Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “differential expression”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 235 records · Page 13Linked to original sources
PubMed2001

[Cloning of drug resistance-related gene fragments differentially expressed on lung adenocarcinoma cell line A549 and its DDP-resistant counterpart A549DDP].

OBJECTIVE: To clone drug resistance-related genes of lung adenocarcinoma. METHOD: The difference in gene expression between A549 and A549DDP was identified by mRNA differential display technique. Genes differentially expressed were cloned and confirmed by Northern blot. RESULTS: Four cDNA fragments of differentially expressed genes were obtained and sequenced. Of the 4 cDNA fragments, 2 (A1 and D1) did not show sequence homology with the existing genes in the GeneBank, one (A2) was 89% homologous with interleukin 1 beta converting enzyme (ICE) gene, and the other (D2) was identical to mouse musculus 45s pre-rRNA (MM45srRNA) gene. Both cDNA fragments A1 and A2 were expressed in A549 but not or barely expressed in A549DDP, while fragments D1 and D2 were expressed in A549DDP but not in A549. CONCLUSION: Four differentially expressed gene fragments between lung adenocarcinoma cell line and its cisplatin-resistant counterpart were identified by mRNA differential display technique. It remains to be studied whether the newly identified gene fragments and those showing sequence homology to ICE and MM45srRNA are indeed positively or negatively related to drug resistance.

Adenocarcinoma↗
PubMed2000

Differential expression of multiple unexpected genes during U937 cell and macrophage differentiation detected by suppressive subtractive hybridization.

OBJECTIVE: The objective of this study was to identify new markers of myelomonocytic differentiation using a sensitive technique that permits detection of rare differential gene expression. MATERIALS AND METHODS: [corrected] Suppressive subtractive hybridization (SSH) was performed between the human myelomonocytic U937 cell line and 1 alpha, 25-dihydroxyvitamin D3 and transforming growth factor beta 1 differentiated U937 cells. cDNA clones with significant increased expression in differentiated U937 cells over nondifferentiated U937 cells were characterized by sequencing. [corrected] The pattern of differential gene expression obtained by SSH was confirmed by cDNA Southern and Northern blots on the undifferentiated vs. differentiated U937 cells, and by reverse transcriptase polymerase chain reaction on undifferentiated human CD34(+) stem cells isolated from bone marrow vs. peripheral blood CD14(+) mature monocytes. RESULTS: Seven cDNAs never associated with in vitro U937 cell myelomonocytic differentiation (prolactin, 11-beta hydroxysteroid dehydrogenase [11 beta-HSD)] haptoglobin alpha (2FS)-beta precursor, GLIPR, RTVP, the RNA helicase P68, and spermidine-spermine N1-acetyltransferase) were identified. The first five of these genes previously were associated with immune function and the last two are important for intermediary metabolism. Differential expression was confirmed in CD34(+)/CD14(+) monocyte differentiation for all genes but 11 beta-HSD. CONCLUSIONS: We identified six new markers of U937 cell differentiation, which also are differentially expressed during normal human myelomonocytic differentiation.

Acetyltransferases↗
PubMed1998

[Re-amplification of differentially expressed mRNA fragments of head-neck cancers without cloning].

BACKGROUND: mRNA expression of healthy and malignant cells can be compared to each other by employing the "differential display" (DD) technique. Most studies describe sequence analysis of differentially expressed fragments after reamplification by a second round of PCR and subsequent molecular cloning to gain a sufficient amount of DNA for sequencing. The aim of this study was to show whether a sufficient amount of differentially expressed mRNA of squamous cell carcinoma cells of the head and neck region can be generated by PCR alone without cloning steps. MATERIAL AND METHODS: mRNA isolated from cultivated keratinocytes and squamous cell carcinoma cells was reverse transcribed into cDNA which was amplified with PCR. Differentially expressed fragments detected after gel electrophoresis were isolated from the gel and reamplified in a second PCR. The resulting cDNA amounts of the second PCR were suitable for cloning but not for direct sequencing. A third round of PCR with the undiluted final product of the second PCR as template regularly failed. Dilutions of the second PCR products between 1:10 and 1:10(10) were prepared. The third round of PCR was carried out with these various template concentrations. RESULTS: A sufficient amount of differentially expressed fragments for sequencing procedures resulted when dilutions of the second PCR products ranging from 1:10(2) to 1:10(7) were used as templates in the third round of PCR. CONCLUSION: Modifications of PCR parameters provide high DNA copy numbers of differentially expressed mRNA fragments from squamous cell carcinoma cells of the upper aerodigestive tract in amounts that are needed for sequence analysis. This may make it possible to avoid labor-intensive cloning procedures requiring high safety standards.

Base Sequence↗
PubMed2000

[Function of one novel gene identified by SSH PCR differentially expressed in HBX transfected HepG2 cells].

OBJECTIVE: To clone full length differentially expressed genes which are related with HBxAg. METHODS: HepG2-cells were infected with prepared recombinant retroviruses encoding the X antigen. The differences in gene expression between HepG2 x and HepG2Cat cells were evaluated by suppression subtractive hybridization and PCR. In situ hybridization (ISH) and Northern blot analysis were carried out to screen the differentially expressed genes. The full length cDNA clone of the gene was obtained by 5' and 3' rapid amplification of cDNA ends(race) PCR. HepG2 cells transiently transfected with the new full length gene were subjected to fluorescence activated cell sorting (FACS) analysis for DNA content. HepG2 cells stably transfected with the new full length gene were tested for anchorage independent growth in soft agar and for tumorigenicity in nude mice. RESULTS: The expression of multiple genes were turned on (8) or off (2) in HepG2X compared to HepG2CAT cells. One differentially expressed gene C2, the human homology of Sui1, encoded a translation initiation factor whose expression was suppressed by X antigen in HepG(2) cells. The full length of this gene was 1.35 kb, which encoded a small protein of 113 amino acids. Introduction of C2 into HepG2 cells could inhibit cell growth in culture, in soft agar, and partially inhibit tumor formation in nude mice. Cells transfected with pcDNA3-HBx showed little or no detectable C2, which was consistent with the suppression of this protein in the presence of HBxAg. C2 was also expressed in nontumor liver, but not in tumor cells from patients with hepatocellular carcinoma. CONCLUSIONS: HBX can regulate the expression of genes whose products may be positive or negative regulators of cell growth. Our work for the first time demonstrates that the mechanism of DNA virus associated carcinogenesis involves altered patterns of gene expression regulated at the level of translation initiation.

Amino Acid Sequence↗
PubMedDate not supplied

A powerful approach for effective finding of significantly differentially expressed genes.

The problem of identifying significantly differentially expressed genes for replicated microarray experiments is accepted as significant and has been tackled by several researchers. Patterns from Gene Expression (PaGE) and q-values are two of the well-known approaches developed to handle this problem. This paper proposes a powerful approach to handle this problem. We first propose a method for estimating the prior probabilities used in the first version of the PaGE algorithm. This way, the problem definition of PaGE stays intact and we just estimate the needed prior probabilities. Our estimation method is similar to Storey's estimator without being its direct extension. Then, we modify the problem formulation to find significantly differentially expressed genes and present an efficient method for finding them. This formulation increases the power by directly incorporating Storey's estimator. We report the preliminary results on the BRCA data set to demonstrate the applicability and effectiveness of our approach.

Algorithms↗
PubMed2003

Differential expression of S100 calcium-binding proteins in epidermoid cysts, branchial cysts, craniopharyngiomas and cholesteatomas.

AIMS: To investigate whether epidermoid cysts, branchial cysts, craniopharyngiomas and cholesteatomas express S100 proteins differentially by immunohistochemical assaying the presence of S100A1, S100A2, S100A3, S100A4, S100A5, S100A6 and S100B. METHODS AND RESULTS: Immunopositivity/negativity was recorded for each S100 protein in a series of 52 cases consisting of 12 epidermoid cysts, 12 branchial cysts, 15 adamantinomatous craniopharyngiomas and 13 acquired cholesteatomas. Except in the case of the craniopharyngiomas, immunoreactivity was assessed independently in the basal membrane and the basal, the internal and the keratin layers. Our data show that in contrast to S100B, which was rarely expressed, S100A1, S100A2, S100A4 and S100A5 were often present in these four types of epithelial lesions. S100A3 and S100A6 and, to a lesser extent, S100A5 were the most differentially expressed proteins across the different histopathological groups analysed. These three proteins are expressed more often in craniopharyngiomas and cholesteatomas, the two more aggressive types of lesions. CONCLUSIONS: This is the first study to report data on the expression of seven S100 proteins in different histopathological groups of epithelial head and neck lesions, whose precise embryological origins are still a matter of debate. S100 proteins could possibly be used as markers to target this embryonic origin, since our results show that S100A3 and S100A6 (and, to a lesser extent, S100A5) are expressed differentially across these different groups of epithelial lesions.

