Abstract:
:By measuring messenger RNA levels for all genes in a sample, RNA-seq provides an attractive option to characterize the global changes in transcription. RNA-seq is becoming the widely used platform for gene expression profiling. However, real transcription signals in the RNA-seq data are confounded with measurement and sequencing errors and other random biological/technical variation. To extract biologically useful transcription process from the RNA-seq data, we propose to use the second ODE for modeling the RNA-seq data. We use differential principal analysis to develop statistical methods for estimation of location-varying coefficients of the ODE. We validate the accuracy of the ODE model to fit the RNA-seq data by prediction analysis and 5-fold cross validation. To further evaluate the performance of the ODE model for RNA-seq data analysis, we used the location-varying coefficients of the second ODE as features to classify the normal and tumor cells. We demonstrate that even using the ODE model for single gene we can achieve high classification accuracy. We also conduct response analysis to investigate how the transcription process responds to the perturbation of the external signals and identify dozens of genes that are related to cancer.
journal_name
Biomed Res Intjournal_title
BioMed research internationalauthors
Li L,Xiong Mdoi
10.1155/2015/916352subject
Has Abstractpub_date
2015-01-01 00:00:00pages
916352eissn
2314-6133issn
2314-6141journal_volume
2015pub_type
杂志文章abstract:OBJECTIVE:This study evaluated the frequencies of allergic symptoms and rate of upper respiratory infections during the past year in the general population, kitchen workers (KW) and health care workers (HCW). METHODS:The European Community Respiratory Health Survey (ECRHS) was used to inquire retrospectively about ast...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2013/285420
更新日期:2013-01-01 00:00:00
abstract::Fatty acids (C6-C18) found in human amniotic fluid, colostrum, and maternal milk reduce behavioral indicators of experimental anxiety in adult Wistar rats. Unknown, however, is whether the anxiolytic-like effects of fatty acids provide a natural mechanism against anxiety in young offspring. The present study assessed ...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2017/8798546
更新日期:2017-01-01 00:00:00
abstract::Diabetic foot ulcers (DFUs) are characterized by an unsatisfactory inflammatory and migratory response. Skin inflammation involves the participation of many cells and particularly macrophages. Macrophage function can be modulated by neuropeptides; however, little is known regarding the role of neurotensin (NT) as a mo...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2013/941764
更新日期:2013-01-01 00:00:00
abstract::Heat shock proteins 70 and heat shock proteins 90 (Hsp70/90) have been implicated in many crucial steps of carcinogenesis: stabilizing oncogenic proteins, inhibiting programmed cell death and replicative senescence, induction of tumor angiogenesis, and activation of the invasion and metastasis. Plenty of cancer relate...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2014/239164
更新日期:2014-01-01 00:00:00
abstract::Elevated levels of resistin and epidermal growth factor receptor (EGFR) facilitate the development of breast cancer, although there are no reports of any correlation between these proteins. This study analyzed 392 human breast cancer tissue specimens and 42 samples of adjacent normal tissue. Rates of positive and stro...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/8835398
更新日期:2020-11-28 00:00:00
abstract:Objective:To characterize and evaluate CT and MRI features of extremity soft tissue adult fibrosarcoma. Methods:CT and MRI images from 10 adult patients with pathologically proven fibrosarcomas were retrospectively analyzed with regard to tumor location, size, number, shape, margins, attenuation, signal intensity, and...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2018/6075705
更新日期:2018-03-06 00:00:00
abstract::Growing evidence indicates that immune-related biomarkers play an important role in tumor processes. This study investigates immune-related gene expression and its prognostic value in lung squamous cell carcinoma (LUSC). A cohort of 493 samples of patients with LUSC was collected and analyzed from data generated by th...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/5024942
更新日期:2020-06-27 00:00:00
abstract:Introduction:The sources of Reactive Oxidative Species (ROS) in the organism are the respiratory processes occurring in cells catalyzed by different enzymes. Operation of ROS is balanced by antioxidants, the compounds; although present in low concentrations, they significantly inhibit the degree of oxidation of particu...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2018/6038106
更新日期:2018-01-02 00:00:00
abstract::28 new pyrrolidine types of compounds as analogues for natural polyhydroxy alkaloids of codonopsinine were evaluated for their anti-MRSA activity using MIC and MBC value determination assay against a panel of S. aureus isolates. One pyrrolidine compound, MFM 501, exhibited good inhibitory activity with MIC value of 15...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/823829
更新日期:2015-01-01 00:00:00
