe...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2011.1416
更新日期:2012-05-01 00:00:00
abstract::Regenerative medicine is a new interdisciplinary field in biomedical science, which aims at the repair or replacement of the defective tissue or organ by congenital defects, age, injury, or disease. Various cell-related techniques such as stem cell-based biotherapy are a hot topic in the current press, and stem cell r...
journal_title:DNA and cell biology
pub_type: 杂志文章,评审
doi:10.1089/dna.2013.2104
更新日期:2013-10-01 00:00:00
abstract::The mdmx gene was shown to possess high homology to the mdm-2 gene and to encode a protein that can bind p53 and block p53 transactivation. Because Mdm-2 protein blocks the growth-suppressive activity of the p53 tumor-suppressor protein through similar activities, we examined the expression patterns of mdmx to determi...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/104454999314971
更新日期:1999-09-01 00:00:00
abstract::The prototypic member of the transforming growth factor beta family is TGFbeta1, which is known to be important in extracellular matrix production, cell proliferation, and cell differentiation. Specifically in the pituitary lactotroph, TGFbeta1 inhibits prolactin (PRL) peptide secretion, PRL mRNA levels, and PRL gene ...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/104454999314863
更新日期:1999-11-01 00:00:00
abstract::To explore the effect of miR-106a in breast cancer cell behavior and sensitivity to chemotherapeutic agents. Tumor tissue and adjacent normal tissue were derived from 40 breast cancer patients, and miR-106a expression was measured by reverse transcription-qPCR. Breast cancer cells, MDA-MB-231 and MCF-7, were treated w...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2018.4282
更新日期:2019-02-01 00:00:00
abstract::Genes involved in the production of nitric oxide (NO) have been suggested as genetic factors for migraine. It has been studied whether polymorphisms in the genes encoding for different types of NO synthase (NOS) could be involved in the liability to migraine; however, most studies yield negative results. The pentanucl...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2010.1102
更新日期:2011-02-01 00:00:00
abstract::FOXO3 is a member of the Forkhead box class O (FOXO) transcription factor family that modulates the transcription of target genes in a variety of cellular functions in lower animals to mammals. It has been implicated in the attenuation of insulin-signaling pathways, including having a potential role in lifespan contro...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2010.1193
更新日期:2011-07-01 00:00:00
abstract::Head and neck cancers (head and neck squamous cell carcinomas [HNSCC]) are a heterogeneous group of neoplasms with varying presenting symptoms, treatment, and expected outcome. There is a need to find an effective way of its treatment at the molecular level. Thus, we should identify the mechanism of cancer cell respon...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2011.1325
更新日期:2012-03-01 00:00:00
abstract::In an effort to develop a more effective genetic immunization strategy for HIV, we developed an HIV-2 env DNA vaccine and evaluated three adjuvant formulations. The gp140 gene from HIV-2(UC2 )was synthesized using mammalian codons and cloned into a plasmid vector that expresses eukaryotic genes at high levels. We foun...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/104454904322759911
更新日期:2004-02-01 00:00:00
abstract::Colorectal cancer (CRC) patients with KRAS mutation are refractory and usually have poor prognosis. We aimed to identify the hub gene associated with KRAS mutant CRCs. Weighted gene coexpression network analysis (WGCNA) was used to calculate the key module and the hub genes in GSE39582. Combined with the protein-prote...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2020.5574
更新日期:2020-09-01 00:00:00
abstract::Epulopiscium sp. type B, a member of the Firmicutes, is a large (up to 300 microm), cigar-shaped bacterial symbiont of surgeonfish that propagates itself by forming multiple intracellular offspring. This unusual form of reproduction is an apparent modification of a developmental program used by some Firmicutes to prod...
journal_title:DNA and cell biology
pub_type: 杂志文章
doi:10.1089/dna.2008.0801
更新日期:2009-02-01 00:00:00