Abstract:
BACKGROUND:Intensive research based on the inverse expression relationship has been undertaken to discover the miRNA-mRNA regulatory modules involved in the infection of Hepatitis C virus (HCV), the leading cause of chronic liver diseases. However, biological studies in other fields have found that inverse expression relationship is not the only regulatory relationship between miRNAs and their targets, and some miRNAs can positively regulate a mRNA by binding at the 5' UTR of the mRNA. RESULTS:This work focuses on the detection of both inverse and positive regulatory relationships from a paired miRNA and mRNA expression data set of HCV patients through a 'change-to-change' method which can derive connected discriminatory rules. Our study uncovered many novel miRNA-mRNA regulatory modules. In particular, it was revealed that GFRA2 is positively regulated by miR-557, miR-765 and miR-17-3p that probably bind at different locations of the 5' UTR of this mRNA. The expression relationship between GFRA2 and any of these three miRNAs has not been studied before, although separate research for this gene and these miRNAs have all drawn conclusions linked to hepatocellular carcinoma. This suggests that the binding of mRNA GFRA2 with miR-557, miR-765, or miR-17-3p, or their combinations, is worthy of further investigation by experimentation. We also report another mRNA QKI which has a strong inverse expression relationship with miR-129 and miR-493-3p which may bind at the 3' UTR of QKI with a perfect sequence match. Furthermore, the interaction between hsa-miR-129-5p (previous ID: hsa-miR-129) and QKI is supported with CLIP-Seq data from starBase. Our method can be easily extended for the expression data analysis of other diseases. CONCLUSION:Our rule discovery method is useful for integrating binding information and expression profile for identifying HCV miRNA-mRNA regulatory modules and can be applied to the study of the expression profiles of other complex human diseases.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Song R,Liu Q,Liu T,Li Jdoi
10.1186/1471-2164-16-S2-S11subject
Has Abstractpub_date
2015-01-01 00:00:00pages
S11issn
1471-2164pii
1471-2164-16-S2-S11journal_volume
16 Suppl 2pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Sub-optimal developmental diets often have adverse effects on long-term fitness and health. One hypothesis is that such effects are caused by mismatches between the developmental and adult environment, and may be mediated by persistent changes in gene expression. However, there are few experimental tests of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3968-z
更新日期:2017-08-22 00:00:00
abstract:BACKGROUND:Nuclear receptors are hormone-regulated transcription factors whose signaling controls numerous aspects of development and physiology. Many receptors recognize DNA hormone response elements formed by direct repeats of RGKTCA motifs separated by 1 to 5 bp (DR1-DR5). Although many known such response elements ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-23
更新日期:2007-01-19 00:00:00
abstract:BACKGROUND:Osteoporosis is a common and debilitating bone disease that is characterised by a low bone mineral density (BMD), a highly heritable trait. Genome-wide association studies (GWAS) have proven to be very successful in identifying common genetic variants associated with BMD adjusted for age, gender and weight, ...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/s12864-016-2481-0
更新日期:2016-02-25 00:00:00
abstract:BACKGROUND:JWB phytoplasma is a kind of insect-transmitted and uncultivable bacterial plant pathogen causeing a destructive Jujube disease. To date, no genome information about JWB phytoplasma has been published, which hindered its characterization at genomic level. To understand its pathogenicity and ecology, the geno...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5075-1
更新日期:2018-09-19 00:00:00
abstract:BACKGROUND:The pattern of point mutation is important for studying mutational mechanisms, genome evolution, and diseases. Previous studies of mutation direction were largely based on substitution data from a limited number of loci. To date, there is no genome-wide analysis of mutation direction or methylation-dependent...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-316
更新日期:2006-12-13 00:00:00
abstract:BACKGROUND:The technological evolution of platforms for detecting genome-wide copy number imbalances has allowed the discovery of an unexpected amount of human sequence that is variable in copy number among individuals. This type of human variation can make an important contribution to human diversity and disease susce...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-573
