Dataset Information

Gene-Family Extension Measures and Correlations.

ABSTRACT: The existence of multiple copies of genes is a well-known phenomenon. A gene family is a set of sufficiently similar genes, formed by gene duplication. In earlier works conducted on a limited number of completely sequenced and annotated genomes it was found that size of gene family and size of genome are positively correlated. Additionally, it was found that several atypical microbes deviated from the observed general trend. In this study, we reexamined these associations on a larger dataset consisting of 1484 prokaryotic genomes and using several ranking approaches. We applied ranking methods in such a way that genomes with lower numbers of gene copies would have lower rank. Until now only simple ranking methods were used; we applied the Kemeny optimal aggregation approach as well. Regression and correlation analysis were utilized in order to accurately quantify and characterize the relationships between measures of paralog indices and genome size. In addition, boxplot analysis was employed as a method for outlier detection. We found that, in general, all paralog indexes positively correlate with an increase of genome size. As expected, different groups of atypical prokaryotic genomes were found for different types of paralog quantities. Mycoplasmataceae and Halobacteria appeared to be among the most interesting candidates for further research of evolution through gene duplication.

SUBMITTER: Carmi G

PROVIDER: S-EPMC5041006 | biostudies-other | 2016 Aug

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Gene-Family Extension Measures and Correlations.

Carmi Gon G Bolshoy Alexander A

Life (Basel, Switzerland) 20160803 3

The existence of multiple copies of genes is a well-known phenomenon. A gene family is a set of sufficiently similar genes, formed by gene duplication. In earlier works conducted on a limited number of completely sequenced and annotated genomes it was found that size of gene family and size of genome are positively correlated. Additionally, it was found that several atypical microbes deviated from the observed general trend. In this study, we reexamined these associations on a larger dataset con ...[more]

PMID: 27527218

Similar Datasets

Project description:The complexity of lung adenocarcinoma (LUAD), the development of which involves many interacting biological processes, makes it difficult to find therapeutic biomarkers for treatment. FK506-binding proteins (FKBPs) are composed of 12 members classified as conservative intracellular immunophilin family proteins, which are often connected to cyclophilin structures by tetratricopeptide repeat domains and have peptidyl prolyl isomerase activity that catalyzes proline from residues and turns the trans form into the cis form. Since FKBPs belong to chaperone molecules and promote protein folding, previous studies demonstrated that FKBP family members significantly contribute to the degradation of damaged, misfolded, abnormal, and foreign proteins. However, transcript expressions of this gene family in LUAD still need to be more fully investigated. In this research, we adopted high-throughput bioinformatics technology to analyze FKBP family genes in LUAD to provide credible information to clinicians and promote the development of novel cancer target drugs in the future. The current data revealed that the messenger (m)RNA levels of FKBP2, FKBP3, FKBP4, FKBP10, FKBP11, and FKBP14 were overexpressed in LUAD, and FKBP10 had connections to poor prognoses among LUAD patients in an overall survival (OS) analysis. Based on the above results, we selected FKBP10 to further conduct a comprehensive analysis of the downstream pathway and network. Through a DAVID analysis, we found that FKBP10 was involved in mitochondrial electron transport, NADH to ubiquinone transport, mitochondrial respiratory chain complex I assembly, etc. The MetaCore pathway analysis also indicated that FKBP10 was involved in "Ubiquinone metabolism", "Translation_(L)-selenoaminoacid incorporation in proteins during translation", and "Transcription_Negative regulation of HIF1A function". Collectively, this study revealed that FKBP family members are both significant prognostic biomarkers for lung cancer progression and promising clinical therapeutic targets, thus providing new targets for treating LUAD patients.

