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Publisher: Hindawi   (Total: 334 journals)

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Showing 1 - 200 of 334 Journals sorted alphabetically
Abstract and Applied Analysis     Open Access   (Followers: 3, SJR: 0.512, h-index: 32)
Active and Passive Electronic Components     Open Access   (Followers: 7, SJR: 0.157, h-index: 15)
Advances in Acoustics and Vibration     Open Access   (Followers: 24, SJR: 0.259, h-index: 6)
Advances in Agriculture     Open Access   (Followers: 7)
Advances in Artificial Intelligence     Open Access   (Followers: 15)
Advances in Artificial Neural Systems     Open Access   (Followers: 4)
Advances in Astronomy     Open Access   (Followers: 35, SJR: 0.351, h-index: 17)
Advances in Bioinformatics     Open Access   (Followers: 18, SJR: 0.421, h-index: 8)
Advances in Biology     Open Access   (Followers: 8)
Advances in Chemistry     Open Access   (Followers: 14)
Advances in Civil Engineering     Open Access   (Followers: 33, SJR: 0.338, h-index: 8)
Advances in Condensed Matter Physics     Open Access   (Followers: 8, SJR: 0.248, h-index: 10)
Advances in Decision Sciences     Open Access   (Followers: 4, SJR: 0.231, h-index: 6)
Advances in Ecology     Open Access   (Followers: 13)
Advances in Electrical Engineering     Open Access   (Followers: 18)
Advances in Endocrinology     Open Access   (Followers: 4)
Advances in Fuzzy Systems     Open Access   (Followers: 5, SJR: 0.258, h-index: 7)
Advances in Hematology     Open Access   (Followers: 9, SJR: 0.892, h-index: 18)
Advances in High Energy Physics     Open Access   (Followers: 20, SJR: 0.892, h-index: 19)
Advances in Human-Computer Interaction     Open Access   (Followers: 19, SJR: 0.439, h-index: 9)
Advances in Materials Science and Engineering     Open Access   (Followers: 32, SJR: 0.263, h-index: 11)
Advances in Mathematical Physics     Open Access   (Followers: 6, SJR: 0.332, h-index: 10)
Advances in Medicine     Open Access   (Followers: 3)
Advances in Meteorology     Open Access   (Followers: 18, SJR: 0.498, h-index: 10)
Advances in Multimedia     Open Access   (Followers: 2, SJR: 0.191, h-index: 10)
Advances in Nonlinear Optics     Open Access   (Followers: 5)
Advances in Numerical Analysis     Open Access   (Followers: 4)
Advances in Nursing     Open Access   (Followers: 21)
Advances in Operations Research     Open Access   (Followers: 11, SJR: 0.343, h-index: 7)
Advances in Optical Technologies     Open Access   (Followers: 3, SJR: 0.283, h-index: 16)
Advances in OptoElectronics     Open Access   (Followers: 5, SJR: 0.973, h-index: 16)
Advances in Orthopedic Surgery     Open Access   (Followers: 9)
Advances in Orthopedics     Open Access   (Followers: 9)
Advances in Pharmacological Sciences     Open Access   (Followers: 6, SJR: 0.695, h-index: 13)
Advances in Physical Chemistry     Open Access   (Followers: 11, SJR: 0.297, h-index: 7)
Advances in Power Electronics     Open Access   (Followers: 24, SJR: 0.26, h-index: 6)
Advances in Preventive Medicine     Open Access   (Followers: 6)
Advances in Public Health     Open Access   (Followers: 20)
Advances in Software Engineering     Open Access   (Followers: 10)
Advances in Tribology     Open Access   (Followers: 10, SJR: 0.267, h-index: 6)
Advances in Urology     Open Access   (Followers: 10, SJR: 0.629, h-index: 16)
Advances in Virology     Open Access   (Followers: 7, SJR: 1.04, h-index: 12)
AIDS Research and Treatment     Open Access   (Followers: 3, SJR: 1.125, h-index: 14)
Analytical Cellular Pathology     Open Access   (Followers: 2, SJR: 0.334, h-index: 12)
Anatomy Research Intl.     Open Access   (Followers: 2)
Anemia     Open Access   (Followers: 4, SJR: 0.991, h-index: 11)
Anesthesiology Research and Practice     Open Access   (Followers: 12, SJR: 0.513, h-index: 12)
Applied and Environmental Soil Science     Open Access   (Followers: 15, SJR: 0.53, h-index: 9)
Applied Bionics and Biomechanics     Open Access   (Followers: 8, SJR: 0.23, h-index: 13)
Applied Computational Intelligence and Soft Computing     Open Access   (Followers: 12)
Archaea     Open Access   (Followers: 3, SJR: 1.248, h-index: 27)
Arthritis     Open Access   (Followers: 4)
Autism Research and Treatment     Open Access   (Followers: 29)
Autoimmune Diseases     Open Access   (Followers: 3, SJR: 0.909, h-index: 17)
Behavioural Neurology     Open Access   (Followers: 7, SJR: 0.696, h-index: 34)
Biochemistry Research Intl.     Open Access   (Followers: 6, SJR: 1.085, h-index: 17)
Bioinorganic Chemistry and Applications     Open Access   (Followers: 9, SJR: 0.286, h-index: 19)
BioMed Research Intl.     Open Access   (Followers: 6, SJR: 0.725, h-index: 59)
Biotechnology Research Intl.     Open Access   (Followers: 2)
Bone Marrow Research     Open Access   (Followers: 2)
Canadian J. of Gastroenterology & Hepatology     Open Access   (Followers: 3, SJR: 0.856, h-index: 53)
Canadian J. of Infectious Diseases and Medical Microbiology     Open Access   (Followers: 4, SJR: 0.409, h-index: 25)
Canadian Respiratory J.     Open Access   (Followers: 1, SJR: 0.503, h-index: 42)
Cardiology Research and Practice     Open Access   (Followers: 7, SJR: 0.941, h-index: 17)
Cardiovascular Psychiatry and Neurology     Open Access   (Followers: 4, SJR: 1.091, h-index: 14)
Case Reports in Anesthesiology     Open Access   (Followers: 10)
Case Reports in Cardiology     Open Access   (Followers: 2)
Case Reports in Critical Care     Open Access   (Followers: 8)
Case Reports in Dentistry     Open Access   (Followers: 3)
Case Reports in Dermatological Medicine     Open Access   (Followers: 2)
Case Reports in Emergency Medicine     Open Access   (Followers: 12)
Case Reports in Endocrinology     Open Access   (SJR: 0.326, h-index: 1)
Case Reports in Gastrointestinal Medicine     Open Access   (Followers: 3)
Case Reports in Genetics     Open Access   (Followers: 1)
Case Reports in Hematology     Open Access   (Followers: 2)
Case Reports in Hepatology     Open Access   (Followers: 1)
Case Reports in Immunology     Open Access   (Followers: 4)
Case Reports in Infectious Diseases     Open Access   (Followers: 5)
Case Reports in Medicine     Open Access   (Followers: 3)
Case Reports in Nephrology     Open Access   (Followers: 4)
Case Reports in Neurological Medicine     Open Access   (Followers: 1)
Case Reports in Obstetrics and Gynecology     Open Access   (Followers: 10)
Case Reports in Oncological Medicine     Open Access   (Followers: 2)
Case Reports in Ophthalmological Medicine     Open Access   (Followers: 2)
Case Reports in Orthopedics     Open Access   (Followers: 7)
Case Reports in Otolaryngology     Open Access   (Followers: 4)
Case Reports in Pathology     Open Access   (Followers: 3)
Case Reports in Pediatrics     Open Access   (Followers: 5)
Case Reports in Psychiatry     Open Access   (Followers: 10)
Case Reports in Pulmonology     Open Access   (Followers: 2)
Case Reports in Radiology     Open Access   (Followers: 8)
Case Reports in Rheumatology     Open Access   (Followers: 4)
Case Reports in Surgery     Open Access   (Followers: 7)
Case Reports in Transplantation     Open Access  
Case Reports in Urology     Open Access   (Followers: 8)
Case Reports in Vascular Medicine     Open Access  
Case Reports in Veterinary Medicine     Open Access   (Followers: 5)
Chemotherapy Research and Practice     Open Access   (Followers: 1)
Child Development Research     Open Access   (Followers: 14)
Chinese J. of Engineering     Open Access   (Followers: 2)
Chinese J. of Mathematics     Open Access  