abstract::Adverse drug reactions (ADRs) are responsible for drug candidate failure during clinical trials. It is crucial to investigate biological pathways contributing to ADRs. Here, we applied a large-scale analysis to identify overrepresented ADR-pathway combinations through merging clinical phenotypic data, biological pathw...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2015/670949
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:The aims of this study were to evaluate the complications that occur after trauma and the characteristics of individuals who develop complications, to identify potential risk factors that increase their incidence, and finally to investigate the relationship between complications and mortality. METHODS:We di...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/473419
更新日期:2014-01-01 00:00:00
abstract::More than one-third of the world's population is infected with one or more helminthic parasites. Helminth infections are prevalent throughout tropical and subtropical regions where malaria pathogens are transmitted. Malaria is the most widespread and deadliest parasitic disease. The severity of the disease is strongly...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2014/913696
更新日期:2014-01-01 00:00:00
abstract::Alterations in pancreatic milieu to adapt to physiological shifts occurring in conditions of obesity and metabolic syndrome (MS) have been documented, though mechanisms leading to such a state have remained elusive so far. The data presented here tries to look at the gravity of metabolic insult during the early and pr...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2013/617569
更新日期:2013-01-01 00:00:00
abstract::In this paper, differences between multichannel EEG signals of artists and nonartists were analyzed during visual perception and mental imagery of some paintings and at resting condition using approximate entropy (ApEn). It was found that ApEn is significantly higher for artists during the visual perception and the me...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/764382
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Although binge drinking prevalence and correlates among young people have been extensively studied in the USA and Northern Europe, less is known for Southern Europe countries with relatively healthier drinking cultures. OBJECTIVE:We aimed at analyzing prevalence and correlates of binge drinking in a represe...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/930795
更新日期:2014-01-01 00:00:00
abstract::The application of chemotherapeutic drug adriamycin (ADR) in cancer therapy is limited by its side effects like high toxicity and insolubility. Nanomedicine offers new hope for overcoming the shortcomings. But how to increase in vivo stability and to control intracellular drug release is a key issue for nano-based for...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/987404
更新日期:2015-01-01 00:00:00
abstract::In our study, we evaluated the feasibility of a new sampling method for splenic stiffness (SS) measurement by Quantitative Acoustic Radiation Force Impulse Elastography (Virtual Touch Tissue Quantification (VTTQ)).We measured SS in 54 patients with HCV-related cirrhosis of whom 28 with esophageal varices (EV), 27 with...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/365982
更新日期:2014-01-01 00:00:00
abstract:OBJECTIVE:To investigate the joint effects of the single nucleotide polymorphisms (SNPs) of genes in the folic acid pathway on homocysteine (Hcy) metabolism. METHODS:Four hundred women with normal pregnancies were enrolled in this study. SNPs were identified by MassARRAY. Serum folic acid and Hcy concentration were me...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/560183
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Varicocele is associated with high levels of DNA damage in spermatozoa due to oxidative stress and elevated levels of sperm DNA fragmentation, which has been currently proposed to be an essential additional diagnostic test to be recommended for patients with clinical varicocele. The aim of this study was to ...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/695713
更新日期:2014-01-01 00:00:00
abstract::L-amino acid oxidases are enzymes found in several organisms, including venoms of snakes, where they contribute to the toxicity of ophidian envenomation. Their toxicity is primarily due to enzymatic activity, but other mechanisms have been proposed recently which require further investigation. L-amino acid oxidases ex...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2014/196754
更新日期:2014-01-01 00:00:00
abstract::Ultrasound tomography (UST) image segmentation is fundamental in breast density estimation, medicine response analysis, and anatomical change quantification. Existing methods are time consuming and require massive manual interaction. To address these issues, an automatic algorithm based on GrabCut (AUGC) is proposed i...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2017/2059036
更新日期:2017-01-01 00:00:00
abstract::Pebisut is a biological adhesive composed of naturally occurring carbohydrates combined with zinc oxide (ZnO) initially used as a coadjutant for healing of anastomoses. Likewise some works demonstrated that carbohydrate complexes exerts anti-inflammatory activity and it is widely known that ZnO modulate inflammation. ...
