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PubMedDate not supplied

Genomic annotation and transcriptome analysis of the zebrafish (Danio rerio) hox complex with description of a novel member, hox b 13a.

The zebrafish (Danio rerio) is an important model in evolutionary developmental biology, and its study is being revolutionized by the zebrafish genome project. Sequencing is at an advanced stage, but annotation is largely the result of in silico analyses. We have performed genomic annotation, comparative genomics, and transcriptional analysis using microarrays of the hox homeobox-containing transcription factors. These genes have important roles in specifying the body plan. Candidate sequences were located in version Z v 4 of the Ensembl genome database by TBLASTN searching with Danio and other vertebrate published Hox protein sequences. Homologies were confirmed by alignment with reference sequences, and by the relative position of genes along each cluster. RT-PCR using adult Tübingen cDNA was used to confirm annotations, to check the genomic sequence and to confirm expression in vivo. Our RT-PCR and microarray data show that all 49 hox genes are expressed in adult zebrafish. Significant expression for all known hox genes could be detected in our microarray analysis. We also find significant expression of hox 8 paralogs and hox b 7 a in the anti-sense direction. A novel gene, D. rerio hox b 13 a, was identified, and a preliminary characterization by in situ hybridization showed expression at 24 hpf at the tip of the developing tail. We are currently characterizing this gene at the functional level. We argue that the oligo design for microarrays can be greatly enhanced by the availability of genomic sequences.

Animals↗

PubMed2000

High-throughput functional annotation of novel gene products using document clustering.

Gene products differentially expressed in healthy vs. diseased tissues may be considered drug targets since the change in their expression level can be related to the cause and progression of the disease studied. A significant portion of the proteins produced by these genes will be unknown and consequently their function must be characterised. The experimental elucidation of biochemical function must be supported by computational tools which can help predicting the possible function of a given protein from its amino acid sequence. We have designed a high-throughput system which automatically analyses amino acid sequences deduced from differentially represented cDNA clones. The system attempts to assign a biological function to protein sequences by carrying out searches in sequence databanks and by locating functionally relevant motifs in the query sequences. The results delivered by the various prediction methods consist of the annotations of matching sequences and/or motifs, which are free-format texts written by humans and therefore may describe the same concept with synonymous words. It is desirable to present the results in such a way that the annotations describing the same biological function are grouped together. To this end we devised an algorithm that enables the hierarchical clustering of free-format documents based on their contents. The system is capable of detecting and flagging conflicting annotations, and will speed up the interpretation of the function prediction results.

Algorithms↗

PubMed1997

Hypnosis for children and adolescents with cancer: an annotated bibliography, 1985-1995.

This annotated bibliography reviews the professional literature published in English, from 1985 to 1995 inclusive, on the subject of the use of hypnosis with pediatric cancer patients. Books, chapters, and journal articles are included; dissertation, theses, and unpublished material are not. This bibliography contains 37 items organized into three categories: (1) General Discussions; (2) Case Reports or Case Studies: and (3) Experimental and Nonexperimental Group Designs. The brief annotations provided are not intended to be reviews or to be evaluative, but, rather, to inform the reader about the content and focus of the publication. This is an update of a previously published annotated bibliography, also presented in this Journal, which explored the relationship between hypnosis and pediatric cancer in journal articles published from 1960 to 1985.

Adolescent↗

PubMed2003

Eval: a software package for analysis of genome annotations.

SUMMARY: Eval is a flexible tool for analyzing the performance of gene annotation systems. It provides summaries and graphical distributions for many descriptive statistics about any set of annotations, regardless of their source. It also compares sets of predictions to standard annotations and to one another. Input is in the standard Gene Transfer Format (GTF). Eval can be run interactively or via the command line, in which case output options include easily parsable tab-delimited files. AVAILABILITY: To obtain the module package with documentation, go to http://genes.cse.wustl.edu/ and follow links for Resources, then Software. Please contact brent@cse.wustl.edu

Computational Biology↗

PubMed2004

Automatic annotation of protein motif function with Gene Ontology terms.

BACKGROUND: Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, a much needed and important task is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO) project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. RESULTS: This paper presents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifs is viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association is found to be a very useful feature. We take advantage of the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correct association. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. CONCLUSIONS: In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about the functions of newly discovered candidate protein motifs.

Amino Acid Motifs↗

PubMed2005

Probabilistic annotation of protein sequences based on functional classifications.

