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At least 811 records · Page 45Linked to original sources
PubMed2000

INE: a rice genome database with an integrated map view.

The Rice Genome Research Program (RGP) launched a large-scale rice genome sequencing in 1998 aimed at decoding all genetic information in rice. A new genome database called INE (INtegrated rice genome Explorer) has been developed in order to integrate all the genomic information that has been accumulated so far and to correlate these data with the genome sequence. A web interface based on Java applet provides a rapid viewing capability in the database. The first operational version of the database has been completed which includes a genetic map, a physical map using YAC (Yeast Artificial Chromosome) clones and PAC (P1-derived Artificial Chromosome) contigs. These maps are displayed graphically so that the positional relationships among the mapped markers on each chromosome can be easily resolved. INE incorporates the sequences and annotations of the PAC contig. A site on low quality information ensures that all submitted sequence data comply with the standard for accuracy. As a repository of rice genome sequence, INE will also serve as a common database of all sequence data obtained by collaborating members of the International Rice Genome Sequencing Project (IRGSP). The database can be accessed at http://www. dna.affrc.go.jp:82/giot/INE. html or its mirror site at http://www.staff.or.jp/giot/INE.html

Chromosomes, Artificial, Yeast↗
PubMed2005

Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters.

BACKGROUND: The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near future. Our objective was to produce extensive collections of ESTs and cDNA clones to support manufacture of cDNA microarrays and gene discovery in white spruce (Picea glauca [Moench] Voss). RESULTS: We produced 16 cDNA libraries from different tissues and a variety of treatments, and partially sequenced 50,000 cDNA clones. High quality 3' and 5' reads were assembled into 16,578 consensus sequences, 45% of which represented full length inserts. Consensus sequences derived from 5' and 3' reads of the same cDNA clone were linked to define 14,471 transcripts. A large proportion (84%) of the spruce sequences matched a pine sequence, but only 68% of the spruce transcripts had homologs in Arabidopsis or rice. Nearly all the sequences that matched the Populus trichocarpa genome (the only sequenced tree genome) also matched rice or Arabidopsis genomes. We used several sequence similarity search approaches for assignment of putative functions, including blast searches against general and specialized databases (transcription factors, cell wall related proteins), Gene Ontology term assignation and Hidden Markov Model searches against PFAM protein families and domains. In total, 70% of the spruce transcripts displayed matches to proteins of known or unknown function in the Uniref100 database (blastx e-value < 1e-10). We identified multigenic families that appeared larger in spruce than in the Arabidopsis or rice genomes. Detailed analysis of translationally controlled tumour proteins and S-adenosylmethionine synthetase families confirmed a twofold size difference. Sequences and annotations were organized in a dedicated database, SpruceDB. Several search tools were developed to mine the data either based on their occurrence in the cDNA libraries or on functional annotations. CONCLUSION: This report illustrates specific approaches for large-scale gene discovery and annotation in an organism that is very distantly related to any of the fully sequenced genomes. The ArboreaSet sequences and cDNA clones represent a valuable resource for investigations ranging from plant comparative genomics to applied conifer genetics.

Arabidopsis↗
PubMed1999

Fidelity probes for DNA arrays.

One current approach to quality control in DNA array manufacturing is to synthesize a small set of test probes that detect variation in the manufacturing process. These fidelity probes consist of identical copies of the same probe, but they are deliberately manufactured using different steps of the manufacturing process. A known target is hybridized to these probes, and those hybridization results are indicative of the quality of the manufacturing process. It is not only desirable to detect variations, but also to analyze the variations that occur, indicating in what process step the manufacture changed. We describe a combinatorial approach which constructs a small set of fidelity probes that not only detect variations, but also point out the manufacturing step in which a variation has occurred. This algorithm is currently being used in mass-production of DNA arrays at Affyetrix.

Algorithms↗
PubMed2005

Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data.

BACKGROUND: Commercial microarray scanners and software cannot distinguish between spectrally overlapping emission sources, and hence cannot accurately identify or correct for emissions not originating from the labeled cDNA. We employed our hyperspectral microarray scanner coupled with multivariate data analysis algorithms that independently identify and quantitate emissions from all sources to investigate three artifacts that reduce the accuracy and reliability of microarray data: skew toward the green channel, dye separation, and variable background emissions. RESULTS: Here we demonstrate that several common microarray artifacts resulted from the presence of emission sources other than the labeled cDNA that can dramatically alter the accuracy and reliability of the array data. The microarrays utilized in this study were representative of a wide cross-section of the microarrays currently employed in genomic research. These findings reinforce the need for careful attention to detail to recognize and subsequently eliminate or quantify the presence of extraneous emissions in microarray images. CONCLUSION: Hyperspectral scanning together with multivariate analysis offers a unique and detailed understanding of the sources of microarray emissions after hybridization. This opportunity to simultaneously identify and quantitate contaminant and background emissions in microarrays markedly improves the reliability and accuracy of the data and permits a level of quality control of microarray emissions previously unachievable. Using these tools, we can not only quantify the extent and contribution of extraneous emission sources to the signal, but also determine the consequences of failing to account for them and gain the insight necessary to adjust preparation protocols to prevent such problems from occurring.

Algorithms↗
PubMed2006

AMarge: Automated Extensive Quality Assessment of Affymetrix chips.

UNLABELLED: AMarge is a web tool for the automatic quality assessment of Affymetrix GeneChip data. It is essential to have a trustworthy set of chips in order to derive gene expression data for phenotypic analysis, and AMarge provides a complete and rigorous web-accessible tool to fulfill this need. The quality assessment steps include image plots of weights derived from a robust linear model fit of the data, a 3'/5' RNA digestion plot, and Affymetrix Microarray Suite version 5.0 (MAS 5.0) quality standard procedures. Furthermore, robust multi-array average expression values are generated in order to have a start-up expression set for the subsequent analysis. The results of the complete analysis are summarised and returned as an HTML report. AVAILABILITY: The AMarge web interface is accessible at http://nin.crg.es/cgi-binf/AMargeWeb.cgi. A mirror server is also available at http://bioinformatics.istge.it/AMarge-bin/AMargeWeb.cgi. The software implementing all these methods is part of the Bioconductor project (http://www.bioconductor.org).

Algorithms↗
PubMed2004

OLIN: optimized normalization, visualization and quality testing of two-channel microarray data.

UNLABELLED: Microarray data are generated in complex experiments and frequently compromised by a variety of systematic errors. Subsequent data normalization aims to correct these errors. Although several normalization methods have recently been proposed, they frequently fail to account for the variability of systematic errors within and between microarray experiments. However, optimal adjustment of normalization procedures to the underlying data structure is crucial for the efficiency of normalization. To overcome this restriction of current methods, we have developed two normalization schemes based on iterative local regression combined with model selection. The schemes have been demonstrated to improve considerably the quality of normalization. They are implemented in a freely available R package. Additionally, functions for visualization and detection of systematic errors in microarray data have been incorporated in the software package. A graphical user interface is also available. AVAILABILITY: The R package can be downloaded from http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN. It underlies the GPL version 2. CONTACT: m.futschik@biologie.hu-berlin.de SUPPLEMENTARY INFORMATION: Further information about the methods used in the OLIN software package can be found at http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN.

Algorithms↗
PubMed2006

Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project.

Microarray-based expression profiling experiments typically use either a one-color or a two-color design to measure mRNA abundance. The validity of each approach has been amply demonstrated. Here we provide a simultaneous comparison of results from one- and two-color labeling designs, using two independent RNA samples from the Microarray Quality Control (MAQC) project, tested on each of three different microarray platforms. The data were evaluated in terms of reproducibility, specificity, sensitivity and accuracy to determine if the two approaches provide comparable results. For each of the three microarray platforms tested, the results show good agreement with high correlation coefficients and high concordance of differentially expressed gene lists within each platform. Cumulatively, these comparisons indicate that data quality is essentially equivalent between the one- and two-color approaches and strongly suggest that this variable need not be a primary factor in decisions regarding experimental microarray design.

Equipment Design↗
PubMed2005

Mitochondrial DNA error prophylaxis: assessing the causes of errors in the GEP'02-03 proficiency testing trial.

We report the results of the Spanish and Portuguese working group (GEP) of the International Society for Forensic Genetics (ISFG) Collaborative Exercise 2002-2003 on mitochondrial DNA (mtDNA) analysis. Six different samples were submitted to the participating laboratories: four blood stains (M1-M2-M3-M4), one mixture blood sample (M5), and two hair shaft fragments (M6). Most of the labs reported consensus results for the blood stains, slightly improving the results of previous collaborative exercises. Although hair shaft analysis is still carried out by a small number of laboratories, this analysis yielded a high rate of success. On the contrary, the analysis of the mixture blood stain (M5) yielded a lower rate of success; in spite of this, the whole results on M5 typing demonstrated the suitability of mtDNA analysis in mixture samples. We have found that edition errors are among the most common mistakes reported by the different labs. In addition, we have detected contamination events as well as other minor problems, i.e. lack of standarization in nomenclature for punctual and length heteroplasmies, and indels. In the present edition of the GEP-ISFG exercise we have paid special attention to the visual phylogenetic inspection for detecting common sequencing errors.

Blood Stains↗
PubMed1997

Insulin lispro: a review of its pharmacological properties and therapeutic use in the management of diabetes mellitus.

Insulin lispro, a recombinant insulin analogue, is identical to human insulin except for the transposition of proline and lysine at positions 28 and 29 in the C-terminus of the B chain. The resultant reduced capacity for self-association in solution translates into more rapid absorption of insulin lispro than human regular insulin from subcutaneous sites. Maximum insulin concentrations are higher and are reached earlier with insulin lispro than with human regular insulin, and insulin concentrations return to baseline values more quickly with insulin lispro; consequently, insulin lispro has a more rapid onset and a shorter duration of glucose-lowering activity. These pharmacological properties provided the rationale for comparative clinical trials of subcutaneous insulin lispro (administered within 15 minutes before meals, preferably immediately before meals) and subcutaneous human regular insulin (administered 20 to 45 minutes before meals) in patients with type 1 diabetes (insulin-dependent diabetes mellitus) or type 2 diabetes (non-insulin-dependent diabetes mellitus) requiring premeal insulin therapy plus basal insulin therapy. Available clinical trials are well designed and results suggest that 1- and 2-hour postprandial blood glucose levels with insulin lispro are similar to or lower than those with human regular insulin; 1- and 2-hourpostprandial glucose excursions are similar to or less pronounced than those with human regular insulin. Glycated haemoglobin A values were generally similar with both agents. Continuous subcutaneous insulin infusion was associated with greater improvements in postprandial blood glucose levels and glycated haemoglobin A1 values with insulin lispro than with human regular insulin. Confirmatory data are required. The incidence of hypoglycaemia with insulin lispro was similar to or lower than that with human regular insulin. In particular insulin lispro appears to be associated with a lower incidence of night-time and severe hypoglycaemic episodes. Evidence also suggests that patients perceive their quality of life to be improved with insulin lispro compared with human regular insulin, and that satisfaction with treatment is greater with the insulin analogue. Thus, in patients with type 1 or 2 diabetes requiring premeal insulin therapy, insulin lispro appears to provide greater postprandial glycaemic control than human regular insulin without increasing the risk of hypoglycaemia. Furthermore, the reduced injection-meal interval with this agent offers greater convenience for the patient than regular human insulin. If longer term clinical experience supports these promising results it is likely that insulin lispro will offer important advantages over human regular insulin.

Amino Acid Sequence↗
PubMed1988

The development of the individuation process from a social-cognitive perspective.

A sequence of four developmental levels for the individuation process, from a social-cognitive perspective, was proposed from late childhood to late adolescence. Individuation is defined as the separation of the self from family. The individuation interview, Selman's self-awareness measure and the Lunzer test were administered in 4th, 7th, 10th grades and a post-high school group (N = 78). Results confirmed age increases in individuation as follows: late childhood subjects consolidate on level I, exhibiting the dominance of parental view over individual perspectives; early adolescents on level 2, demonstrating an increased self-awareness and the beginning decline of parental view; mid-adolescents, on level 3, characterized by conflicts between the recognition of the autonomous self and the parental views; and late adolescents (young adults) on level 3 and level 4, showing the ability to integrate the parental view within the self-system without losing individuality. Further, construct validation confirmed the common as well as the discriminant qualities of the individuation sequence to self-awareness and Piagetian logical development. These results support the uniqueness of the individuation construct within the social-cognitive domain.

Adolescent↗
PubMed2001

ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information.

Experimental approaches for the identification of functionally important regions on the surface of a protein involve mutagenesis, in which exposed residues are replaced one after another while the change in binding to other proteins or changes in activity are recorded. However, practical considerations limit the use of these methods to small-scale studies, precluding a full mapping of all the functionally important residues on the surface of a protein. We present here an alternative approach involving the use of evolutionary data in the form of multiple-sequence alignment for a protein family to identify hot spots and surface patches that are likely to be in contact with other proteins, domains, peptides, DNA, RNA or ligands. The underlying assumption in this approach is that key residues that are important for binding should be conserved throughout evolution, just like residues that are crucial for maintaining the protein fold, i.e. buried residues. A main limitation in the implementation of this approach is that the sequence space of a protein family may be unevenly sampled, e.g. mammals may be overly represented. Thus, a seemingly conserved position in the alignment may reflect a taxonomically uneven sampling, rather than being indicative of structural or functional importance. To avoid this problem, we present here a novel methodology based on evolutionary relations among proteins as revealed by inferred phylogenetic trees, and demonstrate its capabilities for mapping binding sites in SH2 and PTB signaling domains. A computer program that implements these ideas is available freely at: http://ashtoret.tau.ac.il/ approximately rony

Algorithms↗
PubMed1999

Reversed-phase high-performance liquid chromatographic assay for the adenovirus type 5 proteome.

An RP-HPLC assay was developed for a recombinant adenovirus type 5. During chromatography, intact adenovirus dissociated into its structural components (DNA and proteins) and the viral proteome was separated yielding a characteristic fingerprint. The individual components were identified by matrix-assisted laser desorption ionization time-of-flight mass spectroscopy, N-terminal sequencing and amino acid composition. The assay was utilized to measure adenovirus particle concentration through quantification of structural proteins. Each structural protein provided independent measurement of virus concentration allowing verification of accuracy. The assay sensitivity is at or below 2 x 10(8) particles. Contrary to the benchmark spectrophotometric assay, the RP-HPLC assay was shown to be insensitive to contaminants common for partially purified adenovirus preparations.

Adenoviruses, Human↗
PubMed2002

MArray: analysing single, replicated or reversed microarray experiments.

UNLABELLED: MArray is a Matlab toolbox with a graphical user interface that allows the user to analyse single or paired microarray datasets by direct input of the raw data output file from image analysis packages, such as QuantArray or GenePiX. The application provides simple procedures to manually evaluate the quality of each measurement, multiple approaches to both ratio normalization (simple normalization, intensity dependent normalization) and evaluation of the reproducibility of paired experiments (using the techniques 'simple statistical method' and 'quality control ellipse' and 'significance analysis of microarrays'). Specifically, interactive spot evaluation functions are available in MArray and an online gene information database (NCBI UniGene) is linked. The application may provide a valuable aid in selecting and optimizing experimental procedures, as well as serving as an analytical tool for two-state biological comparisons, such as a study of single-dose activation. It is entirely platform independent, and only requires Matlab installed. AVAILABILITY: http://matrise.uio.no/marray/marray.html

Computer Graphics↗
PubMed2006

The Gene Ontology (GO) project in 2006.

The Gene Ontology (GO) project (http://www.geneontology.org) develops and uses a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://song.sourceforge.net/). The GO Consortium continues to improve to the vocabulary content, reflecting the impact of several novel mechanisms of incorporating community input. A growing number of model organism databases and genome annotation groups contribute annotation sets using GO terms to GO's public repository. Updates to the AmiGO browser have improved access to contributed genome annotations. As the GO project continues to grow, the use of the GO vocabularies is becoming more varied as well as more widespread. The GO project provides an ontological annotation system that enables biologists to infer knowledge from large amounts of data.

Database Management Systems↗
PubMed2005

Simultaneous measurement of gene expression for hepatotoxicity in thioacetamide-administered rats by DNA microarrays.

DNA microarray technology was developed as a tool for simultaneously measuring a number of gene expression changes, and has been applied for investigations of toxicity assessments of chemicals. In this study, we used a typical hepatotoxicant, thioacetamide (TA), to find correlations between the extent of hepatotoxicity and certain gene expression patterns or specific gene expression profiles. TA was intraperitoneally administered at high (400 mg/kg), medium (150 mg/kg) or low (50 mg/kg) dose (four rats per group) and then the serum and liver were collected at the indicated time (6, 12, 24, 36 and 48 h). Serum biochemical markers were measured and hepatic mRNA expression profiles were analyzed by a DNA microarray. Serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were increased by TA-administration in a dose-dependent manner and reached the maximum at 24h. Hierarchical clustering analysis of all dosage groups revealed in 2 major clusters, distinguished by an early (6 and 12h) and a late (24, 36 and 48 h) phase. The early and late phase clusters were sorted in time- and dose-dependent manners. The major gene expression profile obtained by quality-threshold (QT) clustering analysis showed the same maximal toxic time as that estimated by the serum biochemical markers. The individual expression profiles of the candidate genes selected in our previous studies and the simultaneous gene expression patterns measured by five typical hepatotoxicants including TA also reflected the hepatotoxicity of TA. These findings suggest that the potential toxic effects appearing as gene expression changes are independent of the dosage of TA. This study suggested that the major gene expression profile estimated by QT clustering would be a sensitive marker of hepatotoxicity.

Alanine Transaminase↗
PubMed2005

OligoFaktory: a visual tool for interactive oligonucleotide design.

SUMMARY: The OligoFaktory is a set of tools for the design, on an arbitrary number of target sequences, of high-quality long oligonucleotide for micro-array, of primer pair for PCR, of siRNA and more. The user-centered interface exists in two flavours: a web portal and a standalone software for Mac OS X Tiger. A unified presentation of results provides overviews with distribution charts and relative location bar graphs, as well as detailed features for each oligonucleotide. Input and output files conform to a common XML interchange file format to allow both automatic generation of input data, archiving, and post-processing of results. The design pipeline can use BLAST servers to evaluate specificity of selected oligonucleotides. AVAILABILITY: The web portal http://ueg.ulb.ac.be/oligofaktory/; the software for Macintosh: http://www.oligofaktory.org/

Algorithms↗
PubMed2026

Protein Language Model Decoys for Target Decoy Competition in Proteomics: Quality Assessment and Benchmarks.

Large-scale proteomics relies heavily on target-decoy competition for false discovery rate estimation in peptide identification, and the performance of this strategy depends strongly on the design of the decoy database. Classical generators such as reversal and shuffling remain widely used. Here, we introduce the first protein language model-based (PLM) decoy generation for peptide identification and benchmark it against classical strategies. We evaluate these approaches using three complementary quality-control layers: sequence-based separability, search-engine-agnostic spectral-space diagnostics, and end-to-end mass spectrometry benchmarks, including pipelines with rescoring. Across these analyses, PLM-based decoys are harder for sequence-only neural networks to distinguish than most classical generators, suggesting fewer obvious sequence-level artifacts. However, this signal is only weakly informative for search performance. Spectral diagnostics further show that short peptides occupy a particularly crowded target-decoy space and are therefore especially prone to local collisions across all generators. In full search pipelines, reverse decoys remain a strong baseline, and current PLM-based generators do not yet provide a clear overall advantage. We therefore view PLM-based decoys not as universal replacements for reverse decoys but as tunable tools for benchmarking, diagnostics, stress testing, and future adaptive decoy optimization, with increasing value as search models become more expressive.

Proteomics↗
PubMed2004

[Sequencing and analyzing of expressed sequence tags (ESTs) of pig fat tissue].

In this paper,the ESTs of pig fat tissue were sequenced and analyzed using the large-scale DNA sequencing method, 7790 high quality ESTs were gained,from which 4354 genes were obtained using cluster analysis with the STACK-PACK software, including 3609 singlet genes and 745 multicopy genes. The 4354 candidate genes were compared with BLASTN to the nr library (e =1e-10), of which 2712 were known genes, containing 1 987 singlet genes and 725 multicopy genes,there are 2 109 unknown genes and new ESTs. Based on the results of BlastN and the index of GenBank Accenssion No., the known gene expression profile of pig fat were constructed. It showed that the genes participating in metabolism held the highest proportion in the 7 sorts, and in some aspects showed the hearty metabolism activity of fat tissue. 257 total reads of the Major Histocompatibility Complex (MHC) genes in the pig fat tissue were found,including 181 singlet genes and 44 multicopy genes. They account for 44.9% of the cell and organism defense, and 5.4% of all known genes,from this we can see that the MHC has a fairly high expression degree. Comparing all ESTs related with MHC (257reads) with known pig BAC we found the partial sequences (approximately 200 bp) of the ESTs distributing to every exon of. We can predict that the ESTs in MHC contain approximately 200 bp highly consistent regions and every exon possesses one of these regions. Although these MHC sequences in different BAC have different protein domains,they are highly consistent and related with immune functions. When the MHC genes transfer to the next generation,they can duplicate repeatly and inherit stably.

Adipose Tissue↗