Cholesterol     Open Access   (Followers: 1, SJR: 0.906, h-index: 12)
Chromatography Research Intl.     Open Access   (Followers: 7)
Complexity     Hybrid Journal   (Followers: 6, SJR: 0.526, h-index: 27)
Computational and Mathematical Methods in Medicine     Open Access   (Followers: 2, SJR: 0.415, h-index: 22)
Computational Intelligence and Neuroscience     Open Access   (Followers: 9, SJR: 0.232, h-index: 30)
Critical Care Research and Practice     Open Access   (Followers: 9, SJR: 0.916, h-index: 14)
Current Gerontology and Geriatrics Research     Open Access   (Followers: 9, SJR: 0.8, h-index: 12)
Dataset Papers in Science     Open Access  
Depression Research and Treatment     Open Access   (Followers: 13, SJR: 0.77, h-index: 11)
Dermatology Research and Practice     Open Access   (Followers: 2, SJR: 0.576, h-index: 15)
Diagnostic and Therapeutic Endoscopy     Open Access   (SJR: 0.651, h-index: 18)
Discrete Dynamics in Nature and Society     Open Access   (Followers: 5, SJR: 0.323, h-index: 24)
Disease Markers     Open Access   (Followers: 1, SJR: 0.774, h-index: 49)
Economics Research Intl.     Open Access   (Followers: 2)
Education Research Intl.     Open Access   (Followers: 18)
Emergency Medicine Intl.     Open Access   (Followers: 6)
Enzyme Research     Open Access   (Followers: 4, SJR: 0.457, h-index: 18)
Epidemiology Research Intl.     Open Access   (Followers: 11)
Epilepsy Research and Treatment     Open Access   (Followers: 3)
Evidence-based Complementary and Alternative Medicine     Open Access   (Followers: 18, SJR: 0.615, h-index: 50)
Experimental Diabetes Research     Open Access   (Followers: 11, SJR: 1.591, h-index: 30)
Gastroenterology Research and Practice     Open Access   (Followers: 3, SJR: 0.664, h-index: 21)
Genetics Research Intl.     Open Access   (Followers: 1)
Hepatitis Research and Treatment     Open Access   (Followers: 6)
HPB Surgery     Open Access   (Followers: 5, SJR: 0.798, h-index: 22)
Indian J. of Materials Science     Open Access  
Infectious Diseases in Obstetrics and Gynecology     Open Access   (Followers: 7, SJR: 0.976, h-index: 34)
Influenza Research and Treatment     Open Access   (Followers: 2)
Interdisciplinary Perspectives on Infectious Diseases     Open Access   (Followers: 2, SJR: 0.763, h-index: 15)
Intl. J. of Aerospace Engineering     Open Access   (Followers: 65, SJR: 0.241, h-index: 6)
Intl. J. of Agronomy     Open Access   (Followers: 8, SJR: 0.223, h-index: 2)
Intl. J. of Alzheimer's Disease     Open Access   (Followers: 11, SJR: 1.193, h-index: 25)
Intl. J. of Analysis     Open Access  
Intl. J. of Analytical Chemistry     Open Access   (Followers: 21, SJR: 0.157, h-index: 2)
Intl. J. of Antennas and Propagation     Open Access   (Followers: 11, SJR: 0.385, h-index: 15)
Intl. J. of Atmospheric Sciences     Open Access   (Followers: 23)
Intl. J. of Bacteriology     Open Access  
Intl. J. of Biodiversity     Open Access   (Followers: 4)
Intl. J. of Biomaterials     Open Access   (Followers: 5, SJR: 0.485, h-index: 10)
Intl. J. of Biomedical Imaging     Open Access   (Followers: 5, SJR: 0.581, h-index: 23)
Intl. J. of Breast Cancer     Open Access   (Followers: 12)
Intl. J. of Carbohydrate Chemistry     Open Access   (Followers: 7)
Intl. J. of Cell Biology     Open Access   (Followers: 4, SJR: 2.658, h-index: 25)
Intl. J. of Chemical Engineering     Open Access   (Followers: 7, SJR: 0.361, h-index: 10)
Intl. J. of Chronic Diseases     Open Access   (Followers: 1)
Intl. J. of Combinatorics     Open Access   (Followers: 1)
Intl. J. of Computer Games Technology     Open Access   (Followers: 11, SJR: 0.213, h-index: 12)
Intl. J. of Corrosion     Open Access   (Followers: 10, SJR: 0.19, h-index: 7)
Intl. J. of Dentistry     Open Access   (Followers: 6, SJR: 0.558, h-index: 11)
Intl. J. of Differential Equations     Open Access   (Followers: 6, SJR: 0.363, h-index: 11)
Intl. J. of Digital Multimedia Broadcasting     Open Access   (Followers: 5, SJR: 0.144, h-index: 10)
Intl. J. of Ecology     Open Access   (Followers: 6, SJR: 0.8, h-index: 11)
Intl. J. of Electrochemistry     Open Access   (Followers: 6)
Intl. J. of Endocrinology     Open Access   (Followers: 3, SJR: 0.961, h-index: 24)
Intl. J. of Engineering Mathematics     Open Access   (Followers: 3)
Intl. J. of Evolutionary Biology     Open Access   (Followers: 9)
Intl. J. of Family Medicine     Open Access   (Followers: 2)
Intl. J. of Food Science     Open Access   (Followers: 3)
Intl. J. of Forestry Research     Open Access   (Followers: 4)
Intl. J. of Genomics     Open Access   (Followers: 2, SJR: 0.721, h-index: 7)
Intl. J. of Geophysics     Open Access   (Followers: 5, SJR: 0.416, h-index: 8)
Intl. J. of Hepatology     Open Access   (Followers: 3)
Intl. J. of Hypertension     Open Access   (Followers: 5, SJR: 0.823, h-index: 20)
Intl. J. of Inflammation     Open Access   (SJR: 0.876, h-index: 14)
Intl. J. of Inorganic Chemistry     Open Access   (Followers: 2)
Intl. J. of Manufacturing Engineering     Open Access   (Followers: 2)
Intl. J. of Mathematics and Mathematical Sciences     Open Access   (Followers: 3, SJR: 0.346, h-index: 27)
Intl. J. of Medicinal Chemistry     Open Access   (Followers: 6)
Intl. J. of Metals     Open Access   (Followers: 4)
Intl. J. of Microbiology     Open Access   (Followers: 5, SJR: 1.006, h-index: 18)
Intl. J. of Microwave Science and Technology     Open Access   (Followers: 3, SJR: 0.167, h-index: 5)
Intl. J. of Molecular Imaging     Open Access  
Intl. J. of Navigation and Observation     Open Access   (Followers: 19, SJR: 0.411, h-index: 7)
Intl. J. of Nephrology     Open Access   (Followers: 2, SJR: 0.926, h-index: 14)
Intl. J. of Oceanography     Open Access   (Followers: 8)
Intl. J. of Optics     Open Access   (Followers: 7, SJR: 0.262, h-index: 7)
Intl. J. of Otolaryngology     Open Access  
Intl. J. of Pediatrics     Open Access   (Followers: 4)
Intl. J. of Peptides     Open Access   (Followers: 4, SJR: 0.73, h-index: 16)
Intl. J. of Photoenergy     Open Access   (Followers: 2, SJR: 0.348, h-index: 28)
Intl. J. of Plant Genomics     Open Access   (Followers: 4, SJR: 1.578, h-index: 20)
Intl. J. of Polymer Science     Open Access   (Followers: 23, SJR: 0.265, h-index: 11)
Intl. J. of Population Research     Open Access   (Followers: 2)
Intl. J. of Proteomics     Open Access   (Followers: 1)
Intl. J. of Quality, Statistics, and Reliability     Open Access   (Followers: 13, SJR: 0.345, h-index: 4)
Intl. J. of Reconfigurable Computing     Open Access   (SJR: 0.182, h-index: 8)
Intl. J. of Reproductive Medicine     Open Access   (Followers: 5)
Intl. J. of Rheumatology     Open Access   (Followers: 4, SJR: 1.015, h-index: 18)
Intl. J. of Rotating Machinery     Open Access   (Followers: 2, SJR: 0.402, h-index: 19)
Intl. J. of Spectroscopy     Open Access   (Followers: 8)
Intl. J. of Stochastic Analysis     Open Access   (Followers: 4, SJR: 0.234, h-index: 19)
Intl. J. of Surgical Oncology     Open Access   (Followers: 1, SJR: 0.753, h-index: 11)
Intl. J. of Telemedicine and Applications     Open Access   (Followers: 3, SJR: 0.757, h-index: 14)
Intl. J. of Vascular Medicine     Open Access   (SJR: 0.865, h-index: 16)
Intl. J. of Vehicular Technology     Open Access   (Followers: 4, SJR: 0.169, h-index: 6)
Intl. J. of Zoology     Open Access   (Followers: 1, SJR: 0.389, h-index: 8)
Intl. Scholarly Research Notices     Open Access   (Followers: 198)
ISRN Astronomy and Astrophysics     Open Access   (Followers: 7)
J. of Addiction     Open Access   (Followers: 10)

