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At least 127 records · Page 7Linked to original sources
PubMed2002

Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns.

All protein sequences from 19 complete chloroplast genomes (cpDNA) have been studied using a new computational method able to analyze functional correlations among series of protein sequences contained in complete proteomes. First, all open reading frames (ORFs) from the cpDNAs, comprising a total of 2266 protein sequences, were compared against the 3168 proteins from Synechocystis PCC6803 complete genome to find functionally related orthologous proteins. Additionally, all cpDNA genomes were pairwise compared to find orthologous groups not present in cyanobacteria. Annotations in the cluster of othologous proteins database and CyanoBase were used as reference for the functional assignments. Following this protocol, new functional assignments were made for ORFs of unknown function and for ycfs (hypothetical chloroplast frames), which still lack a functional assignment. Using this information, a matrix of functional relationships was derived from profiles of the presence and/or absence of orthologous proteins; the matrix included 1837 proteins in 277 orthologous clusters. A factor analysis study of this matrix, followed by cluster analysis, allowed us to obtain accurate phylogenetic reconstructions and the detection of genes probably involved in speciation as phylogenetic correlates. Finally, by grouping common evolutionary patterns, we show that it is possible to determine functionally linked protein networks. This has allowed us to suggest putative associations for some unknown ORFs.

Bacterial Proteins↗
PubMed2006

Predicting Shine-Dalgarno sequence locations exposes genome annotation errors.

In prokaryotes, Shine-Dalgarno (SD) sequences, nucleotides upstream from start codons on messenger RNAs (mRNAs) that are complementary to ribosomal RNA (rRNA), facilitate the initiation of protein synthesis. The location of SD sequences relative to start codons and the stability of the hybridization between the mRNA and the rRNA correlate with the rate of synthesis. Thus, accurate characterization of SD sequences enhances our understanding of how an organism's transcriptome relates to its cellular proteome. We implemented the Individual Nearest Neighbor Hydrogen Bond model for oligo-oligo hybridization and created a new metric, relative spacing (RS), to identify both the location and the hybridization potential of SD sequences by simulating the binding between mRNAs and single-stranded 16S rRNA 3' tails. In 18 prokaryote genomes, we identified 2,420 genes out of 58,550 where the strongest binding in the translation initiation region included the start codon, deviating from the expected location for the SD sequence of five to ten bases upstream. We designated these as RS+1 genes. Additional analysis uncovered an unusual bias of the start codon in that the majority of the RS+1 genes used GUG, not AUG. Furthermore, of the 624 RS+1 genes whose SD sequence was associated with a free energy release of less than -8.4 kcal/mol (strong RS+1 genes), 384 were within 12 nucleotides upstream of in-frame initiation codons. The most likely explanation for the unexpected location of the SD sequence for these 384 genes is mis-annotation of the start codon. In this way, the new RS metric provides an improved method for gene sequence annotation. The remaining strong RS+1 genes appear to have their SD sequences in an unexpected location that includes the start codon. Thus, our RS metric provides a new way to explore the role of rRNA-mRNA nucleotide hybridization in translation initiation.

Base Sequence↗
PubMed2003

Network approaches to genome annotation and the challenge of Anopheles gambiae.

The rapid advancement of current sequencing projects has provided significant challenges for the swift and accurate processing, integration and analysis of biological data. Such challenges will only become greater as a new round of organisms, both well known and obscure, await sequencing and further study. While perhaps less well studied at the molecular level than Drosophila melanogaster, the recently sequenced mosquito, Anopheles gambiae, provides an example of what will be faced by many of these awaiting projects. This review presents a brief overview of some of the challenges associated with these future genome projects (including Anopheles) as well as a description of recent computational approaches that utilize genome context for the prediction of gene and/or protein function. Such approaches show promise not only for the study of Anopheles, but also in the study of biological processes in general.

Animals↗
PubMed2025

The extracellular vesicle transcriptome provides tissue-specific functional genomic annotation relevant to disease susceptibility in obesity.

