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PubMed2025

LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis.

MOTIVATION: Differential expression analysis plays a vital role in omics research enabling precise identification of features that associate with different phenotypes. This process is critical for uncovering biological differences between conditions, such as disease versus healthy states. In proteomics, several statistical methods have been used, ranging from simple t-tests to more advanced methods like DEqMS, limma and ROTS. However, a flexible method for reproducibility-optimized statistics tailored for clinical omics data has been lacking. RESULTS: In this study, we developed LimROTS, a hybrid method that integrates a linear regression model and the empirical Bayes approach with reproducibility optimized statistics, to create a novel moderated ranking statistic, for robust and flexible analysis of proteomics data. We validated its performance using twenty-one proteomics gold standard spike-in datasets with different protein mixtures, MS instruments, and techniques for benchmarking. This hybrid approach improves accuracy and reproducibility of complex proteomics data, making LimROTS a powerful tool for high-dimensional omics data analysis. AVAILABILITY AND IMPLEMENTATION: LimROTS has been implemented as an R/Bioconductor package, available at https://doi.org/doi:10.18129/B9.bioc.LimROTS. Additionally, the code used in this study is available in GitHub repository https://github.com/AliYoussef96/LimROTSmanuscript.

Bayes Theorem↗
PubMed2005

DEPD: a novel database for differentially expressed proteins.

SUMMARY: The Differentially Expressed Protein Database was designed to store the output of comparative proteomics studies and provides a publicly available query and analysis platform for data mining. The database contains information about more than 3000 differentially expressed proteins (DEPs) manually extracted from the published literature, including relevant biological, experimental and methodological elements. Tools for visualization and functional analysis of DEPs are provided via a user-friendly webinterface. AVAILABILITY: http://protchem.hunnu.edu.cn/depd/.

Computational Biology↗
PubMed1998

Identification of differentially expressed genes in human trophoblast cells by differential-display RT-PCR.

Molecular mechanisms controlling human trophoblast invasiveness are still poorly understood. In the present investigation, mRNA patterns of trophoblast cells isolated from first trimester (high invasiveness) and term placentae (no/low invasiveness) were compared by differential-display reverse transcriptase polymerase chain reaction (DDRT-PCR) revealing differential expression of numerous genes. Of 18 differentially expressed DDRT-PCR products analysed, 11 were unknown, four showed homologies with expressed sequence tag sequences, and three others were homologous to integrin-beta1, ATP-synthetase U6 (both showing higher expression in first trimester) or to aldose-reductase (higher expression at term), respectively. One of the unknown transcripts (PBK1, accession number: AJ007398) was cloned from a first trimester placenta cDNA library and was characterized. The 1908-bp gene fragment contains an open reading frame of 1551 bp and an Alu-sequence in the 3' non-coding region. According to Northern blot analysis on JAr choriocarcinoma cells, the fragment is close to full-length cDNA. By in situ hybridization, PBK1 was detected only in first trimester but not term placentae in the proximal parts of cell islands and in closely adjacent villous cytotrophoblast. This expression pattern suggests that the newly identified molecule, PBK1, could be involved in the regulation of proliferation/ differentiation and potentially in invasion of trophoblast cells.

ATP Synthetase Complexes↗
PubMed2002

Identification of differentially expressed genes during cyclic adenosine monophosphate-induced neuroendocrine differentiation in the human prostatic adenocarcinoma cell line LNCaP.

The LNCaP cell line is a versatile and useful model suitable for the study of human prostate cancer in vitro. It has been determined that the elevation of LNCaP intracellular cyclic adenosine monophosphate (cAMP) levels through the addition of membrane-permeable cAMP analogs, phosphodiesterase inhibitors, adenylate cyclase activators, or components of the cAMP signal-transduction pathway can induce reversible neuroendocrine (NE) differentiation. Elucidation of those genes that are differentially expressed between undifferentiated prostate cancer cells and prostate cancer cells that have been induced to differentiate may present new insights into the molecular mechanisms governing NE differentiation, early detection of prostate cancer, and potential targets for gene therapy. In this study, differential display polymerase chain reaction (PCR) was used to identify 226 differentially expressed PCR products. Twelve of the differential display PCR products were confirmed by Northern blot analysis and were cloned. DNA sequencing and database comparisons were performed. To our knowledge, this is the first report of the use of differential gene expression techniques to analyze gene expression during cAMP-induced NE differentiation in LNCaP cells. Confirmation of NE differentiation reversibility also was accomplished.