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Journal Cover International Journal of Genomics
  [SJR: 0.721]   [H-I: 7]   [2 followers]  Follow
    
  This is an Open Access Journal Open Access journal
   ISSN (Print) 2314-436X - ISSN (Online) 2314-4378
   Published by Hindawi Homepage  [334 journals]
  • Differential Analysis of Genetic, Epigenetic, and Cytogenetic
           Abnormalities in AML

    • Abstract: Acute myeloid leukemia (AML) is a haematological malignancy characterized by the excessive proliferation of immature myeloid cells coupled with impaired differentiation. Many AML cases have been reported without any known cytogenetic abnormalities and carry no mutation in known AML-associated driver genes. In this study, 200 AML cases were selected from a publicly available cohort and differentially analyzed for genetic, epigenetic, and cytogenetic abnormalities. Three genes (FLT3, DNMT3A, and NPMc) are found to be predominantly mutated. We identified several aberrations to be associated with genome-wide methylation changes. These include Del (5q), T (15; 17), and NPMc mutations. Four aberrations—Del (5q), T (15; 17), T (9; 22), and T (9; 11)—are significantly associated with patient survival. Del (5q)-positive patients have an average survival of less than 1 year, whereas T (15; 17)-positive patients have a significantly better prognosis. Combining the methylation and mutation data reveals three distinct patient groups and four clusters of genes. We speculate that combined signatures have the better potential to be used for subclassification of AML, complementing cytogenetic signatures. A larger sample cohort and further investigation of the effects observed in this study are required to enable the clinical application of our patient classification aided by DNA methylation.
      PubDate: Tue, 20 Jun 2017 00:00:00 +000
       
  • Recent Advances in High Throughput Sequencing Analysis

    • PubDate: Mon, 19 Jun 2017 07:42:32 +000
       
  • Antioxidant System Response and cDNA-SCoT Marker Profiling in Phoenix
           dactylifera L. Plant under Salinity Stress