BACKGROUND: One of the most evident achievements of bioinformatics is the development of methods that transfer biological knowledge from characterised proteins to uncharacterised sequences. This mode of protein function assignment is mostly based on the detection of sequence similarity and the premise that functional properties are conserved during evolution. Most automatic approaches developed to date rely on the identification of clusters of homologous proteins and the mapping of new proteins onto these clusters, which are expected to share functional characteristics. RESULTS: Here, we inverse the logic of this process, by considering the mapping of sequences directly to a functional classification instead of mapping functions to a sequence clustering. In this mode, the starting point is a database of labelled proteins according to a functional classification scheme, and the subsequent use of sequence similarity allows defining the membership of new proteins to these functional classes. In this framework, we define the Correspondence Indicators as measures of relationship between sequence and function and further formulate two Bayesian approaches to estimate the probability for a sequence of unknown function to belong to a functional class. This approach allows the parametrisation of different sequence search strategies and provides a direct measure of annotation error rates. We validate this approach with a database of enzymes labelled by their corresponding four-digit EC numbers and analyse specific cases. CONCLUSION: The performance of this method is significantly higher than the simple strategy consisting in transferring the annotation from the highest scoring BLAST match and is expected to find applications in automated functional annotation pipelines.

Algorithms↗

PubMed2005

Columba: an integrated database of proteins, structures, and annotations.

BACKGROUND: Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. DESCRIPTION: COLUMBA currently integrates twelve different databases, including PDB, KEGG, Swiss-Prot, CATH, SCOP, the Gene Ontology, and ENZYME. The database can be searched using either keyword search or data source-specific web forms. Users can thus quickly select and download PDB entries that, for instance, participate in a particular pathway, are classified as containing a certain CATH architecture, are annotated as having a certain molecular function in the Gene Ontology, and whose structures have a resolution under a defined threshold. The results of queries are provided in both machine-readable extensible markup language and human-readable format. The structures themselves can be viewed interactively on the web. CONCLUSION: The COLUMBA database facilitates the creation of protein structure data sets for many structure-based studies. It allows to combine queries on a number of structure-related databases not covered by other projects at present. Thus, information on both many and few protein structures can be used efficiently. The web interface for COLUMBA is available at http://www.columba-db.de.

Base Sequence↗

PubMed2006

ProFAT: a web-based tool for the functional annotation of protein sequences.

BACKGROUND: The functional annotation of proteins relies on published information concerning their close and remote homologues in sequence databases. Evidence for remote sequence similarity can be further strengthened by a similar biological background of the query sequence and identified database sequences. However, few tools exist so far, that provide a means to include functional information in sequence database searches. RESULTS: We present ProFAT, a web-based tool for the functional annotation of protein sequences based on remote sequence similarity. ProFAT combines sensitive sequence database search methods and a fold recognition algorithm with a simple text-mining approach. ProFAT extracts identified hits based on their biological background by keyword-mining of annotations, features and most importantly, literature associated with a sequence entry. A user-provided keyword list enables the user to specifically search for weak, but biologically relevant homologues of an input query. The ProFAT server has been evaluated using the complete set of proteins from three different domain families, including their weak relatives and could correctly identify between 90% and 100% of all domain family members studied in this context. ProFAT has furthermore been applied to a variety of proteins from different cellular contexts and we provide evidence on how ProFAT can help in functional prediction of proteins based on remotely conserved proteins. CONCLUSION: By employing sensitive database search programs as well as exploiting the functional information associated with database sequences, ProFAT can detect remote, but biologically relevant relationships between proteins and will assist researchers in the prediction of protein function based on remote homologies.

Algorithms↗

PubMed2004

Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

BACKGROUND: Heterocellular hereditary persistence of fetal hemoglobin (HPFH) is a common multifactorial trait characterized by a modest increase of fetal hemoglobin levels in adults. We previously localized a Quantitative Trait Locus for HPFH in an extensive Asian-Indian kindred to chromosome 6q23. As part of the strategy of positional cloning and a means towards identification of the specific genetic alteration in this family, a thorough annotation of the candidate interval based on a strategy of in silico / wet biology approach with comparative genomics was conducted. RESULTS: The ~1.5 Mb candidate region was shown to contain five protein-coding genes. We discovered a very large uncharacterized gene containing WD40 and SH3 domains (AHI1), and extended the annotation of four previously characterized genes (MYB, ALDH8A1, HBS1L and PDE7B). We also identified several genes that do not appear to be protein coding, and generated 17 kb of novel transcript sequence data from re-sequencing 97 EST clones. CONCLUSION: Detailed and thorough annotation of this 1.5 Mb interval in 6q confirms a high level of aberrant transcripts in testicular tissue. The candidate interval was shown to exhibit an extraordinary level of alternate splicing - 19 transcripts were identified for the 5 protein coding genes, but it appears that a significant portion (14/19) of these alternate transcripts did not have an open reading frame, hence their functional role is questionable. These transcripts may result from aberrant rather than regulated splicing.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed2005

CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences.