We characterized circulating extracellular vesicles (EVs) in obese and lean humans, identifying transcriptional cargo differentially expressed in obesity (277 unique genes; false discovery rate < 10%). Since circulating EVs may have broad origin, we compared this obesity EV transcriptome with expression from human visceral-adipose-tissue-derived EVs from freshly collected and cultured biopsies from the same obese individuals, observing high concordance. Using a comprehensive set of adipose-specific epigenomic and chromatin conformation assays, we found that the differentially expressed transcripts from the EVs were those regulated in adipose by body mass index-associated SNPs (p < 5 &#xd7; 10-8) from a large-scale genome-wide association study (GWAS). Using a phenome-wide association study of the regulatory SNPs for the EV-derived transcripts, we identified a substantial enrichment for inflammatory phenotypes, including type 2 diabetes. Collectively, these findings represent the convergence of the GWAS (genetics), epigenomics (transcript regulation), and EV (liquid biopsy) fields, enabling powerful future genomic studies of complex diseases.

Humans↗
PubMed2004

Genomic annotation of the meningioma tumor suppressor locus on chromosome 1p34.

Meningioma is a frequently occurring tumor of the meninges surrounding the central nervous system. Loss of the short arm of chromosome 1 (1p) is the second most frequent chromosomal abnormality observed in these tumors. Previously, we identified a 3.7 megabase (Mb) region of consistent deletion on 1p33-p34 in a panel of 157 tumors. Loss of this region was associated with advanced disease and predictive for tumor relapse. In this report, a high-resolution integrated map of the region was constructed (CompView) to identify all markers in the smallest region of overlapping deletion (SRO). A regional somatic cell hybrid panel was used to more precisely localize those markers identified in CompView as within or overlapping the region. Additional deletion mapping using microsatellites localized to the region narrowed the SRO to approximately 2.8 Mb. The 88 markers remaining in the SRO were used to screen genomic databases to identify large-insert clones. Clones were assembled into a physical map of the region by PCR-based, sequence-tagged site (STS) content mapping. A sequence from clones was used to validate STS content by electronic PCR and to identify transcripts. A minimal tiling path of 43 clones was constructed across the SRO. Sequence data from the most current sequence assembly were used for further validation. A total of 59 genes were ordered within the SRO. In all, 17 of these were selected as likely candidates based on annotation using Gene Ontology Consortium terms, including the MUTYH, PRDX1, FOXD2, FOXE3, PTCH2, and RAD54L genes. This annotation of a putative tumor suppressor locus provides a resource for further analysis of meningioma candidate genes.

Chromosomes, Human, Pair 1↗
PubMed2003

Multi-species sequence comparison: the next frontier in genome annotation.

Multi-species comparisons of DNA sequences are more powerful for discovering functional sequences than pairwise DNA sequence comparisons. Most current computational tools have been designed for pairwise comparisons, and efficient extension of these tools to multiple species will require knowledge of the ideal evolutionary distance to choose and the development of new algorithms for alignment, analysis of conservation, and visualization of results.

Animals↗
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

Integrative bioinformatics for functional genome annotation: trawling for G protein-coupled receptors.

G protein-coupled receptors (GPCR) are amongst the best studied and most functionally diverse types of cell-surface protein. The importance of GPCRs as mediates or cell function and organismal developmental underlies their involvement in key physiological roles and their prominence as targets for pharmacological therapeutics. In this review, we highlight the requirement for integrated protocols which underline the different perspectives offered by different sequence analysis methods. BLAST and FastA offer broad brush strokes. Motif-based search methods add the fine detail. Structural modelling offers another perspective which allows us to elucidate the physicochemical properties that underlie ligand binding. Together, these different views provide a more informative and a more detailed picture of GPCR structure and function. Many GPCRs remain orphan receptors with no identified ligand, yet as computer-driven functional genomics starts to elaborate their functions, a new understanding of their roles in cell and developmental biology will follow.

Algorithms↗
PubMed2003

rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation.

The analysis of gene regulatory networks has become one of the most challenging problems of the postgenomic era. Earlier we developed rSNP_Guide (http://util.bionet.nsc.ru/databases/rsnp.html), a computer system and database devoted to prediction of transcription factor (TF) binding sites (TF sites), which can be responsible for disease phenotypes. The prediction results were confirmed by 70 known relationships between TF sites and diseases, as well as by site-directed mutagenesis data. The rSNP_Guide is being investigated as a tool for TF site annotation. Previously analyzed and characterized cases of altered TF sites were used to annotate potential sites of the same type and at the same location in homologous genes. Based on 20 TF sites with known alterations in TF binding to DNA, we localized 245 potential TF sites in homologous genes. For these potential TF sites, rSNP_Guide estimates TF-DNA interaction according to three categories: 'present', 'weak', and 'absent'. The significance of each assignment is statistically measured.