journal_title:BioMed research international
pub_type: 临床试验,杂志文章
doi:10.1155/2014/712312
更新日期:2014-01-01 00:00:00
abstract:Introduction:We investigated the proportion of myeloid-derived suppressor cells (MDSCs) and their subsets in patients with rheumatic diseases and clarified the association between these cells and the patient clinical data. Methods:Patients with rheumatic diseases and healthy controls were recruited. The clinical chara...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2018/5474828
更新日期:2018-06-26 00:00:00
abstract::In clinical endodontics, preoperative estimation of root canal curvature is crucial regarding the prevention of iatrogenic errors. Reproduction of the two-dimensional radiographic images causes certain proximal view curvatures not seen. Therefore, the present study is aimed at investigating the degree of root canal cu...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2021/6699635
更新日期:2021-01-13 00:00:00
abstract::Big data bioinformatics aims at drawing biological conclusions from huge and complex biological datasets. Added value from the analysis of big data, however, is only possible if the data is accompanied by accurate metadata annotation. Particularly in high-throughput experiments intelligent approaches are needed to kee...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/958302
更新日期:2015-01-01 00:00:00
abstract::The white-rot fungus Phanerochaete chrysosporium was investigated for its capacity to degrade the herbicide diuron in liquid stationary cultures. The presence of diuron increased the production of lignin peroxidase in relation to control cultures but only barely affected the production of manganese peroxidase. The her...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2013/251354
更新日期:2013-01-01 00:00:00
abstract:OBJECTIVE:There is an unmet need for a specific cardiovascular risk (CV) algorithm for rheumatoid arthritis (RA) patients. Lipoprotein data are often not available in RA cohorts but could be obtained from frozen blood samples. The objective of this study was to estimate the storage effect on lipoproteins in long-term (...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/930925
更新日期:2014-01-01 00:00:00
abstract::The most frequently seen types of tremor are essential (ET) and parkinsonian tremor (PT) and in some patients clinical characteristics of these tremor types overlap. It is vital to distinguish between these two types of tremor in order to reach the right diagnosis and select the appropriate treatment. One of the widel...
journal_title:BioMed research international
pub_type: 临床试验,杂志文章
doi:10.1155/2014/934746
更新日期:2014-01-01 00:00:00
abstract::The chromosomal changes accompanying bivalve evolution are an area about which few reports have been published. To improve our understanding on chromosome evolution in Veneridae, ribosomal RNA gene clusters were mapped by fluorescent in situ hybridization (FISH) to chromosomes of five species of venerid clams (Venerup...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/754012
更新日期:2014-01-01 00:00:00
abstract:Background:Osteonecrosis of the femoral head (ONFH) is a challenge for surgeons and is still without effective treatment method. This study is aimed at evaluating the combined pharmacotherapy with alendronate and desferoxamine for preventing glucocorticoid-induced osteonecrosis of the femoral head (GIOFH) and evaluatin...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/3120458
更新日期:2020-09-21 00:00:00