BACKGROUND: With the recent progress made in large-scale genome sequencing projects a vast amount of novel data is becoming available. A comparative sequence analysis, exploiting sequence information from various resources, can be used to uncover hidden information, such as genetic variation. Although there are enormous amounts of SNPs for a wide variety of organisms submitted to NCBI dbSNP and annotated in most genome assembly viewers like Ensembl and the UCSC Genome Browser, these platforms do not easily allow for extensive annotation and incorporation of experimental data supporting the polymorphism. However, such information is very important for selecting the most promising and useful candidate polymorphisms for use in experimental setups. DESCRIPTION: The CASCAD database is designed for presentation and query of candidate SNPs that are retrieved by in silico mining of high-throughput sequencing data. Currently, the database provides collections of laboratory rat (Rattus norvegicus) and zebrafish (Danio rerio) candidate SNPs. The database stores detailed information about raw data supporting the candidate, extensive annotation and links to external databases (e.g. GenBank, Ensembl, UniGene, and LocusLink), verification information, and predictions of a potential effect for non-synonymous polymorphisms in coding regions. The CASCAD website allows search based on an arbitrary combination of 27 different parameters related to characteristics like candidate SNP quality, genomic localization, and sequence data source or strain. In addition, the database can be queried with any custom nucleotide sequences of interest. The interface is crosslinked to other public databases and tightly coupled with primer design and local genome assembly interfaces in order to facilitate experimental verification of candidates. CONCLUSIONS: The CASCAD database discloses detailed information on rat and zebrafish candidate SNPs, including the raw data underlying its discovery. An advanced web-based search interface http://cascad.niob.knaw.nl allows universal access to the database content and allows various queries supporting many types of research utilizing single nucleotide polymorphisms.

Animals↗

PubMed2000

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).

BACKGROUND: Standard archival sequence databases have not been designed as tools for genome annotation and are far from being optimal for this purpose. We used the database of Clusters of Orthologous Groups of proteins (COGs) to reannotate the genomes of two archaea, Aeropyrum pernix, the first member of the Crenarchaea to be sequenced, and Pyrococcus abyssi. RESULTS: A. pernix and P. abyssi proteins were assigned to COGs using the COGNITOR program; the results were verified on a case-by-case basis and augmented by additional database searches using the PSI-BLAST and TBLASTN programs. Functions were predicted for over 300 proteins from A. pernix, which could not be assigned a function using conventional methods with a conservative sequence similarity threshold, an approximately 50% increase compared to the original annotation. A. pernix shares most of the conserved core of proteins that were previously identified in the Euryarchaeota. Cluster analysis or distance matrix tree construction based on the co-occurrence of genomes in COGs showed that A. pernix forms a distinct group within the archaea, although grouping with the two species of Pyrococci, indicative of similar repertoires of conserved genes, was observed. No indication of a specific relationship between Crenarchaeota and eukaryotes was obtained in these analyses. Several proteins that are conserved in Euryarchaeota and most bacteria are unexpectedly missing in A. pernix, including the entire set of de novo purine biosynthesis enzymes, the GTPase FtsZ (a key component of the bacterial and euryarchaeal cell-division machinery), and the tRNA-specific pseudouridine synthase, previously considered universal. A. pernix is represented in 48 COGs that do not contain any euryarchaeal members. Many of these proteins are TCA cycle and electron transport chain enzymes, reflecting the aerobic lifestyle of A. pernix. CONCLUSIONS: Special-purpose databases organized on the basis of phylogenetic analysis and carefully curated with respect to known and predicted protein functions provide for a significant improvement in genome annotation. A differential genome display approach helps in a systematic investigation of common and distinct features of gene repertoires and in some cases reveals unexpected connections that may be indicative of functional similarities between phylogenetically distant organisms and of lateral gene exchange.

Archaea↗

PubMed2001

A draft annotation and overview of the human genome.

BACKGROUND: The recent draft assembly of the human genome provides a unified basis for describing genomic structure and function. The draft is sufficiently accurate to provide useful annotation, enabling direct observations of previously inferred biological phenomena. RESULTS: We report here a functionally annotated human gene index placed directly on the genome. The index is based on the integration of public transcript, protein, and mapping information, supplemented with computational prediction. We describe numerous global features of the genome and examine the relationship of various genetic maps with the assembly. In addition, initial sequence analysis reveals highly ordered chromosomal landscapes associated with paralogous gene clusters and distinct functional compartments. Finally, these annotation data were synthesized to produce observations of gene density and number that accord well with historical estimates. Such a global approach had previously been described only for chromosomes 21 and 22, which together account for 2.2% of the genome. CONCLUSIONS: We estimate that the genome contains 65,000-75,000 transcriptional units, with exon sequences comprising 4%. The creation of a comprehensive gene index requires the synthesis of all available computational and experimental evidence.