    • Abstract: Many Phoenix dactylifera (date palm) cultivars are grown in the arid and semiarid regions of the world, including Saudi Arabia. P. dactylifera is highly tolerant to salinity stress. To investigate the response of Khalas cultivar of P. dactylifera, two-month-old plants were treated with sodium chloride (50, 100, and 150 mM NaCl) for three months. Our result showed that proline content was higher in all treated plants compared to control plants. Thiobarbituric acid reactive substances (TBARS) were increased at 100 and 150 mM NaCl treatments; however, the result was found nonsignificant between control and plants treated at 50 mM NaCl. Similarly, enzyme activities of catalase (CAT) and superoxide dismutase (SOD) were 0.805 and 0.722 U/mg protein/min, respectively, and were greater at 100 and 150 mM NaCl treatments compared to the control plants. Total chlorophyll content and fresh weight of shoots and roots decreased substantially with the increase of salinity. A cDNA start codon-targeted (cDNA-SCoT) marker showed a variation in different gene expressions profiling between treated and untreated plants under various NaCl concentrations.
      PubDate: Sun, 18 Jun 2017 00:00:00 +000
       
  • Coexpression Analysis of Transcriptome on AIDS and Other Human Disease
           Pathways by Canonical Correlation Analysis

    • Abstract: Acquired immune deficiency syndrome is a severe disease in humans caused by human immunodeficiency virus. Several human genes were characterized as host genetic factors that impact the processes of AIDS disease. Recent studies on AIDS patients revealed a series disease is complicating with AIDS. To resolve gene interaction between AIDS and complicating diseases, a canonical correlation analysis was used to identify the global correlation between AIDS and other disease pathway genes expression. The results showed that HLA-B, HLA-A, MH9, ZNED1, IRF1, TLR8, TSG101, NCOR2, and GML are the key AIDS-restricted genes highly correlated with other disease pathway genes. Furthermore, pathway genes in several diseases such as asthma, autoimmune thyroid disease, and malaria were globally correlated with ARGs. It suggests that these diseases are a high risk in AIDS patients as complicating diseases.
      PubDate: Wed, 14 Jun 2017 00:00:00 +000
       
  • Discovery of MicroRNAs and Their Target Genes Related to Drought in
           Paulownia “Yuza 1” by High-Throughput Sequencing

    • Abstract: Understanding the role of miRNAs in regulating the molecular mechanisms responsive to drought stress was studied in Paulownia “yuza 1.” Two small RNA libraries and two degradome libraries were, respectively, constructed and sequenced in order to detect miRNAs and their target genes associated with drought stress. A total of 107 miRNAs and 42 putative target genes were identified in this study. Among them, 77 miRNAs were differentially expressed between drought-treated Paulownia “yuza 1” and the control (60 downregulated and 17 upregulated). The predicted target genes were annotated using the GO, KEGG, and Nr databases. According to the functional classification of the target genes, Paulownia “yuza 1” may respond to drought stress via plant hormone signal transduction, photosynthesis, and osmotic adjustment. Furthermore, the expression levels of seven miRNAs (ptf-miR157b, ptf-miR159b, ptf-miR398a, ptf-miR9726a, ptf-M2153, ptf-M2218, and ptf-M24a) and their corresponding target genes were validated by quantitative real-time PCR. The results provide relevant information for understanding the molecular mechanism of Paulownia resistance to drought and reference data for researching drought resistance of other trees.
      PubDate: Sun, 11 Jun 2017 06:32:18 +000
       
  • An Exploration of Gene-Gene Interactions and Their Effects on Hypertension

    • Abstract: Hypertension tends to perpetuate in families and the heritability of hypertension is estimated to be around 20–60%. So far, the main proportion of this heritability has not been found by single-locus genome-wide association studies. Therefore, the current study explored gene-gene interactions that have the potential to partially fill in the missing heritability. A two-stage discovery-confirmatory analysis was carried out in the Framingham Heart Study cohorts. The first stage was an exhaustive pairwise search performed in 2320 early-onset hypertensive cases with matched normotensive controls from the offspring cohort. Then, identified gene-gene interactions were assessed in an independent set of 694 subjects from the original cohort. Four unique gene-gene interactions were found to be related to hypertension. Three detected genes were recognized by previous studies, and the other 5 loci/genes (MAN1A1, LMO3, NPAP1/SNRPN, DNAL4, and RNA5SP455/KRT8P5) were novel findings, which had no strong main effect on hypertension and could not be easily identified by single-locus genome-wide studies. Also, by including the identified gene-gene interactions, more variance was explained in hypertension. Overall, our study provides evidence that the genome-wide gene-gene interaction analysis has the possibility to identify new susceptibility genes, which can provide more insights into the genetic background of blood pressure regulation.
      PubDate: Wed, 31 May 2017 00:00:00 +000
       
  • Chimeric Genes in Deletions and Duplications Associated with Intellectual
           Disability

    • Abstract: We report on three nonrelated patients with intellectual disability and CNVs that give rise to three new chimeric genes. All the genes forming these fusion transcripts may have an important role in central nervous system development and/or in gene expression regulation, and therefore not only their deletion or duplication but also the resulting chimeric gene may contribute to the phenotype of the patients. Deletions and duplications are usually pathogenic when affecting dose-sensitive genes. Alternatively, a chimeric gene may also be pathogenic by different gain-of-function mechanisms that are not restricted to dose-sensitive genes: the emergence of a new polypeptide that combines functional domains from two different genes, the deregulated expression of any coding sequence by the promoter region of a neighboring gene, and/or a putative dominant-negative effect due to the preservation of functional domains of partially truncated proteins. Fusion oncogenes are well known, but in other pathologies, the search for chimeric genes is disregarded. According to our findings, we hypothesize that the frequency of fusion transcripts may be much higher than suspected, and it should be taken into account in the array-CGH analyses of patients with intellectual disability.
      PubDate: Wed, 24 May 2017 08:53:26 +000
       
  • Evidence of Divergent Amino Acid Usage in Comparative Analyses of R5- and
           X4-Associated HIV-1 Vpr Sequences

    • Abstract: Vpr is an HIV-1 accessory protein that plays numerous roles during viral replication, and some of which are cell type dependent. To test the hypothesis that HIV-1 tropism extends beyond the envelope into the vpr gene, studies were performed to identify the associations between coreceptor usage and Vpr variation in HIV-1-infected patients. Colinear HIV-1 Env-V3 and Vpr amino acid sequences were obtained from the LANL HIV-1 sequence database and from well-suppressed patients in the Drexel/Temple Medicine CNS AIDS Research and Eradication Study (CARES) Cohort. Genotypic classification of Env-V3 sequences as X4 (CXCR4-utilizing) or R5 (CCR5-utilizing) was used to group colinear Vpr sequences. To reveal the sequences associated with a specific coreceptor usage genotype, Vpr amino acid sequences were assessed for amino acid diversity and Jensen-Shannon divergence between the two groups. Five amino acid alphabets were used to comprehensively examine the impact of amino acid substitutions involving side chains with similar physiochemical properties. Positions 36, 37, 41, 89, and 96 of Vpr were characterized by statistically significant divergence across multiple alphabets when X4 and R5 sequence groups were compared. In addition, consensus amino acid switches were found at positions 37 and 41 in comparisons of the R5 and X4 sequence populations. These results suggest an evolutionary link between Vpr and gp120 in HIV-1-infected patients.
      PubDate: Tue, 23 May 2017 00:00:00 +000
       
  • Neurodevelopmental Disorders and Environmental Toxicants: Epigenetics as
           an Underlying Mechanism

    • Abstract: The increasing prevalence of neurodevelopmental disorders, especially autism spectrum disorders (ASD) and attention deficit hyperactivity disorder (ADHD), calls for more research into the identification of etiologic and risk factors. The Developmental Origin of Health and Disease (DOHaD) hypothesizes that the environment during fetal and childhood development affects the risk for many chronic diseases in later stages of life, including neurodevelopmental disorders. Epigenetics, a term describing mechanisms that cause changes in the chromosome state without affecting DNA sequences, is suggested to be the underlying mechanism, according to the DOHaD hypothesis. Moreover, many neurodevelopmental disorders are also related to epigenetic abnormalities. Experimental and epidemiological studies suggest that exposure to prenatal environmental toxicants is associated with neurodevelopmental disorders. In addition, there is also evidence that environmental toxicants can result in epigenetic alterations, notably DNA methylation. In this review, we first focus on the relationship between neurodevelopmental disorders and environmental toxicants, in particular maternal smoking, plastic-derived chemicals (bisphenol A and phthalates), persistent organic pollutants, and heavy metals. We then review studies showing the epigenetic effects of those environmental factors in humans that may affect normal neurodevelopment.
      PubDate: Mon, 08 May 2017 10:10:35 +000
       
  • Evolution of the Apicomplexan Sugar Transporter Gene Family Repertoire

    • Abstract: Apicomplexan protist parasites utilize host sugars transported into the parasite by sugar transporter proteins for use as an energy source. We performed a phylum-wide phylogenetic analysis of the apicomplexan sugar transporter repertoire. Phylogenetic analyses revealed six major subfamilies of apicomplexan sugar transporters. Transporters in one subfamily have undergone expansions in Piroplasma species and Gregarina niphandrodes, while other subfamilies are highly divergent and contain genes found in only one or two species. Analyses of the divergent apicomplexan subfamilies revealed their presence in ciliates, indicating their alveolate ancestry and subsequent loss in chromerids and many apicomplexans.
      PubDate: Sun, 07 May 2017 00:00:00 +000
       
  • Comparative Transcriptome Analyses of Resistant and Susceptible
           Near-Isogenic Wheat Lines following Inoculation with Blumeria graminis f.
           sp. tritici

    • Abstract: Powdery mildew is one of the most important diseases of wheat. In this study, the leaf RNA samples of wheat NILs carrying powdery mildew resistant and susceptible Pm2 alleles (L031 and Chancellor) and its F1 hybrid at two time points (16 h and 96 h postinoculation) were used for RNA-seq analysis. We carry comparison between similar materials at different times and between different materials at same times. The overlapping DEGs between the dominant phenotypes (L031 and F1 hybrid) and the recessive phenotype (Chancellor) were 1028 and 2214 DEGs, which were clearly lower than those between the dominant and recessive parents and thus could provide relatively accurate and valuable information. GO and KEGG enrichment analysis of DEGs revealed that other than the expected defense-related genes, differential up- and downregulation of genes from many other signaling networks were also involved. Comparative transcriptome analysis also revealed that early-stage postinoculation is important and suitable time points to study expression profiles and signaling pathways of resistance-related genes following fungal inoculation. qRT-PCR analyses showed highly consistent expression patterns of genes with RNA-seq data. The results will aid in the identification of genes and signaling pathways involved in powdery mildew response in wheat.
      PubDate: Tue, 02 May 2017 00:00:00 +000
       
  • Genome-Wide Identification of bZIP Family Genes Involved in Drought and
           Heat Stresses in Strawberry (Fragaria vesca)

    • Abstract: Basic leucine zipper (bZIP) genes are known to play a crucial role in response to various processes in plant as well as abiotic or biotic stress challenges. We have performed an identification and characterization of 50 bZIP genes across the woodland strawberry (Fragaria vesca) genome, which were divided into 10 clades according to the phylogenetic relationship of the strawberry bZIP proteins with those in Arabidopsis and rice. Five categories of intron patterns were observed within basic and hinge regions of the bZIP domains. Some additional conserved motifs have been found with the group specificity. Further, we predicted DNA-binding specificity of the basic and hinge regions as well as dimerization properties of leucine zipper regions, which was consistent with our phylogenetic clade and classified into 20 subfamilies. Across the different developmental stages of 15 organs and two types of fruits, the clade A bZIP members showed different tissue-specific expression patterns and the duplicated genes were differentially regulated, indicating a functional diversification coupled with the expansion of this gene family in strawberry. Under normal growth conditions, mrna11837 and mrna30280 of clade A showed very weak expression levels in organs and fruits, respectively; but higher expression was observed with different set of genes following drought and heat treatment, which may be caused by the separate response pathway between drought and heat treatments.
      PubDate: Tue, 11 Apr 2017 00:00:00 +000
       
  • Naturally Occurring Canine Invasive Urinary Bladder Cancer: A
           Complementary Animal Model to Improve the Success Rate in Human Clinical
           Trials of New Cancer Drugs

