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At least 307 records · Page 17Linked to original sources

PubMed2002

Genomic functional annotation using co-evolution profiles of gene clusters.

BACKGROUND: The current speed of sequencing already exceeds the capability of annotation, creating a potential bottleneck. A large proportion of the genes in microbial genomes remains uncharacterized. Here we propose a new method for functional annotation using the conservation patterns of gene clusters. If several gene clusters show the same coevolution pattern across different genomes it is reasonable to infer they are functionally related. The gene cluster phylogenetic profile integrates chromosomal proximity information and phylogenetic profile information and allows us to infer functional dependences between the gene clusters even at great distance on the chromosome. RESULTS: As a proof of concept, we applied our method to the genome of Escherichia coli K12 strain. Our method establishes functional relationships among 176 gene clusters, comprising 738 E. coli genes. The accuracy of pair phylogenetic profiles was compared with the single-gene phylogenetic profile and was shown to be higher. As a result, we are able to suggest functional roles for several previously unknown genes or unknown genomic regions in E. coli. We also examined the robustness of coevolution signals across a larger set of genomes and suggest a possible upper limit of accuracy for the phylogenetic profile methods. CONCLUSIONS: The higher-order phylogenetic profiles, such as the gene-pair phylogenetic profiles, can detect functional dependences that are missed by using conventional single-gene phylogenetic profile or the chromosomal proximity method only. We show that the gene-pair phylogenetic profile is more accurate than the single-gene phylogenetic profiles.

Alleles↗

PubMed2003

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

BACKGROUND: As a biomarker of cellular activities, the transcriptome of a specific tissue or cell type during development and disease is of great biomedical interest. We have generated and analyzed 10,000 expressed sequence tags (ESTs) from three mouse eye tissue cDNA libraries: embryonic day 15.5 (M15E) eye, postnatal day 2 (M2PN) eye and adult retina (MRA). RESULTS: Annotation of 8,633 non-mitochondrial and non-ribosomal high-quality ESTs revealed that 57% of the sequences represent known genes and 43% are unknown or novel ESTs, with M15E having the highest percentage of novel ESTs. Of these, 2,361 ESTs correspond to 747 unique genes and the remaining 6,272 are represented only once. Phototransduction genes are preferentially identified in MRA, whereas transcripts for cell structure and regulatory proteins are highly expressed in the developing eye. Map locations of human orthologs of known genes uncovered a high density of ocular genes on chromosome 17, and identified 277 genes in the critical regions of 37 retinal disease loci. In silico expression profiling identified 210 genes and/or ESTs over-expressed in the eye; of these, more than 26 are known to have vital retinal function. Comparisons between libraries provided a list of temporally regulated genes and/or ESTs. A few of these were validated by qRT-PCR analysis. CONCLUSIONS: Our studies present a large number of potentially interesting genes for biological investigation, and the annotated EST set provides a useful resource for microarray and functional genomic studies.

Aging↗

PubMed2023

Pervasive correlations between causal disease effects of proximal SNPs vary with functional annotations and implicate stabilizing selection.

The genetic architecture of human diseases and complex traits has been extensively studied, but little is known about the relationship of causal disease effect sizes between proximal SNPs, which have largely been assumed to be independent. We introduce a new method, LD SNP-pair effect correlation regression (LDSPEC), to estimate the correlation of causal disease effect sizes of derived alleles between proximal SNPs, depending on their allele frequencies, LD, and functional annotations; LDSPEC produced robust estimates in simulations across various genetic architectures. We applied LDSPEC to 70 diseases and complex traits from the UK Biobank (average N=306K), meta-analyzing results across diseases/traits. We detected significantly nonzero effect correlations for proximal SNP pairs (e.g., -0.37±0.09 for low-frequency positive-LD 0-100bp SNP pairs) that decayed with distance (e.g., -0.07±0.01 for low-frequency positive-LD 1-10kb), varied with allele frequency (e.g., -0.15±0.04 for common positive-LD 0-100bp), and varied with LD between SNPs (e.g., +0.12±0.05 for common negative-LD 0-100bp) (because we consider derived alleles, positive-LD and negative-LD SNP pairs may yield very different results). We further determined that SNP pairs with shared functions had stronger effect correlations that spanned longer genomic distances, e.g., -0.37±0.08 for low-frequency positive-LD same-gene promoter SNP pairs (average genomic distance of 47kb (due to alternative splicing)) and -0.32±0.04 for low-frequency positive-LD H3K27ac 0-1kb SNP pairs. Consequently, SNP-heritability estimates were substantially smaller than estimates of the sum of causal effect size variances across all SNPs (ratio of 0.87±0.02 across diseases/traits), particularly for certain functional annotations (e.g., 0.78±0.01 for common Super enhancer SNPs)-even though these quantities are widely assumed to be equal. We recapitulated our findings via forward simulations with an evolutionary model involving stabilizing selection, implicating the action of linkage masking, whereby haplotypes containing linked SNPs with opposite effects on disease have reduced effects on fitness and escape negative selection.

Journal Article↗

PubMed1976

SAM Complex Coordinator and Multidimensional Pursuit Test: annotated bibliographies.

A brief description of the SAM Complex Coordinator (Mashburn Apparatus) and the SAM Multidimensional Pursuit Test (MDP or MPT) and annotated bibliographies including 144 and 51 citations respectively are presented. All references are annotated as to subject matter within six categories; Factor Analytic-Task Taxonomy, Aircrew Selection-Classification, Learning Phenomena, Stress Effects, History and Development, General Reviews.

Aerospace Medicine↗

PubMed1998

Primary prevention of alcohol misuse: overview and annotated bibliography.

Following an overview of conceptual and methodological issues related to alcohol misuse primary prevention and a brief discussion of the most frequently employed primary prevention strategies, a comprehensive annotated bibliography of the alcohol misuse primary prevention literature is presented. Several benefits of presenting detailed annotations, such as allowing readers to (a) examine the various prevention program components, (b) identify the presence or absence of methodological shortcomings, (c) identify whether or not high-risk groups were included as program participants, and (d) evaluate the feasibility of program implementation, are also highlighted. The present article complements previous reviews which have often mixed together the findings of primary and secondary prevention studies and which have typically reported the effects of prevention programming on multiple substance misuse outcomes simultaneously. The practice of simultaneously reporting multiple substance misuse outcomes has made it difficult to interpret the specific effects that primary prevention programs have had on alcohol misuse per se.

Alcoholism↗

PubMed2003

Functional annotation of putative aminoglycoside antibiotic modifying proteins in Mycobacterium tuberculosis H37Rv.

The growing availability of sequences of bacterial genomes has revealed a number of open reading frames predicted by sequence alignment to encode antibiotic resistance proteins. The presence of these putative resistance genes within bacterial genomes raises important questions regarding potential reservoirs of resistance elements and their evolution. Here we examine four gene products encoding predicted aminoglycoside-aminocyclitol antibiotic modifying enzymes, two phosphotransferases and two acetyltransferases, derived from analysis of the genome sequence of Mycobacterium tuberculosis strain H37Rv with the goal of assigning biochemical function by purification of each protein and characterization of their ability to modify aminoglycoside antibiotics. Only one of these enzymes, the previously characterized aminoglycoside acetyltransferase AAC(2')-Ic, displayed compelling aminoglycoside modifying activity. While the putative phosphotransferase encoded by the Rv3225c gene did display low levels of aminoglycoside kinase activity, the predicted kinase encoded by the Rv3817 gene lacked any such activity. A potential aminoglycoside 6'-acetyltransferase, encoded by the Rv1347c gene, did not show antibiotic acylation activity but did demonstrate selective thioesterase activity with numerous acyl-CoAs. This activity, together with the genomic environment of the Rv1347c gene in a likely polyketide synthesis cluster, suggests a role for this protein in secondary metabolism and not in antibiotic modification. It was thus shown that only one of four putative aminoglycosides modifying enzymes derived from the whole genome sequencing of M. tuberculosis H37Rv showed sufficient predicted enzyme activity to be annotated as an aminoglycoside resistance element. This study demonstrates the necessity of biochemical annotation methods as a follow up to in silico sequence alignment-based methods of assigning gene product function.

Acetyltransferases↗

PubMed1999

Position-specific annotation of protein function based on multiple homologs.

I present in this work an algorithm for deriving protein functional annotations which are position-specific. The input is based on the results of a sequence similarity search of the query sequence against a sequence database. Strings of words are extracted from the descriptions of the proteins, and the correlation between proteins having the same descriptors and the amino acid conservation is used to compute a score that indicates which descriptor is likely to describe better the function of each particular residue. Analysis of the score curves and comparison of different functions allows an easy detection of parts of the sequence associated to different function. Different levels of functional specificity can be compared, allowing to choose the one that suits better the function of the protein. Immediate applications of this algorithm are, support for (automated) methods of protein functional annotation, and database coherence check.