Chromosome Mapping↗

PubMed2002

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome.

BACKGROUND: It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be determined. RESULTS: We analyzed conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of the D. melanogaster genome. All D. melanogaster genes (and 78-82% of coding exons) identified in divergent species such as D. pseudoobscura show evidence of functional constraint. Addition of a third species can reveal functional constraint in otherwise non-significant pairwise exon comparisons. Microsynteny is largely conserved, with rearrangement breakpoints, novel transposable element insertions, and gene transpositions occurring in similar numbers. Rates of amino-acid substitution are higher in uncharacterized genes relative to genes that have previously been studied. Conserved non-coding sequences (CNCSs) tend to be spatially clustered with conserved spacing between CNCSs, and clusters of CNCSs can be used to predict enhancer sequences. CONCLUSIONS: Our results provide the basis for choosing species whose genome sequences would be most useful in aiding the functional annotation of coding and cis-regulatory sequences in Drosophila. Furthermore, this work shows how decoding the spatial organization of conserved sequences, such as the clustering of CNCSs, can complement efforts to annotate eukaryotic genomes on the basis of sequence conservation alone.

Animals↗

PubMed1986

An annotated bibliography on respite care for children and families.

With an increasing emphasis on home care, more and more children with severe disabilities and chronic-acute health impairments will be cared for at home. Care of these children places great financial, physical, and emotional strains on families. Adequate support for families is essential to prevent costly rehospitalization, foster placement, or worse. Respite care is a supportive service that is an important part of every effective plan for home care. This bibliography offers annotations on a range of materials directly addressing or closely related to the topic of respite care for children and families. The bibliography will be useful for the reader searching for general material on the topic as well as the reader interested in specific aspects of respite care, including family perceptions, program models, funding issues, and training. Annotations on articles, reports, books, and some government materials are provided. Additionally, a listing of training materials, and where they can be obtained, is provided without annotations after the bibliography.

Bibliographies as Topic↗

PubMed2000

Annotating sequence data using Genotator.

In this postgenomic era, it is no longer necessary to argue the need for automated methods for sequence annotation. Many researchers have designed tools for analyzing DNA sequences, but running multiple tools and interpreting the results can be tedious and confusing. In the last few years, many analysis workbenches have been developed to help streamline the process of sequence annotation. Genotator, developed in 1996, is still a popular choice owing to its ease of use and its configurability. This article will review annotating sequence data using the Genotator.

Amino Acid Sequence↗

PubMed2005

Chemical and biological profiling of an annotated compound library directed to the nuclear receptor family.

Nuclear receptors form a family of ligand-activated transcription factors that regulate a wide variety of biological processes and are thus generally considered relevant targets in drug discovery. We have constructed an annotated compound library directed to nuclear receptors (NRacl) as a means for integrating the chemical and biological data being generated within this family. Special care has been put in the appropriate storage of annotations by using hierarchical classification schemes for both molecules and nuclear receptors, which takes the ability to extract knowledge from annotated compound libraries to another level. Analysis of NRacl has ultimately led to the identification of scaffolds with highly promiscuous nuclear receptor profiles and to the classification of nuclear receptor groups with similar scaffold promiscuity patterns. This information can be exploited in the design of probing libraries for deorphanization activities as well as for devising screening batteries to address selectivity issues.

Combinatorial Chemistry Techniques↗

PubMedDate not supplied

I2Cnet medical image annotation service.

I2Cnet (Image Indexing by Content network) aims to provide services related to the content-based management of images in healthcare over the World-Wide Web. Each I2Cnet server maintains an autonomous repository of medical images and related information. The annotation service of I2Cnet allows specialists to interact with the contents of the repository, adding comments or illustrations to medical images of interest. I2Cnet annotations may be communicated to other users via e-mail or posted to I2Cnet for inclusion in its local repositories. This paper discusses the annotation service of I2Cnet and argues that such services pave the way towards the evolution of active digital medical image libraries.

Computer Communication Networks↗

PubMedDate not supplied

Stents. An annotated bibliography of selected references.

This is an annotated bibliography of selected references on stents. It includes 90 annotated references and 6 others that were not annotated. It has been structured to include pertinent details about each citation, including the site at which the device was used (coronary or peripheral), the type of article in which the research was reported (clinical paper, case report, abstract, review, editorial), the number of subjects and lesions treated, the design of the study (case study, single group, group comparison, or randomized trial), acute and late results, and comments about the study and its findings.

Coronary Disease↗