    • Abstract: Genomic analyses are defining numerous new targets for cancer therapy. Therapies aimed at specific genetic and epigenetic targets in cancer cells as well as expanded development of immunotherapies are placing increased demands on animal models. Traditional experimental models do not possess the collective features (cancer heterogeneity, molecular complexity, invasion, metastasis, and immune cell response) critical to predict success or failure of emerging therapies in humans. There is growing evidence, however, that dogs with specific forms of naturally occurring cancer can serve as highly relevant animal models to complement traditional models. Invasive urinary bladder cancer (invasive urothelial carcinoma (InvUC)) in dogs, for example, closely mimics the cancer in humans in pathology, molecular features, biological behavior including sites and frequency of distant metastasis, and response to chemotherapy. Genomic analyses are defining further intriguing similarities between InvUC in dogs and that in humans. Multiple canine clinical trials have been completed, and others are in progress with the aim of translating important findings into humans to increase the success rate of human trials, as well as helping pet dogs. Examples of successful targeted therapy studies and the challenges to be met to fully utilize naturally occurring dog models of cancer will be reviewed.
      PubDate: Sun, 09 Apr 2017 00:00:00 +000
       
  • Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain

    • Abstract: The Chinese Kunming (KM) mouse is a widely used outbred mouse stock in China. However, its genetic structure remains unclear. In this study, we sequenced the genome of the C57BL/6J-Chr1KM (B6-Chr1KM) strain, the chromosome 1 (Chr 1) of which was derived from one KM mouse. With 36.6× average coverage of the entire genome, 0.48 million single nucleotide polymorphisms (SNPs) and 96,679 indels were detected on Chr 1 through comparison with reference strain C57BL/6J. Moreover, 46,590 of them were classified as novel mutations. Further functional annotation identified 155 genes harboring potentially functional variants, among which 27 genes have been associated with human diseases. We then performed sequence similarity and Bayesian concordance analysis using the SNPs identified on Chr 1 and their counterparts in three subspecies, Mus musculus domesticus, M. m. musculus, and M. m. castaneus. Both analyses suggested that the Chr 1 sequence of B6-Chr1KM was predominantly derived from M. m. domesticus while 9.7% of the sequence was found to be from M. m. musculus. In conclusion, our analysis provided a detailed description of the genetic variations on Chr 1 of B6-Chr1KM and a new perspective on the subspecies origin of KM mouse which can be used to guide further genetic studies with this mouse strain.
      PubDate: Sun, 09 Apr 2017 00:00:00 +000
       
  • An Integrating Approach for Genome-Wide Screening of MicroRNA
           Polymorphisms Mediated Drug Response Alterations

    • Abstract: MicroRNAs (miRNAs) are a class of evolutionarily conserved small noncoding RNAs, ~22 nt in length, and found in diverse organisms and play important roles in the regulation of mRNA translation and degradation. It was shown that miRNAs were involved in many key biological processes through regulating the expression of targets. Genetic polymorphisms in miRNA target sites may alter miRNA regulation and therefore result in the alterations of the drug targets. Recent studies have demonstrated that SNPs in miRNA target sites can affect drug efficiency. However, there are still a large number of specific genetic variants related to drug efficiency that are yet to be discovered. We integrated large scale of genetic variations, drug targets, gene interaction networks, biological pathways, and seeds region of miRNA to identify miRNA polymorphisms affecting drug response. In addition, harnessing the abundant high quality biological network/pathways, we evaluated the cascade distribution of tarSNP impacts. We showed that the predictions can uncover most of the known experimentally supported cases as well as provide informative candidates complementary to existing methods/tools. Although there are several existing databases predicting the gain or loss of targeting function of miRNA mediated by SNPs, such as PolymiRTS, miRNASNP, MicroSNiPer, and MirSNP, none of them evaluated the influences of tarSNPs on drug response alterations. We developed a user-friendly online database of this approach named Mir2Drug.
      PubDate: Wed, 05 Apr 2017 08:07:32 +000
       
  • Transcriptome Analysis of Orange Head Chinese Cabbage (Brassica rapa L.
           ssp. pekinensis) and Molecular Marker Development

    • Abstract: Due to the visual appearance and high carotenoid content, orange inner leaves are a desirable trait for the Chinese cabbage. To understand the molecular mechanism underlying the formation of orange inner leaves, the BrCRTISO (Bra031539) gene, as the Br-or candidate gene, was analyzed among the white and orange varieties, and 7 single nucleotide polymorphisms (SNPs) were identified. However, only one SNP (C952 to T952) altered the amino acid sequence, resulting in a mutation from Leu318 to Phe318 in the orange varieties. Additionally, we analyzed differentially expressed genes (DEGs) between the orange and white F2 individuals (14-401 × 14-490) and found four downregulated genes were involved in the carotenoid biosynthesis pathway, which may lead to the accumulation of prolycopene and other carotenoid pigments in the orange inner leaves. In addition, we developed a novel InDel marker in the first intron, which cosegregates with the phenotypes of orange color inner leaves. In conclusion, these findings enhance our understanding of the underlying mechanism of pigment accumulation in the inner leaves of the Chinese cabbage. Additionally, the SNP (C952 to T952) and the InDel marker will facilitate the marker-assisted selection during Chinese cabbage breeding.
      PubDate: Sun, 02 Apr 2017 00:00:00 +000
       
  • The Promise of Genomic Studies on Human Diseases: From Basic Science to
           Clinical Application

    • PubDate: Wed, 29 Mar 2017 00:00:00 +000
       
  • Application of Genomic In Situ Hybridization in Horticultural Science

    • Abstract: Molecular cytogenetic techniques, such as in situ hybridization methods, are admirable tools to analyze the genomic structure and function, chromosome constituents, recombination patterns, alien gene introgression, genome evolution, aneuploidy, and polyploidy and also genome constitution visualization and chromosome discrimination from different genomes in allopolyploids of various horticultural crops. Using GISH advancement as multicolor detection is a significant approach to analyze the small and numerous chromosomes in fruit species, for example, Diospyros hybrids. This analytical technique has proved to be the most exact and effective way for hybrid status confirmation and helps remarkably to distinguish donor parental genomes in hybrids such as Clivia, Rhododendron, and Lycoris ornamental hybrids. The genome characterization facilitates in hybrid selection having potential desirable characteristics during the early hybridization breeding, as this technique expedites to detect introgressed sequence chromosomes. This review study epitomizes applications and advancements of genomic in situ hybridization (GISH) techniques in horticultural plants.
      PubDate: Tue, 28 Mar 2017 10:30:14 +000
       
  • Temporal Changes in Gene Expression Profile during Mature Adipocyte
           Dedifferentiation

    • Abstract: Objective. To characterize changes in gene expression profile during human mature adipocyte dedifferentiation in ceiling culture. Methods. Subcutaneous (SC) and omental (OM) adipose tissue samples were obtained from 4 participants paired for age and BMI. Isolated adipocytes were dedifferentiated in ceiling culture. Gene expression analysis at days 0, 4, 7, and 12 of the cultures was performed using Affymetrix Human Gene 2.0 STvi arrays. Hierarchical clustering according to similarity of expression changes was used to identify overrepresented functions. Results. Four clusters gathered genes with similar expression between day 4 to day 7 but decreasing expression from day 7 to day 12. Most of these genes coded for proteins involved in adipocyte functions (LIPE, PLIN1, DGAT2, PNPLA2, ADIPOQ, CEBPA, LPL, FABP4, SCD, INSR, and LEP). Expression of several genes coding for proteins implicated in cellular proliferation and growth or cell cycle increased significantly from day 7 to day 12 (WNT5A, KITLG, and FGF5). Genes coding for extracellular matrix proteins were differentially expressed between days 0, 4, 7, and 12 (COL1A1, COL1A2, and COL6A3, MMP1, and TGFB1). Conclusion. Dedifferentiation is associated with downregulation of transcripts encoding proteins involved in mature adipocyte functions and upregulation of genes involved in matrix remodeling, cellular development, and cell cycle.
      PubDate: Sun, 19 Mar 2017 00:00:00 +000
       
  • The Promise of Agriculture Genomics

    • PubDate: Sun, 05 Mar 2017 00:00:00 +000
       
  • Racial Differences in Expression Levels of miRNA Machinery-Related Genes,
           Dicer, Drosha, DGCR8, and AGO2, in Asian Korean Papillary Thyroid
           Carcinoma and Comparative Validation Using the Cancer Genome Atlas

    • Abstract: Aberrant regulation of microRNA (miRNA) machinery components is associated with various human cancers, including papillary thyroid carcinoma (PTC), which is the most common type of thyroid cancer, and a higher prevalent female malignancy. The purpose of this study is to investigate racial differences in mRNA expression levels of four miRNA machinery components, Dicer, Drosha, DGCR8, and AGO2, and their correlations with clinicopathological characteristics. Forty PTC samples from female Asian Korean PTC patients were enrolled. Using qPCR, we examined mRNA expression levels of the components and next validated our results by comparison with results of female white American in the TCGA PTC project. Interestingly, mRNA expression levels of the selected factors were altered in the TCGA PTC samples. However, only Drosha showed a significantly lower expression level in Asian Korean PTC samples. Furthermore, the mRNA expression levels of the four components showed no association with clinicopathological characteristics in both groups. On the other hand, positive correlations were observed between altered mRNA expression levels of Dicer and Drosha and DGCR8 and Drosha in TCGA PTC samples. These findings collectively revealed that altered mRNA expression levels of miRNA machinery components might be responsible for racial differences in the carcinogenesis of PTC.
      PubDate: Thu, 02 Mar 2017 08:26:25 +000
       
  • A Review of Recent Advancement in Integrating Omics Data with Literature
           Mining towards Biomedical Discoveries

    • Abstract: In the past decade, the volume of “omics” data generated by the different high-throughput technologies has expanded exponentially. The managing, storing, and analyzing of this big data have been a great challenge for the researchers, especially when moving towards the goal of generating testable data-driven hypotheses, which has been the promise of the high-throughput experimental techniques. Different bioinformatics approaches have been developed to streamline the downstream analyzes by providing independent information to interpret and provide biological inference. Text mining (also known as literature mining) is one of the commonly used approaches for automated generation of biological knowledge from the huge number of published articles. In this review paper, we discuss the recent advancement in approaches that integrate results from omics data and information generated from text mining approaches to uncover novel biomedical information.
      PubDate: Sun, 26 Feb 2017 07:10:14 +000
       
  • Case Study of Somaclonal Variation in Resistance Genes Mlo and Pme3 in
           Flaxseed (Linum usitatissimum L.) Induced by Nanoparticles

    • Abstract: Nanoparticles influence on genome is investigated worldwide. The appearance of somaclonal variation is a cause of great concern for any micropropagation system. Somaclonal variation describes the tissue-culture-induced phenotypic and genotypic variations. This paper shows the results of somaclonal variation in two resistance genes pectin methylesterase and Mlo-like protein in all tissue culture development stages, as donor plant, calluses, and regenerants of Linum usitatissimum induced by gold and silver nanoparticles. In this paper, it was essential to obtain DNA material from all tissue culture development stages from one donor plant to record changes in each nucleotide sequence. Gene region specific primers were developed for resistance genes such as Mlo and Pme3 to define the genetic variability in tissue culture of L. usitatissimum. In recent years, utilization of gold and silver nanoparticles in tissue culture is increased and the mechanisms of changes in genome induced by nanoparticles still remain unclear. Obtained data show the somaclonal variation increase in calluses obtained from one donor plant and grown on medium supplemented by gold nanoparticles (Mlo ; Pme3 ) or silver nanoparticles (Mlo ; Pme3 ) and decrease in regenerants. Morphological parameters of calluses showed a number of differences between each investigated culture group.
      PubDate: Thu, 23 Feb 2017 08:20:23 +000
       
  • Genomewide Expression and Functional Interactions of Genes under Drought
           Stress in Maize

    • Abstract: A genomewide transcriptome assay of two subtropical genotypes of maize was used to observe the expression of genes at seedling stage of drought stress. The number of genes expressed differentially was greater in HKI1532 (a drought tolerant genotype) than in PC3 (a drought sensitive genotype), indicating primary differences at the transcriptional level in stress tolerance. The global coexpression networks of the two genotypes differed significantly with respect to the number of modules and the coexpression pattern within the modules. A total of 174 drought-responsive genes were selected from HKI1532, and their coexpression network revealed key correlations between different adaptive pathways, each cluster of the network representing a specific biological function. Transcription factors related to ABA-dependent stomatal closure, signalling, and phosphoprotein cascades work in concert to compensate for reduced photosynthesis. Under stress, water balance was maintained by coexpression of the genes involved in osmotic adjustments and transporter proteins. Metabolism was maintained by the coexpression of genes involved in cell wall modification and protein and lipid metabolism. The interaction of genes involved in crucial biological functions during stress was identified and the results will be useful in targeting important gene interactions to understand drought tolerance in greater detail.
      PubDate: Thu, 23 Feb 2017 00:00:00 +000
       
  • Exploration of Nitrate Reductase Metabolic Pathway in Corynebacterium
           pseudotuberculosis

    • Abstract: Based on the ability of nitrate reductase synthesis, Corynebacterium pseudotuberculosis is classified into two biovars: Ovis and Equi. Due to the presence of nitrate reductase, the Equi biovar can survive in absence of oxygen. On the other hand, Ovis biovar that does not have nitrate reductase is able to adapt to various ecological niches and can grow on certain carbon sources. Apart from these two biovars, some other strains are also able to carry out the reduction of nitrate. The enzymes that are involved in electron transport chain are also identified by in silico methods. Findings about pathogen metabolism can contribute to the identification of relationship between nitrate reductase and the C. pseudotuberculosis pathogenicity, virulence factors, and discovery of drug targets.
      PubDate: Mon, 20 Feb 2017 11:44:33 +000
       
  • Integrating Biological Covariates into Gene Expression-Based Predictors of
           Radiation Sensitivity

    • Abstract: The use of gene expression-based classifiers has resulted in a number of promising potential signatures of patient diagnosis, prognosis, and response to therapy. However, these approaches have also created difficulties in trying to use gene expression alone to predict a complex trait. A practical approach to this problem is to integrate existing biological knowledge with gene expression to build a composite predictor. We studied the problem of predicting radiation sensitivity within human cancer cell lines from gene expression. First, we present evidence for the need to integrate known biological conditions (tissue of origin, RAS, and p53 mutational status) into a gene expression prediction problem involving radiation sensitivity. Next, we demonstrate using linear regression, a technique for incorporating this knowledge. The resulting correlations between gene expression and radiation sensitivity improved through the use of this technique (best-fit adjusted increased from 0.3 to 0.84). Overfitting of data was examined through the use of simulation. The results reinforce the concept that radiation sensitivity is not driven solely by gene expression, but rather by a combination of distinct parameters. We show that accounting for biological heterogeneity significantly improves the ability of the model to identify genes that are associated with radiosensitivity.
      PubDate: Wed, 08 Feb 2017 12:44:50 +000
       
  • Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice
           Landraces as a Comprehensive Information Resource for Marker-Assisted
           Selection

    • Abstract: Next generation sequencing technologies have provided numerous opportunities for application in the study of whole plant genomes. In this study, we present the sequencing and bioinformatic analyses of five typical rice landraces including three indica and two japonica with potential blast resistance. A total of 688.4 million 100 bp paired-end reads have yielded approximately 30-fold coverage to compare with the Nipponbare reference genome. Among them, a small number of reads were mapped to both chromosomes and organellar genomes. Over two million and eight hundred thousand single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) in indica and japonica lines have been determined, which potentially have significant impacts on multiple transcripts of genes. SNP deserts, contiguous SNP-low regions, were found on chromosomes 1, 4, and 5 of all genomes of rice examined. Based on the distribution of SNPs per 100 kilobase pairs, the phylogenetic relationships among the landraces have been constructed. This is the first step towards revealing several salient features of rice genomes in Vietnam and providing significant information resources to further marker-assisted selection (MAS) in rice breeding programs.
      PubDate: Tue, 07 Feb 2017 08:32:54 +000
       
  • The Draft Genome and Transcriptome of the Atlantic Horseshoe Crab, Limulus
           polyphemus

    • Abstract: The horseshoe crab, Limulus polyphemus, exhibits robust circadian and circatidal rhythms, but little is known about the molecular mechanisms underlying those rhythms. In this study, horseshoe crabs were collected during the day and night as well as high and low tides, and their muscle and central nervous system tissues were processed for genome and transcriptome sequencing, respectively. The genome assembly resulted in contigs with N50 of 4,736, while the transcriptome assembly resulted in contigs and N50 of 3,497. Analysis of functional completeness by the identification of putative universal orthologs suggests that the transcriptome has three times more total expected orthologs than the genome. Interestingly, RNA-Seq analysis indicated no statistically significant changes in expression level for any circadian core or accessory gene, but there was significant cycling of several noncircadian transcripts. Overall, these assemblies provide a resource to investigate the Limulus clock systems and provide a large dataset for further exploration into the taxonomy and biology of the Atlantic horseshoe crab.
      PubDate: Mon, 06 Feb 2017 13:20:51 +000
       
  • The Numerical Predominance and Large Transcriptome Differences of
           Neutrophils in Peripheral Blood Together Inevitably Account for a Reported
           Pulmonary Tuberculosis Signature

    • Abstract: Previous transcriptomic analysis revealed a 393-transcript signature (PTBsig), which is dominated by interferon inducible genes, in whole blood of pulmonary tuberculosis (PTB) patients. Comparisons with a limited set of interferon-driven genes among separated monocytes, CD4+ T cells, CD8+ T cells, and neutrophils indicated that the signature is due to changes in neutrophils, the overwhelmingly predominant cell type. By extending the analysis to the entire 393 transcripts of PTBsig and by switching the cell proportions between separated monocytes, CD4+ T cells, CD8+ T cells, and neutrophils, we create putative PTBsig for whole blood (pPTBsig) in which CD4+ or CD8+ T cells or monocytes predominated or in which the cell proportions were unchanged. These putative signatures are then compared to the actual reported PTBsig. We show that, because of their predominance in peripheral blood and their larger transcriptional responses, neutrophils were indeed almost exclusively responsible for PTBsig. We caution that the functional significance of changes in other cell types might escape notice in transcriptome analysis that is based upon whole blood.
      PubDate: Mon, 06 Feb 2017 11:48:06 +000
       
  • Characteristics and Validation Techniques for PCA-Based Gene-Expression
           Signatures

    • Abstract: Background. Many gene-expression signatures exist for describing the biological state of profiled tumors. Principal Component Analysis (PCA) can be used to summarize a gene signature into a single score. Our hypothesis is that gene signatures can be validated when applied to new datasets, using inherent properties of PCA. Results. This validation is based on four key concepts. Coherence: elements of a gene signature should be correlated beyond chance. Uniqueness: the general direction of the data being examined can drive most of the observed signal. Robustness: if a gene signature is designed to measure a single biological effect, then this signal should be sufficiently strong and distinct compared to other signals within the signature. Transferability: the derived PCA gene signature score should describe the same biology in the target dataset as it does in the training dataset. Conclusions. The proposed validation procedure ensures that PCA-based gene signatures perform as expected when applied to datasets other than those that the signatures were trained upon. Complex signatures, describing multiple independent biological components, are also easily identified.
      PubDate: Mon, 06 Feb 2017 09:57:36 +000
       
 
 
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