Algorithms↗

PubMed2000

Standardized annotation of nuclear medicine images.

There are no generally accepted standards for annotating nuclear medicine images. This is a potential problem whenever hardcopies from other centers are being evaluated, reinterpreted or compared to actual images of the same patient. Proposals for image annotation are elaborated to support image evaluation by a third party. In this paper, examples are given of lung scintigraphy, thyroid scintigraphy, bone scintigraphy both in planar and SPECT techniques, renal function scintigraphy, myocardial perfusion scintigraphy, and PET. They are presented to stimulate discussion in the nuclear medicine community.

Forms and Records Control↗

PubMed2001

Improving delivery of preventive health care with the comprehensive annotated reminder tool (CART).

OBJECTIVES: We assessed the effect of the Comprehensive Annotated Reminder Tool (CART) on physician adherence to preventive services recommendations. STUDY DESIGN: Using a randomized pretest/posttest control group design, we assigned physicians to the CART group or the control group, followed up prospectively, and evaluated for appropriate adherence to guidelines. The 3 age-specific versions of the CART annotated history and physical examination form contained up to 49 preventive services recommendations. POPULATION: All resident physicians in a large family practice residency program were studied over the course of 1 academic year. OUTCOMES MEASURED: We performed blinded chart reviews to assess the appropriateness of preventive services ordered by the physicians before the introduction of the CART, during its use, and after its removal. A multiple-choice test completed before and after the use of the CART forms assessed knowledge. RESULTS: When the CART was used, the appropriateness of physician preventive behavior increased by 21% overall. The appropriateness of history, physical examination, and laboratory interventions increased by 33%. When the CART was removed, physician behavior returned to baseline (P < or = .0025 for 16 of 20 interventions). No significant differences were observed in the control group over time. Knowledge increased over the study period for all physicians (P < or = .005) but did not differ significantly between the treatment and control groups (P = .608). CONCLUSIONS: Use of the CART significantly improved physician performance in the appropriate delivery of preventive care.

Delivery of Health Care↗

PubMed2002

The CATH protein family database: a resource for structural and functional annotation of genomes.

Over the last decade, there have been huge increases in the numbers of protein sequences and structures determined. In parallel, many methods have been developed for recognising similarities between these proteins, arising from their common evolutionary background, and for clustering such relatives into protein families. Here we review some of the protein family resources available to the biologist and describe how these can be used to provide structural and functional annotations for newly determined sequences. In particular we describe recent developments to the CATH domain database of protein structural families which have facilitated genome annotation and which have also revealed important caveats that must be considered when transferring functional data between homologous proteins.

Databases, Protein↗

PubMed2001

Bioinformatics issues for automating the annotation of genomic sequences.

The rapid explosion in the amount of biological data being generated worldwide is surpassing efforts to manage analysis of the data. As part of an ongoing project to automate and manage bioinformatics analysis, the authors have designed and implemented a simple automated annotation system, which is described in this paper. The system is applied to existing GenBank/DDBJ/EMBL entries and compared with existing annotations to illustrate not only potential errors but also that they are generally not up-to-date, as a result of new versions of analysis tools and updates of genomic repositories. We highlight the important Bioinformatics issues of storage and management of information to ensure data and results are kept up-to-date in light of new information becoming available. Surprisingly, from just four database entries, a significant number of new features were found. We describe the results as well as identify important issues that need to be addressed in order to automate the re-analysis/re-annotation of genomic sequences within a reasonable timeframe.

Computational Biology↗

PubMed2002

Representation and processing of complex DNA spatial architecture and its annotated genomic content.

This paper presents a new general approach for the spatial representation and visualization of DNA molecule and its annotated information. This approach is based on a biological 3D model that predicts the complex spatial trajectory of huge naked DNA. With such modeling, a global vision of the sequence is possible, which is different and complementary to other representations as textual, linguistics or syntactic ones. The DNA is well known as a three-dimensional structure. Whereas, the spatial information plays a great part during its evolution and its interaction with the other biological elements This work will motivate investigations in order to launch new bioinformatics studies for the analysis of the spatial architecture of the genome. Besides, in order to obtain a friendly interactive visualization, a powerful graphic modeling is proposed including DNA complex trajectory management and its annotated-based content structuring. The paper describes spatial architecture modeling, with consideration of both biological and computational constraints. This work is implemented through a powerful graphic software tool, named ADN-Viewer. Several examples of visualization are shown for various organisms and biological elements.

DNA↗

PubMed1999

The Feasibility of Using Proteome Expression Profile for Genome Annotation.

By investigating into the expression data from ECO2DBASE (Edition 6),the feasibility of using proteome expression profile for genome annotation was tested. Based on our newly developed CRC (cellular role cluster) method,79 proteins extracted from ECO2DBASE were clustered into 4 CRCs. Function related proteins tend to be clustered into same CRC. Total 9 aminoacyl-tRNA synthetases were clustered into CRC2, whereas 4 heat-shock proteins into CRC3. These results indicate with enough proteome expression data and the efficient algorithm, proteome expression profile can provide very important information for genome annotation, while this kind of information is sequence-independent.

Journal Article↗

PubMed2002

[Annotation of complete genomic sequence of 3p24-p25 478 kb of human DNA].

OBJECTIVE: To annotate the human genome 3p24-p25 478 kb complete sequence. METHODS: The protein-coding genes in the genomic sequence were identified by using ab initio gene finding, homology-based similarity database searching and all or partial mRNA aligning with genomic sequence, and the content feature of the genomic sequence were analyzed by using EMBOSS package. RESULTS: Two known genes SLC6A1 and SLC6A11 were identified; as well as the GC content of this genomic sequence was 47% and 3 putative CpG islands were predicted in the genomic sequence, located in 130,685-131,516 bp, 307,090-307,870 bp and 415,585-416,308 bp, respectively. CONCLUSIONS: The methods, as mentioned above, might be used for annotating the biological information in the genomic sequence, such as gene structure, GC content, CpG island.

Base Sequence↗

PubMed2003

Open-source toolkit for simple XML annotation.

Use of Extensible Markup Language (XML) is increasingly prevalent among medical informatics projects. Many of these projects involve, at some point, the interaction between a researcher and specialized XML documents for the purpose of annotating the XML data. We offer a simple toolkit to assist these researchers. Our solution is a simple, yet fully functional, annotation system that can easily be adapted to the needs of the researcher. All of the materials for this toolkit are freely available.

Algorithms↗

PubMed1992

Use of neurodevelopmental treatment as an intervention: annotated listing of studies 1980-1990.

This annotated bibliography presents a listing of research investigations on the effectiveness of neurodevelopmental treatment, an approach developed by the Bobaths in managing the neuromotor problems of infants, toddlers, children, and adults with neuromotor disorders. The annotated listing of 19 articles appearing in peer-reviewed journals between 1980 and 1990 is presented by category of experimental design (single-subject, quasi-experimental, and experimental). Each research article was reviewed for research question, conceptual framework, research design, findings, and limitations. The bibliography should be useful for educators, clinicians, and researchers in evaluating current research and in developing strategic plans for research. The implications for clinical practice and program development are discussed.

Activities of Daily Living↗

PubMed1992

An annotated algorithm approach to clinical guideline development.

The Urinary Incontinence in Adults Guideline Panel facilitated the ready elucidation of its guideline's management recommendations through the use of an annotated algorithm approach. The algorithms created as part of this guideline differ from previous algorithms in two ways: (1) they employ systematic annotation to link explicitly the algorithms' recommendations to the literature, and (2) they contain patient counseling and decision nodes to depict the major preference-dependent decision or branch points in the algorithm. We believe that these two innovations can help ensure the clinical validity of guidelines' algorithms while preserving appropriate clinical flexibility and respecting patient preferences.

Algorithms↗

PubMed1990

Annotated bibliography on the reuse of hemodialyzers.

The following annotated bibliography on the reuse of hemodialyzers is offered as a service to nephrology nurses needing information on this subject. The articles with the exception of two, are those published in the medical literature from 1980-1989. For ease of access, the articles are divided into the following categories: general information/reading, dialyzer performance, disinfectant, physiologic response, and infection control. Additionally, very brief descriptions of the primary contents of the articles are included. Many of the articles also contain material in addition to that summarized in the annotation. The bibliography is a selection of the hundreds available. For a more thorough study of reuse, we recommend that the reader access the additional citations listed in the bibliographies of the individual articles included herein. No attempt was made to critique the quality of the studies being reported. Readers are encouraged to examine the articles first hand, incorporating the findings into their own clinical settings.

Bibliographies as Topic↗