Project description:AIM:The aim of this study was to explore associations between reduced stereoacuity and clinical measures of accommodation, vergences, and symptoms which could facilitate the development of quick and reliable screening tools. METHODS:Using a multi-stage random cluster sampling, 1211 high school students (481 males and 730 females) between 13 and 18 years of age, were selected and examined. Visual acuity, stereoacuity and suppression, refractive errors, near point of convergence, heterophoria and fusional vergences, as well as, amplitude of accommodation, accommodative response, facility and relative accommodation were evaluated. Correlations among variables and the validity of Randot stereoacuity to distinguish between children with and without defective clinical measures as well as symptomatic versus asymptomatic children were characterized by the sensitivity and specificity of the tests. RESULTS:The overall mean stereoacuity was 43.9?±?25.23?s arc, and 18.9% [95% Confidence Interval, 16.6-21.4%)] of the participants had reduced stereoacuity (defined as ?60). Stereoacuity values and symptoms scores were worse in children with defective clinical measures. The Receiver Operation Curve showed that maximum sensitivity and specificity was obtained with near point of convergence break (?10?cm) of (0.70 95% confidence interval: 0.63-0.77) with Randot stereoacuity test (defined as ?60?s arc). The correlations between reduced stereoacuity and symptoms scores was moderately strong and statistically significant (Pearson's, r?=?0.507, p?=?0.01). The Receiver Operation Curve showed that maximum sensitivity and specificity obtained with the Convergence Insufficiency Symptoms Survey was 0.57 (95% Confidence interval?=?0.53-0.62, p?=?0.001), sensitivity of 90.26%, and specificity 15.26% with the Randot stereoacuity test. CONCLUSION:Reduced stereoacuity, defective clinical measures and symptoms of asthenopia were prevalent among sample of school children studied. Randot stereoacuity test could fairly distinguish between defective and normal clinical measures; though the accuracy to differentiate between symptomatic and asymptomatic school children is poor. These findings highlight the need for validation of a simple and fast screening tool in school settings. Further studies to confirm above findings will be needed.

Project description:ImportanceMeasurement of the quality of care is important for alternative payment models in oncology, yet the ability to distinguish high-quality from low-quality care across oncology practices remains uncertain.ObjectiveTo assess the reliability of cancer care quality measures across oncology practices using registry and claims-based measures of process, utilization, end-of-life (EOL) care, and survival, and to assess the correlations of practice-level performance across measure and cancer types.Design, setting, and participantsThis cross-sectional study used the Surveillance, Epidemiology, and End Results (SEER) Program registry linked to Medicare administrative data to identify individuals with lung cancer, breast cancer, or colorectal cancer (CRC) that was newly diagnosed between January 1, 2011, and December 31, 2015, and who were treated in oncology practices with 20 or more patients. Data were analyzed from January 2018 to December 2020.Main outcomes and measuresReceipt of guideline-recommended treatment and surveillance, hospitalizations or emergency department visits during 6-month chemotherapy episodes, care intensity in the last month of life, and 12-month survival were measured. Summary measures for each domain in each cohort were calculated. Practice-level rates for each measure were estimated from hierarchical linear models with practice-level random effects; practice-level reliability (reproducibility) for each measure based on the between-measure variance, within-measure variance, and distribution of patients treated in each practice; and correlations of measures across measure and cancer types.ResultsIn this study of SEER registry data linked to Medicare administrative data from 49 715 patients with lung cancer treated in 502 oncology practices, 21 692 with CRC treated in 347 practices, and 52 901 with breast cancer treated in 492 practices, few practices had 20 or more patients who were eligible for most process measures during the 5-year study period. Patients were 65 years or older; approximately 50% of the patients with lung cancer and CRC and all of the patients with breast cancer were women. Most measures had limited variability across practices. Among process measures, 0 of 6 for lung cancer, 0 of 6 for CRC, and 3 of 11 for breast cancer had a practice-level reliability of 0.75 or higher for the median-sized practice. No utilization, EOL care, or survival measure had reliability across practices of 0.75 or higher. Correlations across measure types were low (r ≤ 0.20 for all) except for a correlation between the CRC process and 1-year survival summary measures (r = 0.35; P < .001). Summary process measures had limited or no correlation across lung cancer, breast cancer, and CRC (r ≤ 0.16 for all).Conclusions and relevanceThis study found that quality measures were limited by the small numbers of Medicare patients with newly diagnosed cancer treated in oncology practices, even after pooling 5 years of data. Measures had low reliability and had limited to no correlation across measure and cancer types, suggesting the need for research to identify reliable quality measures for practice-level quality assessments.

Dataset Information

Gene-Family Extension Measures and Correlations.

Publications

Gene-Family Extension Measures and Correlations.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets