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Results for “differential analysis”

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At least 307 records · Page 17Linked to original sources
PubMed2005

[Methods of statistical analysis in differential diagnostics of the degree of brain glioma anaplasia during preoperative stage].

The authors proposed a possible preoperative diagnostics of the degree of supratentorial brain gliom anaplasia using statistical analysis methods. It relies on a complex examination of 934 patients with I-IV degree anaplasias, which had been treated in the Institute of Neurosurgery from 1990 to 2004. The use of statistical analysis methods for differential diagnostics of the degree of brain gliom anaplasia may optimize a diagnostic algorithm, increase reliability of obtained data and in some cases avoid carrying out irrational operative intrusions. Clinically important signs for the use of statistical analysis methods directed to preoperative diagnostics of brain gliom anaplasia have been defined

Adult↗
PubMed2006

ADGO: analysis of differentially expressed gene sets using composite GO annotation.

MOTIVATION: Genes are typically expressed in modular manners in biological processes. Recent studies reflect such features in analyzing gene expression patterns by directly scoring gene sets. Gene annotations have been used to define the gene sets, which have served to reveal specific biological themes from expression data. However, current annotations have limited analytical power, because they are classified by single categories providing only unary information for the gene sets. RESULTS: Here we propose a method for discovering composite biological themes from expression data. We intersected two annotated gene sets from different categories of Gene Ontology (GO). We then scored the expression changes of all the single and intersected sets. In this way, we were able to uncover, for example, a gene set with the molecular function F and the cellular component C that showed significant expression change, while the changes in individual gene sets were not significant. We provided an exemplary analysis for HIV-1 immune response. In addition, we tested the method on 20 public datasets where we found many 'filtered' composite terms the number of which reached approximately 34% (a strong criterion, 5% significance) of the number of significant unary terms on average. By using composite annotation, we can derive new and improved information about disease and biological processes from expression data. AVAILABILITY: We provide a web application (ADGO: http://array.kobic.re.kr/ADGO) for the analysis of differentially expressed gene sets with composite GO annotations. The user can analyze Affymetrix and dual channel array (spotted cDNA and spotted oligo microarray) data for four species: human, mouse, rat and yeast. CONTACT: chu@kribb.re.kr SUPPLEMENTARY INFORMATION: http://array.kobic.re.kr/ADGO.

Algorithms↗
PubMed2005

Proteomic profiling for cancer progression: Differential display analysis for the expression of intracellular proteins between regressive and progressive cancer cell lines.

Tumor development and progression consist of a series of complex processes involving multiple changes in gene expression (Paolo et al. Physiol. Rev., 1993, 73, 161-195; Lance et al. Cell., 1991, 64, 327-336). Tumor cells acquire an invasive and metastatic phenotype that is the main cause of death for cancer patients. Therefore, for early diagnosis and effective therapeutic intervention, we need to detect the alterations associated with transition from benign to malignant tumor cells on a molecular basis. To unravel alterations concerned with tumor progression, the proteomic approach has attracted great attention because it can identify qualitative and quantitative changes in protein composition, including post-translational modifications. In this study, we performed proteomic differential display analysis for the expression of intracellular proteins in the regressive cancer cell line QR-32 and the inflammatory cell-promoting progressive cancer cell line QRsP-11 of murine fibrosarcoma by two-dimensional gel electrophoresis and mass spectrometry using an Agilent 1100 LC/MSD Trap XCT. We found 11 protein spots whose expression was different between QR-32 and QRsP-11 cells and identified nine proteins, seven of which, calreticulin precursor, tropomyosin 1 alpha chain, annexin A5, heat shock protein (HSP)90-alpha, HSP90-beta, PEBP, and Prx II, were over-expressed, and two, Anp32e and HDGF, which were down-regulated. The results suggest an important complementary role for proteomics in identification of molecular abnormalities in tumor progression.

Animals↗
PubMed2005

Characterization of pollen tube development in Pinus strobus (Eastern white pine) through proteomic analysis of differentially expressed proteins.

The differentially expressed proteins in pollen tubes indicate their specific roles in this stage of male gametophyte development. To isolate these proteins, 2-DE was done using ungerminated pollen and 2-day-old pollen tubes of Pinus strobus. Results show that 645 and 647 protein spots were clearly resolved from pollen grains and pollen tubes, respectively. Thirty-eight protein spots were expressed only in pollen tubes, while 19 increased in intensity. MALDI-TOF MS was used to generate tryptic peptide masses that were submitted to Mascot for identification. Of the differentially expressed proteins, 12% matched with hypothetical proteins, 33% did not hit any protein, and for the 55%, a putative function was assigned based on similarity of sequences with previously characterized proteins. Therefore, pollen tube development can be characterized by the cellular activities that involve metabolism, stress/defense response, gene regulation, signal transduction, and cell wall formation. This study expands our understanding of the changes in protein expression associated with pollen tube development and provides insights into the molecular programs that separate the development of the pollen tubes from pollen grains. This is the first report that describes a global analysis of differentially expressed proteins from the pollen tube of any seed plant.