更新日期:2008-11-28 00:00:00
abstract:BACKGROUND:Cottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving efficient genetic improvement of the traits. However, it is not yet clear about their genetic archit...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4837-0
更新日期:2018-06-13 00:00:00
abstract:BACKGROUND:The molecular mechanisms of transcriptional regulation are poorly understood in Plasmodium falciparum. In addition, most of the genes in Plasmodium falciparum are transcriptionally poised and only a handful of cis-regulatory elements are known to operate in transcriptional regulation. Here, we employed an ep...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4052-4
更新日期:2017-08-23 00:00:00
abstract:BACKGROUND:Triptolide is a therapeutic diterpenoid derived from the Chinese herb Tripterygium wilfordii Hook f. Triptolide has been shown to induce apoptosis by activation of pro-apoptotic proteins, inhibiting NFkB and c-KIT pathways, suppressing the Jak2 transcription, activating MAPK8/JNK signaling and modulating the...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1614-1
更新日期:2015-06-30 00:00:00
abstract:BACKGROUND:The principal toxicity of acute organophosphate (OP) pesticide poisoning is the disruption of neurotransmission through inhibition of acetylcholinesterase (AChE). However, other mechanisms leading to persistent effects and neurodegeneration remain controversial and difficult to detect. Because Caenorhabditis...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-291
更新日期:2013-04-30 00:00:00
abstract:BACKGROUND:The Pacific oyster Crassostrea gigas is an important fishery resource that is sensitive to temperature fluctuations. Thus, it has evolved a protection mechanism against heat stress by increasing the expression of the gene coding for heat shock protein (HSP) 70 under elevated temperatures. In other animals, h...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6003-8
更新日期:2019-08-08 00:00:00
abstract:BACKGROUND:Rapid acquisition of accurate genotyping information is essential for all genetic marker-based studies. For species with relatively small genomes, complete genome resequencing is a feasible approach for genotyping; however, for species with large and highly repetitive genomes, the acquisition of whole genome...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-448
更新日期:2013-07-05 00:00:00
abstract:BACKGROUND:Dimension reduction is a critical issue in the analysis of microarray data, because the high dimensionality of gene expression microarray data set hurts generalization performance of classifiers. It consists of two types of methods, i.e. feature selection and feature extraction. Principle component analysis ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S2-S24
更新日期:2008-09-16 00:00:00
abstract:BACKGROUND:Candida albicans is an opportunistic pathogenic yeast, which could become pathogenic in various stressful environmental factors including the spaceflight environment. In this study, we aim to explore the phenotypic changes and possible mechanisms of C. albicans after exposure to spaceflight conditions. RESU...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6476-5
更新日期:2020-01-17 00:00:00
abstract:BACKGROUND:Intensive selection has resulted in increased growth rates and muscularity in broiler chickens, in addition to adverse effects, including delayed organ development, sudden death syndrome, and altered metabolic rates. The biological mechanisms underlying selection responses remain largely unknown. Non-artific...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3845-9
更新日期:2017-06-20 00:00:00
abstract:BACKGROUND:Genomic selection based on genotyping-by-sequencing (GBS) data could accelerate alfalfa yield gains, if it displayed moderate ability to predict parent breeding values. Its interest would be enhanced by predicting ability also for germplasm/reference populations other than those for which it was defined. Pre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2212-y
更新日期:2015-12-01 00:00:00
abstract:BACKGROUND:Mycoviruses are viruses that naturally infect and replicate in fungi. Aspergillus fumigatus, an opportunistic pathogen causing fungal lung diseases in humans and animals, was recently shown to harbour several different types of mycoviruses. A well-characterised defence against virus infection is RNA silencin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3773-8
更新日期:2017-05-30 00:00:00