Adenocarcinoma↗
PubMed2005

[Screening of differentially expressed genes in colorectal cancer using human whole genomic oligonucleotide microarrays].

OBJECTIVE: To screen the differentially expressed genes in human colorectal cancer (CRC) tissue. METHODS: Affymetrix oligonucleotide microarrays HG-U133 representing 32,264 human genes including 19,308 known genes and 12,956 expressed sequence tags (ESTs) were used to detect the gene expressions of CRC tissue paired with normal mucosa tissue. The microarray findings were confirmed by real-time quantitative reverse transcriptase-polymerase chain reaction (FQ-PCR). The gene expression profiles were analyzed by intersection and complement, rank sum test and t test. RESULTS: Totally 3,125 genes and ESTs expressed differentially were detected in normal and cancer tissues, consisting of 974 up-regulated and 2,151 down-regulated genes with 247 ESTs present in CRC tissue and absent in normal mucosa and 162 ESTs absent in CRC tissue but present in normal mucosa. A percent of 80.1% of the differentially expressed genes were not reported in the literatures. CONCLUSION: The strategy of data mining provides a foundation for filtering molecular markers and interpreting molecular carcinogenesis of CRC.

Colorectal Neoplasms↗
PubMed2002

Differential expression of proteins in renal cortex and medulla: a proteomic approach.

BACKGROUND: Western blotting has previously been used to identify changes in protein expression in renal tissue. However, only a few proteins can be studied in each experiment by Western blot. We have used proteomic tools to construct protein maps of rat kidney cortex and medulla. METHODS: Expression of proteins was determined by silver stain after two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Protein spots were excised and digested with trypsin. Peptide masses were identified by MALDI-TOF mass spectrometry. The Mascot search engine was used to analyze the peptide masses and identify the proteins. RESULTS: Seventy-two proteins were identified (54 unique proteins) out of approximately 1000 spots visualized on each gel. Most of the spots were expressed both in cortex and medulla. Of the identified proteins, three were expressed only in medulla and one only in cortex. Nine proteins were expressed in both regions but to a greater extent in cortex and three proteins were expressed more in medulla. Differential expression was confirmed for three proteins by Western blot. CONCLUSIONS: A large group of proteins and their relative expression levels from cortical and medullary portions of rat kidneys were found. Sixteen proteins are differentially expressed. Proteomics can be used to identify differential expression of proteins in the kidney on a large scale. Proteomics should be useful to detect changes in renal protein expression in response to a large range of physiological and pathophysiological stimuli.

Animals↗
PubMed2005

Glial-derived nexin, a differentially expressed gene during neuronal differentiation, transforms HEK cells into neuron-like cells.

Glial-derived nexin (GDN) is a proteinase inhibitor secreted from glial cells and it can enhance neuronal function. However, its expression and function in neuronal differentiation are not, as yet, well-known. In the present study, we analyzed glial-derived nexin gene expression in dissociated neural stem/progenitor cells (NS/PCs) (D0) from the embryonic mouse cerebral cortex, expanded NS/PC cultures (D4 and D10 cultures) and cultured neurons (E15) using a semi-quantitative RT-PCR assay. Our data suggest that mouse GDN, homologue of human GDN, was significantly up-regulated in the expanded NS/PC cultures and cultured neurons. To analyze its function in neuronal differentiation, human GDN cDNA was cloned into bicistronic plasmids containing green fluorescent protein (GFP) and the resulting plasmids were transfected into rodent primary NS/PCs and non-neuronal human embryonic kidney (HEK) cells. Our data suggest that the ectopic expression of human GDN triggered the expression of the neuronal marker TuJ1 in both NS/PCs and HEK cells. We conclude that GDN is up-regulated during neuronal differentiation and plays a role in transforming non-neuronal HEK cells into neuron-like cells.

Amyloid beta-Protein Precursor↗
PubMed2003

[Identification of differential expression ESTs in pig muscle tissue by DHPLC].

The differential expression ESTs in muscle tissue of Large Yorkshire pig and Lantang pig, one of the local pig breeds in Guangdong province, were identified with DHPLC system and graphic analysis software LabWork4.0, and both methods verified the true differential display bands. The results showed that DHPLC can quickly and accurately detect differential expression mRNA profiles of different tissues, and can be widely used to study mRNA expression, differential expression of different animal tissues under variant environments.

Animals↗
PubMed2002

Differential expression of genes during TPA-induced differentiation of human prostatic cancer TSU-Pr1 cells.

We are interested in the possibility of a new prostate cancer therapy that would control tumor malignancy via induction of terminal cell differentiation. We previously reported that 12-O-tetra-decanoylphorbol-13-acetate (TPA) induces differentiation into cells with characteristics of microglia and decreases the malignant characteristics of human prostatic cancer TSU-Pr1 cells. To investigate the mechanism underlying differentiation of TSU-Pr1 cells, we attempted to identify genes expressed during differentiation using differential display. We identified four genes expressed differentially after TPA treatment. Levels of expression of two genes, human flavoprotein subunit of complex II and JKTBP, were downregulated by TPA, and expression of two genes, human golgin p245 and bcl-xL, was upregulated. Moreover, we found that the changes in expression of flavo-protein, JKTBP and bcl-xL induced by TPA were blocked by treatment with protein kinase C (PKC) or mitogen-activated protein (MAP) kinase inhibitors that prevent TPA-induced differentiation of TSU-Pr1 cells. These results suggest that the differential expression of these genes is associated with TPA-induced differentiation of TSU-Pr1 cells. We expect that understanding the roles of these genes during differentiation will provide for new approaches and therapeutic targets for treatment of prostate cancer.

Antineoplastic Agents↗
PubMed2006

A comparison of statistical tests for detecting differential expression using Affymetrix oligonucleotide microarrays.

Signal quantification and detection of differential expression are critical steps in the analysis of Affymetrix microarray data. Many methods have been proposed in the literature for each of these steps. The goal of this paper is to evaluate several signal quantification methods (GCRMA, RSVD, VSN, MAS5, and Resolver) and statistical methods for differential expression (t test, Cyber-T, SAM, LPE, RankProducts, Resolver RatioBuild). Our particular focus is on the ability to detect differential expression via statistical tests. We have used two different datasets for our evaluation. First, we have used the HG-U133 Latin Square spike in dataset developed by Affymetrix. Second, we have used data from an in-house rat liver transcriptomics study following 30 different drug treatments generated using the Affymetrix RAE230A chip. Our overall recommendation based on this study is to use GCRMA for signal quantification. For detection of differential expression, GCRMA coupled with Cyber-T or SAM is the best approach, as measured by area under the receiver operating characteristic (ROC) curve. The integrated pipeline in Resolver RatioBuild combining signal quantification and detection of differential expression is an equally good alternative for detecting differentially expressed genes. For most of the differential expression algorithms we considered, the performance using MAS5 signal quantification was inferior to that of the other methods we evaluated.

Animals↗
PubMed2002

Two isoforms of vasa homologs in a teleost fish: their differential expression during germ cell differentiation.

Two isoforms of vasa mRNA and protein are present in a teleost fish, tilapia. One (vas-s) lacks a part of the N-terminal region found in the other isoform (vas). Both isoforms are expressed in oocytes through the embryonic stage when primordial germ cells (PGCs) localize in the lateral plate mesoderm. After PGC localization in the gonadal anlagen, vas-s expression increased and vas expression became undetectable. Expression of both isoforms was observed again after morphological gonadal sex differentiation, irrespective of genotypic sex. In ovary, compared with vas expression vas-s expression predominated throughout oogenesis. In testis, vas expression was predominant compared with vas-s during spermatogenesis. These results indicate that relative expression of two vasa isoforms is dependent upon germ cell differentiation and sex.

Amino Acid Sequence↗
PubMed2004

Replicated studentized-deviate detection applied to the identification of differentially expressed genes in TNF-alpha-stimulated cells.

Among the applications of DNA microarray expression data, identification of differentially expressed genes is widely used to search for genes involved in specific biological processes. Previous studies have shown that replication is necessary to reliably identify differentially expressed genes. In practice, however, further guidelines are required to provide references for experiment design, that is, to fulfill the needs for determining the replication number on a desired confidence level or the detection sensitivity of the microarrays. Here, we performed simulations to build a simple statistical table of general guidelines adapted specifically for identifying differentially expressed genes using replications of a microarray experiment, and we present an accompanying nonparametric method, replicated studentized-deviate detection (RSD). The analysis results of the TNF-alpha-stimulated cells showed that RSD is simple and robust, and that the resulting statistical table is plausible.

Algorithms↗
PubMed2002

Identification of differentially expressed transcripts in the human pathogenic fungus Paracoccidioides brasiliensis by differential display.