Cell Wall↗
PubMed1999

Long-term analysis of differentiation in human myoblasts repopulated with mitochondria harboring mtDNA mutations.

Short-term analysis of myogenesis in respiration-deficient myoblasts demonstrated that respiratory chain dysfunction impairs muscle differentiation. To investigate long-term consequences of a deficiency in oxidative phosphorylation on myogenesis, we quantitated myoblast fusion and expression of sarcomeric myosin in respiration-deficient myogenic cybrids. We produced viable myoblasts harboring exclusively mtDNA with large-scale deletions by treating wild-type myoblasts with rhodamine 6G and fusing them with cytoplasts homoplasmic for two different mutated mtDNAs. Recovery of growth in transmitochondrial myoblasts demonstrated that respiratory chain function is not required for recovery of rhodamine 6G-treated cells. Both transmitochondrial respiration-deficient cultures exhibited impaired myoblast fusion. Expression of sarcomeric myosin was also delayed in deficient myoblasts. However, 4 weeks after induction of differentiation, one cell line was able to quantitatively recover its capacity to form postmitotic muscle cells. This indicates that while oxidative phosphorylation is an important source of ATP for muscle development, myoblast differentiation can be supported entirely by glycolysis.

Biomarkers↗
PubMed2007

Genetic network and pathway analysis of differentially expressed proteins during critical cellular events in fracture repair.

Bone repair consists of inflammation, intramembranous ossification, chondrogenesis, endochondral ossification, and remodeling. To better understand the translational regulation of these distinct but interrelated cellular events, we used the second generation of BD Clontechtrade mark Antibody Microarray to dissect and functionally characterize proteins differentially expressed between intact and fractured rat femur at each of these cellular events. Genetic network analysis showed that proteins differentially expressed within a given cellular event tend to be physically or functionally correlated. Seventeen such interacting networks were established over five cellular events that were most frequently associated with cell cycle, cell death, cell-to-cell signaling and interaction, and cell growth and proliferation. Eighteen molecular pathways were significantly enriched during the bone repair process, of which ERK/MAPK, NF-kB, PDGF, and T-cell receptor signaling pathways were significant during three or more cellular events. The analyses revealed dynamic temporal expression patterns and cellular-event-specific functions. The inflammation event on Day 1 was characteristic of the cell cycle-related molecular changes. The relative quiet stage of intramembranous ossification on Day 4 and the molecularly most active stage of chondrogenesis on Day 7 were featured by coordinated cell death and cell-proliferation signals. Endochondral ossification on Day 14 experienced a clear transition from the molecular/cellular function to the physiological system development/function. The osteoclast-mediated remodeling on Day 28 was highlighted by the integrin signaling pathway. The distinct changes in protein expression during these cellular events provide a molecular basis for developing cellular event-targeted therapeutic strategy to accelerate bone healing.

Animals↗
PubMed1993

Rapid quantitative analysis of differential PCR products by high-performance liquid chromatography.

We describe the use of high-performance liquid chromatography (HPLC) for the rapid quantitative analysis of short DNA fragments generated in differential PCR, where a target gene and a control gene are in vitro coamplified in one single reaction. Using an anion-exchange nonporous column, both separation and quantitation of the differential PCR products are achieved in about 5 min per sample. The performance of this technique proved to be superior to that of conventional gel electrophoresis and subsequent analysis by a laser densitometer, a solid-state scanner and a charge coupled device video camera imaging system. The usefulness for clinical testing is described in the example of the quantitative analysis of the c-erbB-2 oncogene copy number of human breast carcinomas by differential PCR. The combined use of differential PCR and automated HPLC analysis of the PCR products may well substitute for classical Southern blot hybridization in routine clinical analysis of oncogene amplification.

Base Sequence↗
PubMed2004

Gene expression profile of human bone marrow stromal cells determined by restriction fragment differential display analysis.

Using an in vitro osteogenic culture system, we carried out a restriction fragment differential display (RFDD-PCR) to identify genes expressed by these cells in their undifferentiated stage and not expressed, or expressed at a lower level, in a closely related but distinct cell type: bone marrow stromal cells (BMSC)-derived osteoblasts (BDO). Forty-seven candidate regulated genes, selected by RFDD, were analyzed by RT-PCR analysis in three cell clones and in primary cultures from seven different donors. A subset of three genes were confirmed as upregulated in BMSC relative to BDO in every primary culture and cloned population examined: betaIG-h3, IGFbp3, and LOXL2. Their differential expression was confirmed by Northern analysis and the corresponding proteins were detected by immunolocalization in BMSC.

Adolescent↗
PubMed1991

The F9-EC cell line as a model for the analysis of differentiation.

The teratocarcinoma stem cell line F9 has been widely used as a model for the analysis of molecular mechanisms associated with differentiation. This cell line has been considered to be nullipotent and able to differentiate into endodermal-like derivatives upon treatment with retinoic acid. Nevertheless, under definite culture conditions, F9 cells are able to differentiate into derivatives of all three germ layers. The F9 cells express characteristics of early mouse embryonal cells and possess all repression factors known to be present in cells of the early mouse embryogenesis. Induction of differentiation can be achieved not only by adding chemical agents to the culture medium but also by transfection of several oncogenic sequences. In somatic cell genetic experiments, immortalized, differentiated F9-like cells have been shown to express dominantly genes responsible for the appearance of the differentiated phenotype.

Animals↗
PubMed1998

Differential genome analysis of bacteria by genomic subtractive hybridization and pulsed field gel electrophoresis.

A comprehensive analysis of the differences between the genomes of two closely related bacterial strains should give insight into the molecular basis of their individual phenotypic and genotypic characteristics. Here we present an integrative approach including two different strategies for the thorough investigation of genomic divergence. We have combined two techniques including genomic subtractive hybridization and comparative genome mapping by pulsed field gel electrophoresis (PFGE) techniques. The subtractive method for which a protocol is given herein results in the production of a library of specific DNA sequence tags present only in one strain, while the construction of macrorestriction maps of the bacterial chromosomes yields data about the overall genome organization and the arrangement and distance of gene loci. Comparison of the physical and genetic maps and determination of the map positions of the strain-specific DNA sequences reveals gross chromosomal modifications, insertions or deletions of additional genetic material, and transpositional events. The further investigation of the strain-specific regions yields information about the nature and origin of the acquired DNA and their influence on the evolution of the individual bacterial genome. The two methods were applied to differential genome analysis of clonal divergence in Pseudomonas aeruginosa choosing two clone C isolates from diverse habitats.

Chromosomes, Bacterial↗
PubMedDate not supplied

Differentiated DNA analysis in relation to steroid receptor status, grading, and staging in human breast cancer.

Flow cytometric DNA analysis was performed in 100 cases of human breast cancer. Using a category system of six ploidy groups, ploidy status was distributed as follows: The majority of the neoplasias were either diploid (45%), hyperdiploid (21%), or tetraploid (15%), whereas the remaining marginal ploidy groups, i.e. hypodiploid (4%), hypertetraploid (9%), and multiploid (6%) were less frequent. In an attempt to evaluate the prognostic significance of DNA content, ploidy status was correlated with steroid hormone receptor status, histopathological grade, and TNM data. The higher incidence of negative estrogen and progestin receptor status and higher histopathological grade in hyperdiploid malignancies was significantly different from the prognostically more favorable positive receptor status and lower grade in diploid tumors. Tetraploid neoplasias statistically resembled the latter group with respect to both parameters. As far as TNM data are concerned, tendencies towards less favorable staging were observed in hyperdiploid as compared to diploid and tetraploid tumors. A definite statement of the prognostic significance of the marginal ploidy groups cannot be made at present. In order to characterize diploid malignancies more closely, proliferative activity expressed by %S-phase was analyzed. Steroid receptor status of diploid tumors exhibiting more than 6% S-phase did not differ statistically from that of hyperdiploid neoplasias. In contrast, diploid tumors expressing less than 6% S-phase closely resembled tetraploid ones. Our data emphasize the prognostic significance of differentiated DNA analysis.

Breast Neoplasms↗
PubMed2026

DiaReport: reproducible workflow for differential expression analysis and interactive reporting in DIA-based proteomics.

MOTIVATION: Data-independent acquisition (DIA) has become the preferred data acquisition method for mass spectrometry-based proteomics, yet, reproducible workflows for differential expression (DE) analysis and results reporting remain limited. We present DiaReport, an R package that performs precursor- and protein-level DE analysis from DIA-NN output using MSqRob and QFeatures, while generating high-quality, interactive HTML reports through Quarto. DiaReport integrates precursor data, filtering of missing values, normalization, protein summarization and statistical modeling within a single function, supporting both simple pairwise as well as complex experimental designs. The package provides structured outputs and configuration files to ensure computational reproducibility across different studies. To accommodate diverse research needs, DiaReport includes multiple reporting templates tailored to different proteomic applications. Applying DiaReport to an extracellular vesicle (EV) proteomics dataset demonstrates its ability to efficiently analyze DIA data and provide rapid insights into sample quality and protein level differences. AVAILABILITY: DiaReport is an open-source R package available at https://github.com/Gevaert-Lab/diareport (DOI: 10.5281/zenodo.20120604). The package is platform-independent and distributed under the MIT license. Reports are generated using Quarto and require only standard R dependencies. Detailed documentation, installation guides and usage vignettes are provided within the repository. The interactive HTML reports discussed in this study, including the UPS2 benchmark and EV case study, are archived on Zenodo (10.5281/zenodo.20122506 and 10.5281/zenodo.20123378).

Proteomics↗
PubMedDate not supplied

Quantitative proteome analysis using differential stable isotopic labeling and microbore LC-MALDI MS and MS/MS.

We demonstrate an approach for global quantitative analysis of protein mixtures using differential stable isotopic labeling of the enzyme-digested peptides combined with microbore liquid chromatography (LC) matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS). Microbore LC provides higher sample loading, compared to capillary LC, which facilitates the quantification of low abundance proteins in protein mixtures. In this work, microbore LC is combined with MALDI MS via a heated droplet interface. The compatibilities of two global peptide labeling methods (i.e., esterification to carboxylic groups and dimethylation to amine groups of peptides) with this LC-MALDI technique are evaluated. Using a quadrupole-time-of-flight mass spectrometer, MALDI spectra of the peptides in individual sample spots are obtained to determine the abundance ratio among pairs of differential isotopically labeled peptides. MS/MS spectra are subsequently obtained from the peptide pairs showing significant abundance differences to determine the sequences of selected peptides for protein identification. The peptide sequences determined from MS/MS database search are confirmed by using the overlaid fragment ion spectra generated from a pair of differentially labeled peptides. The effectiveness of this microbore LC-MALDI approach is demonstrated in the quantification and identification of peptides from a mixture of standard proteins as well as E. coli whole cell extract of known relative concentrations. It is shown that this approach provides a facile and economical means of comparing relative protein abundances from two proteome samples.

Chromatography, High Pressure Liquid↗
PubMedDate not supplied

Proteomic analysis of differential protein expression in atherosclerosis.

Although recent studies have shown that several pro-inflammatory proteins can be used as biomarkers for atherosclerosis, the mechanism of atherogenesis is unclear and little information is available regarding proteins involved in development of the disease. Atherosclerotic tissue samples were collected from patients in order to identify the proteins involved in atherogenesis. The protein expression profile of atherosclerosis patients was analysed using two-dimensional electrophoresis-based proteomics. Thirty-nine proteins were detected that were differentially expressed in the atherosclerotic aorta compared with the normal aorta. Twenty-seven of these proteins were identified in the MS-FIT database. They are involved in a number of biological processes, including calcium-mediated processes, migration of vascular smooth muscle cells, matrix metalloproteinase activation and regulation of pro-inflammatory cytokines. Confirmation of differential protein expression was performed by Western blot analysis. Potential applications of the results include the identification and characterization of signalling pathways involved in atherogenesis, and further exploration of the role of selected identified proteins in atherosclerosis.

Aortic Diseases↗
PubMed1992

Outer membrane protein profiles and multilocus enzyme electrophoresis analysis for differentiation of clinical isolates of Proteus mirabilis and Proteus vulgaris.

Outer membrane protein (MP) profiles and multilocus enzyme electrophoresis (MEE) analysis were used as tools for differentiating clinical isolates of Proteus spp. Fourteen distinct MP profiles were established by sodium dodecyl sulfate-urea polyacrylamide gel electrophoresis in 54 clinical isolates of Proteus spp. (44 strains identified as P. mirabilis and 10 strains identified as P. vulgaris). Forty-one isolates of P. mirabilis and eight isolates of P. vulgaris were grouped within six and three MP profiles, respectively. The remaining P. mirabilis and P. vulgaris isolates had unique profiles. MEE analysis was used to further discriminate among the strains belonging to the same MP groups. Thirty-five distinct electrophoretic types (ETs) were identified among P. mirabilis isolates. The isolates of P. mirabilis from the four most common MP groups were subgrouped into 30 ETs. All of the P. vulgaris strains had unique ETs. The results suggest that upon biochemical classification of Proteus isolates as P. mirabilis or P. vulgaris, further differentiation among strains of the same species can be obtained by the initial determination of MP profiles followed by MEE analysis of strains with identical MPs.

Bacterial Outer Membrane Proteins↗