Binding Sites↗
PubMed2004

Whole-genome annotation by using evidence integration in functional-linkage networks.

The advent of high-throughput biology has catalyzed a remarkable improvement in our ability to identify new genes. A large fraction of newly discovered genes have an unknown functional role, particularly when they are specific to a particular lineage or organism. These genes, currently labeled "hypothetical," might support important biological cell functions and could potentially serve as targets for medical, diagnostic, or pharmacogenomic studies. An important challenge to the scientific community is to associate these newly predicted genes with a biological function that can be validated by experimental screens. In the absence of sequence or structural homology to known genes, we must rely on advanced biotechnological methods, such as DNA chips and protein-protein interaction screens as well as computational techniques to assign putative functions to these genes. In this article, we propose an effective methodology for combining biological evidence obtained in several high-throughput experimental screens and integrating this evidence in a way that provides consistent functional assignments to hypothetical genes. We use the visualization method of propagation diagrams to illustrate the flow of functional evidence that supports the functional assignments produced by the algorithm. Our results contain a number of predictions and furnish strong evidence that integration of functional information is indeed a promising direction for improving the accuracy and robustness of functional genomics.

Chromosome Mapping↗
PubMed1995

Human chromosome-specific cDNA libraries: new tools for gene identification and genome annotation.

To date, only a small percentage of human genes have been cloned and mapped. To facilitate more rapid gene mapping and disease gene isolation, chromosome 5-specific cDNA libraries have been constructed from five sources. DNA sequencing and regional mapping of 205 unique cDNAs indicates that 25 are from known chromosome 5 genes and 138 are from new chromosome 5 genes (a frequency of 79.5%). Sequence complexity estimates indicate that each library contains -20% of the approximately 5000 genes that are believed to reside on chromosome 5. This study more than doubles the number of genes mapped to chromosome 5 and describes an important new tool for disease gene isolation.

Base Sequence↗
PubMed2006

Chemosensory proteins in the honey bee: Insights from the annotated genome, comparative analyses and expressional profiling.

Small chemosensory proteins (CSPs) belong to a conserved, but poorly understood protein family that has been implicated in transporting chemical stimuli within insect sensilla. However, their expression patterns suggest that these molecules are also critical for other functions including early development. Here we used both bioinformatics and experimental approaches to characterize the CSP gene family in a social insect, the Western honey bee Apis mellifera, and then compared its members to CSPs in other arthropods. The number of CSPs in the honey bee genome (six) is similar to that found in the sequenced dipteran species (four-seven), but is much lower than the number of CSPs in the moth or in the beetle (around 20 each). These differences seem to be the result of lineage specific expansions. Our analysis of CSPs in a number of arthropods reveals a conserved gene family found in both Mandibulates and Chelicerates. Expressional profiling in diverse tissues and throughout development reveals broader than expected patterns of expression with none of the CSPs restricted to the antennae and one found only in the queen ovaries and in embryos. We conclude that CSPs are multifunctional context-dependent proteins involved in diverse cellular processes ranging from embryonic development to chemosensory signal transduction. Some CSPs may function in cuticle synthesis, consistent with their evolutionary origins in the arthropods.

Amino Acid Sequence↗
PubMed2005

Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge.

UNLABELLED: Centrifuge is a user-friendly system to simultaneously access Arabidopsis gene annotations and intra- and inter-organism sequence comparison data. The tool allows rapid retrieval of user-selected data for each annotated Arabidopsis gene providing, in any combination, data on the following features: predicted protein properties such as mass, pI, cellular location and transmembrane domains; SWISS-PROT annotations; Interpro domains; Gene Ontology records; verified transcription; BLAST matches to the proteomes of A.thaliana, Oryza sativa (rice), Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. The tool lends itself particularly well to the rapid analysis of contigs or of tens or hundreds of genes identified by high-throughput gene expression experiments. In these cases, a summary table of principal predicted protein features for all genes is given followed by more detailed reports for each individual gene. Centrifuge can also be used for single gene analysis or in a word search mode. AVAILABILITY: http://centrifuge.unil.ch/ CONTACT: edward.farmer@unil.ch.

Arabidopsis↗
PubMed2005

A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context.

An important step in understanding the regulation of a prokaryotic genome is the generation of its transcription unit map. The current strongest operon predictor depends on the distributions of intergenic distances (IGD) separating adjacent genes within and between operons. Unfortunately, experimental data on these distance distributions are limited to Escherichia coli and Bacillus subtilis. We suggest a new graph algorithmic approach based on comparative genomics to identify clusters of conserved genes independent of IGD and conservation of gene order. As a consequence, distance distributions of operon pairs for any arbitrary prokaryotic genome can be inferred. For E.coli, the algorithm predicts 854 conserved adjacent pairs with a precision of 85%. The IGD distribution for these pairs is virtually identical to the E.coli operon pair distribution. Statistical analysis of the predicted pair IGD distribution allows estimation of a genome-specific operon IGD cut-off, obviating the requirement for a training set in IGD-based operon prediction. We apply the method to a representative set of eight genomes, and show that these genome-specific IGD distributions differ considerably from each other and from the distribution in E.coli.

Algorithms↗
PubMed2001

Massive sequence comparisons as a help in annotating genomic sequences.

An all-by-all comparison of all the publicly available protein sequences from plants has been performed, followed by a clusterization process. Within each of the 1064 resulting clusters-containing sequences that are orthologous as well as paralogous-the sequences have been submitted to a pyramidal classification and their domains delineated by an automated procedure à la. This process provides a means for easily checking for any apparent inconsistency in a cluster, for example, whether one sequence is shorter or longer than the others, one domain is missing, etc. In such cases, the alignment of the DNA sequence of the gene with that of a close homologous protein often reveals (in 10% of the clusters) probable sequencing errors (leading to frameshifts) or probable wrong intron/exon predictions. The composition of the clusters, their pyramidal classifications, and domain decomposition, as well as our comments when appropriate, are available from http://chlora.infobiogen.fr:1234/PHYTOPROT.

Amino Acid Sequence↗
PubMed2003

An extensible application for assembling annotation for genomic data.

SUMMARY: AnnBuilder is an R package for assembling genomic annotation data. The system currently provides parsers to process annotation data from LocusLink, Gene Ontology Consortium, and Human Gene Project and can be extended to new data sources via user defined parsers. AnnBuilder differs from other existing systems in that it provides users with unlimited ability to assemble data from user selected sources. The products of AnnBuilder are files in XML format that can be easily used by different systems. AVAILABILITY: (http://www.bioconductor.org). Open source.

Database Management Systems↗
PubMed2002

SUPFAM--a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes.

Members of a superfamily of proteins could result from divergent evolution of homologues with insignificant similarity in the amino acid sequences. A superfamily relationship is detected commonly after the three-dimensional structures of the proteins are determined using X-ray analysis or NMR. The SUPFAM database described here relates two homologous protein families in a multiple sequence alignment database of either known or unknown structure. The present release (1.1), which is the first version of the SUPFAM database, has been derived by analysing Pfam, which is one of the commonly used databases of multiple sequence alignments of homologous proteins. The first step in establishing SUPFAM is to relate Pfam families with the families in PALI, which is an alignment database of homologous proteins of known structure that is derived largely from SCOP. The second step involves relating Pfam families which could not be associated reliably with a protein superfamily of known structure. The profile matching procedure, IMPALA, has been used in these steps. The first step resulted in identification of 1280 Pfam families (out of 2697, i.e. 47%) which are related, either by close homologous connection to a SCOP family or by distant relationship to a SCOP family, potentially forming new superfamily connections. Using the profiles of 1417 Pfam families with apparently no structural information, an all-against-all comparison involving a sequence-profile match using IMPALA resulted in clustering of 67 homologous protein families of Pfam into 28 potential new superfamilies. Expansion of groups of related proteins of yet unknown structural information, as proposed in SUPFAM, should help in identifying 'priority proteins' for structure determination in structural genomics initiatives to expand the coverage of structural information in the protein sequence space. For example, we could assign 858 distinct Pfam domains in 2203 of the gene products in the genome of Mycobacterium tubercolosis. Fifty-one of these Pfam families of unknown structure could be clustered into 17 potentially new superfamilies forming good targets for structural genomics. SUPFAM database can be accessed at http://pauling.mbu.iisc.ernet.in/~supfam.

Animals↗