abstract:BACKGROUND:Acinetobacter baumannii is a significant hospital pathogen, particularly due to the dissemination of highly multidrug resistant isolates. Genome data have revealed that A. baumannii is highly genetically diverse, which correlates with major variations seen at the phenotypic level. Thus far, comparative genom...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1020
更新日期:2014-11-25 00:00:00
abstract:BACKGROUND:Tubulin isotypes and expression patterns are highly regulated in diverse organisms. The genome sequence of the protozoan parasite Leishmania major contains three distinct beta-tubulin loci. To investigate the diversity of beta-tubulin genes, we have compared the published genome sequence to draft genome sequ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-137
更新日期:2006-06-06 00:00:00
abstract:BACKGROUND:In many eukaryotes, microRNAs (miRNAs) bind to complementary sites in the 3'-untranslated regions (3'-UTRs) of target messenger RNAs (mRNAs) and regulate their expression at the stage of translation. Recent studies have revealed that many miRNAs are evolutionarily conserved; however, the evolution of their t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-101
更新日期:2010-02-09 00:00:00
abstract:BACKGROUND:There is strong but mostly circumstantial evidence that genetic factors modulate the severity of influenza infection in humans. Using genetically diverse but fully inbred strains of mice it has been shown that host sequence variants have a strong influence on the severity of influenza A disease progression. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-411
更新日期:2012-08-20 00:00:00
abstract:BACKGROUND:Cotton is an important fiber crop but has serious heterosis effects, and cytoplasmic male sterility (CMS) is the major cause of heterosis in plants. However, to the best of our knowledge, no studies have investigated CMS Yamian A in cotton with the genetic background of Australian wild Gossypium bickii. Conj...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07261-y
更新日期:2020-12-02 00:00:00
abstract:BACKGROUND:Of the hundreds of Vibrio cholerae serogroups, O1 and O139 are the main epidemic-causing ones. Although non-O1/non-O139 serogroups rarely cause epidemics, the possibility exists for strains within them to have pathogenic potential. RESULTS:We selected 25 representative strains within 16 V. cholerae serogrou...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5603-7
更新日期:2019-03-25 00:00:00
abstract:BACKGROUND:Quantitative trait locus (QTL) studies show that variation in salinity tolerance in Arctic charr and rainbow trout has a genetic basis, even though both these species have low to moderate salinity tolerance capacities. QTL were observed to localize to homologous linkage group segments within putative chromos...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-420
更新日期:2012-08-24 00:00:00
abstract:BACKGROUND:Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4656-3
更新日期:2018-04-16 00:00:00
abstract:BACKGROUND:Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens ar...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2376-0
更新日期:2016-01-12 00:00:00
abstract:BACKGROUND:Antimicrobial resistance is one of our most serious health threats. Antimicrobial peptides (AMPs), effecter molecules of innate immune system, can defend host organisms against microbes and most have shown a lowered likelihood for bacteria to form resistance compared to many conventional drugs. Thus, AMPs ar...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06978-0
更新日期:2020-08-28 00:00:00
abstract:BACKGROUND:Adjuvant Radiotherapy (RT) after surgical removal of tumors proved beneficial in long-term tumor control and treatment planning. For many years, it has been well concluded that radio-sensitivities of tumors upon radiotherapy decrease according to the sizes of tumors and RT models based on Poisson statistics ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S2-S9
更新日期:2008-09-16 00:00:00
abstract:BACKGROUND:Zoysia matrella, widely used in lawns and sports fields, is of great economic and ecological value. Z. matrella is an allotetraploid species (2n = 4x = 40) in the genus zoysia under the subfamily Chloridoideae. Despite its ecological impacts and economic importance, the subfamily Chloridoideae has received l...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2969-7
更新日期:2016-08-08 00:00:00
abstract:BACKGROUND:Relationships between an organism and its environment can be fundamental in the understanding how populations change over time and species arise. Local ecological conditions can shape variation at multiple levels, among these are the evolutionary history and trajectories of coding genes. This study examines ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6097-z
更新日期:2019-10-12 00:00:00