Paracoccidioides brasiliensis is a dimorphic human pathogenic fungus that is the causal agent of paracoccidioidomycosis, a systemic disease that predominantly affects rural communities in South and Central America. Dimorphism is a common characteristic of systemic human pathogenic fungi. Here we describe the use of differential display (DD) to isolate and identify differentially expressed genes of P. brasiliensis, in the two cell types, yeast (Y) and mycelium (M), as well as at different time intervals during temperature-induced M to Y transition. Using two oligo-deoxythymidine-anchored primers combined with 10 arbitrary ones, we were able to detect the presence of at least 20 differentially transcribed cDNA fragments. Some of these fragments were further analysed by reverse-northern blot and northern blot in order to confirm their differential expression. The M32, M51 and M73 cDNA fragments were specific for the mycelial form of P. brasiliensis. Furthermore, we found two cDNA fragments (M-Y1 and M-Y2) that were upregulated during M-Y transition. This method was efficient and useful in the detection of differentially expressed genes in P. brasiliensis.

DNA, Complementary↗
PubMed2004

Multivariate search for differentially expressed gene combinations.

BACKGROUND: To identify differentially expressed genes, it is standard practice to test a two-sample hypothesis for each gene with a proper adjustment for multiple testing. Such tests are essentially univariate and disregard the multidimensional structure of microarray data. A more general two-sample hypothesis is formulated in terms of the joint distribution of any sub-vector of expression signals. RESULTS: By building on an earlier proposed multivariate test statistic, we propose a new algorithm for identifying differentially expressed gene combinations. The algorithm includes an improved random search procedure designed to generate candidate gene combinations of a given size. Cross-validation is used to provide replication stability of the search procedure. A permutation two-sample test is used for significance testing. We design a multiple testing procedure to control the family-wise error rate (FWER) when selecting significant combinations of genes that result from a successive selection procedure. A target set of genes is composed of all significant combinations selected via random search. CONCLUSIONS: A new algorithm has been developed to identify differentially expressed gene combinations. The performance of the proposed search-and-testing procedure has been evaluated by computer simulations and analysis of replicated Affymetrix gene array data on age-related changes in gene expression in the inner ear of CBA mice.

Aging↗
PubMed2005

Differential expression of CXCR4 is associated with the metastatic potential of human non-small cell lung cancer cells.

PURPOSE: To evaluate the relation between CXCR4 expression and the presence of metastatic disease in human non-small cell lung cancer (NSCLC) patients and investigate whether modulation of CXCR4 expression could serve as a potential pathway in preventing metastasis of NSCLC. EXPERIMENTAL DESIGN: CXCR4 expression in 36 patients with NSCLC and 10 normal lung tissues was detected by real-time PCR and immunohistochemistry. CXCR4 expression in two human NSCLC clones (95C and 95D) with different metastatic potential was determined by real-time PCR and flow cytometry. 95C and 95D cells were transfected with the plasmid DNA containing CXCR4 coding gene or CXCR4 antisense nucleotide fragment, respectively, and the effects on in vitro cell migration, invasion, and adhesion and in vivo metastasis were measured. RESULTS: Up-regulated expression of CXCR4 was detected in 34 tumors, which were further divided into 17 high expression cancers and 17 low expression cancers by their staining intensities. High CXCR4 tumors (13 of 17) were more prone to clinical metastasis in comparison with low expression tumors. CXCR4 was differentially expressed in 95C and 95D cells with low or high metastatic potential, and the surface expression of CXCR4 were 50% up-regulated or down-regulated following the stable transfection. The metastatic potential of NSCLC in vitro, such as migration, invasion, and adhesion, were significantly enhanced or impaired. In addition, neutralizing the interactions of stromal cell-derived factor-1/CXCR4 in vitro with CXCR4-specific antibodies inhibited the CXCR4-dependent migration, invasion, and adhesion. Furthermore, s.c. inoculation of lung cancer cells with low expression of CXCR4 in nude mice showed 0- to 2-fold decrease in lung metastatic foci than that with high expression of CXCR4. CONCLUSIONS: Differential expression of CXCR4 is associated with the metastatic potential of human NSCLC, raising the possibility that blockade of CXCR4/stromal cell-derived factor-1 interaction may lead the way to design novel therapeutic tools for the treatment of metastatic NSCLC patients.

Animals↗
PubMed2001

Antigraft antibody-mediated expression of metalloproteinases on endothelial cells. Differential expression of TIMP-1 and ADAM-10 depends on antibody specificity and isotype.

Endothelial cell (EC) interaction with antigraft antibodies (Abs) mediates EC injury and activation involved in vascular graft rejection. The aim of this study was to identify EC genes regulated in response to antigraft Ab binding that contribute to the endothelium alterations implicated in graft rejection or survival. By means of RNA differential display, 13 cDNA fragments corresponding to genes differentially expressed in ECs incubated with antigraft Abs were identified. Among these cDNAs were found the tissue inhibitor of metalloproteinase-1 (TIMP-1) and a desintegrin and metalloproteinase (ADAM-10). We demonstrated that TIMP-1 and ADAM-10 mRNA and protein expression was rapidly upregulated in ECs in response to antigraft Ab binding. Our data showed that TIMP-1 was upregulated in response to human IgG but not IgM and anti-galactosyl (Gal) alpha1-3Gal human xenogeneic Abs. In contrast, upregulation of ADAM-10 in ECs was shown to be mostly mediated by anti-Galalpha1-3Gal IgM Abs. Specific effects of human IgG and IgM xenogeneic Abs on endothelial transcripts indicate that different isotypes and specificities of Abs may mediate different EC changes. Our results suggest that interaction of ECs with antigraft Abs, according to their specificity, selectively induces synthesis and release of metalloproteinases and inhibitors, controlling proteolytic processes and immunological events that respectively contribute to graft rejection or survival.

Amyloid Precursor Protein Secretases↗
PubMed1980

Differential expression of lectin receptors during hemopoietic differentiation: enrichment for granulocyte-macrophage progenitor cells.

Molecular changes occur at the surface of hemopoietic cells during differentiation from progenitor cells to mature granulocytes and macrophages. The differential expression of surface carbohydrate residues has been probed using lectins and the results used to purify normal mouse granulocyte-macrophage progenitor cells. Ten different lectins were screened for selective interaction with mouse hemopoietic colony-forming cells (CFCs), using agglutination or a quantitative analysis of the number of fluoresceinated lectin molecules bound per cell using a fluorescence activated cell sorter (FACS). Pokeweed mitogen (PWM), Helix pomatia agglutinin (HPA), soybean agglutinin (SBA), and peanut agglutinin (PNA) preferentially bound to CFCs so that it was possible to enrich 4 to 10-fold for these progenitor cells by sorting for the highly fluorescent cells. Further analysis of the low and high angle light scattering characteristics of the CFCs indicated that these cells were polydisperse, but could be enriched ten-fold by selecting for cells with high intensity low angle (0 degrees) scatter and low intensity high angle (90 degrees) scatter. PWM gave the best enrichment (10 to 15-fold) for adult bone marrow CFCs, for CFCs from fetal sources (fetal liver, fetal blood), and for CFCs from the spleens of mice injected previously with outer membrane lipoprotein from E. coli. Three parameter sorting for CFC using the FACS (low angle scatter, high angle scatter, and PWM-fluorescence) resulted in large enrichment factors (16 to 50-fold) for CFCs from all the above sources. Over 7% of the cells sorted from bone marrow, 10% of the cells sorted from post-lipoprotein spleen, and 28% of the cells sorted from fetal peripheral blood were hemopoietic CFCs. Ninety percent of the cells in these fractions had the morphology of blast cells or myelocytes. Thus, it was possible to identify the morphological characteristics of the hemopoietic progenitor cells. Screening of other developmental systems using quantitation of fluorescence with lectins should prove of general value for the purification of selected differentiation states.

Animals↗
PubMed2001

A strategy to identify differentially expressed genes using representational difference analysis and cDNA arrays.

Representational difference analysis (RDA) combined with cDNA arrays is an effective approach to identify differentially expressed genes. To identify differentially expressed genes in c-Myc transgenic mouse liver, we compared the virtues of probing commercially available cDNA arrays with either radiolabeled cDNA pools or radiolabeled difference products (DP2) derived from RDA using c-Myc transgenic and normal mouse liver. Probing commercial and custom arrays with DP2 products led to the identification of transcripts of low abundance that were missed when the arrays were initially probed with PCR-amplified cDNA pools. Although DP2 probes also detected abundant transcripts that are highly differentially expressed, they failed to identify abundant transcripts with low differential expression that were detected with cDNA pools. The combined use of radiolabeled cDNA and DP2 products to probe arrays allows a more comprehensive identification of differentially expressed transcripts that are abundant or rare. Our method has the additional benefit of eliminating false-positive transcripts that lack true differential expression and frequently contaminate DP2 pools. Using this method we identified 16 differentially expressed genes in c-Myc transgenic liver, one of which is novel.

Animals↗