Adolescent↗
PubMed2002

Global analysis of differentially expressed genes in early gestational decidua and chorionic villi using a 9600 human cDNA microarray.

The global gene expression profiles of the decidua and chorionic villi of early human pregnancies were analysed by using cDNA microarray technology. Decidual and villous placental tissues were obtained from first trimester abortus and mRNA was extracted for cDNA microarray analysis. The human cDNA microarray [9600 clones, including known regulatory genes and expressed sequence tags (EST)] with colorimetric detection was used to identify differentially expressed genes between early gestational decidua and villi. According to cDNA microarray analysis, we have identified 641 genes with highly expressed mRNA in both decidua and villi, 49 genes with higher expressions in decidua, and 75 genes with higher expression in chorionic villi. These differentially expressed genes were further grouped into categories by their putative functions, including: cell growth-related factors, hormones/cytokines, cell adhesion molecules, signal transduction molecules, apoptosis-related factors, cytoskeleton/extracellular matrix proteins, and EST. Immunohistochemical stainings of cathepsin L, leukaemia inhibitory factor-receptor, and proliferative cell nuclear antigen showed results consistent with the microarray data. Identification of the differentially expressed genes between decidua and villi by microarray provide a global profiling of the gene expression pattern. This work adds to our understanding of placentation by reporting the gene expression profiles during first trimester human pregnancies using cDNA microarray.

Adult↗
PubMed2000

Identification of genes that are differentially expressed in extraocular and limb muscle.

The extraocular muscles (EOM) are anatomically and physiologically distinct from other striated muscles in mammals. Among other differences, they can be driven to generate individual twitch contractions at an extremely high frequency and are resistant to [Ca(2+)]-induced myonecrosis. While EOM are preferentially targeted in some neuromuscular diseases such as myasthenia gravis and congenital fibrosis of the extraocular muscles, they are enigmatically spared in Duchenne's muscular dystrophy, despite the widespread damage seen in all other skeletal muscle groups during the course of this disease. To address the molecular mechanisms that specify the EOM-phenotype, we characterized the transcriptional profile of genes expressed in rat EOM versus limb muscle using a differential display strategy. Ninety-five putative differentially expressed cDNA tags were cloned, from which fourteen were confirmed as being differentially expressed by RNA slot blot and Northern blot analysis. Ten of these cDNAs were homologous to known human or murine genes and ESTs, while four genes that were upregulated in EOM were novel, and have been named expressed in ocular muscle (eom) 1-4. The identification of these differentially expressed genes may provide mechanistic clues toward understanding the unique patho-physiological phenotype of EOM.

Animals↗
PubMed2026

Comprehensive analysis of differentially expressed mRNAs, lncRNAs, and miRNAs involved in ovarian differentiation and development in Qihe gibel carp (Carassius gibelio var. Qihe).

Qihe gibel carp (Carassius gibelio var. Qihe) exhibits diverse reproductive modes including gynogenesis and sexual reproduction, yet the molecular mechanisms of ovarian differentiation remain poorly understood. Ovarian tissues at 20, 30, and 60 days after hatching (dah), representing key stages covering early ovarian differentiation and primary oocyte growth, were subjected to whole-transcriptome sequencing. A total of 27,259 mRNAs, 2622 lncRNAs, and 2467 miRNAs were differentially expressed. Cell cycle, transcription, translation, and DNA replication pathways were significantly upregulated from 20 to 60 dah. Oocyte meiosis was enriched from 20 and 30 dah, whereas metabolic pathways (lipid, carbohydrate, and nucleotide metabolism) were enriched from 30 to 60 dah, indicating sequential progression from meiosis initiation to primary oocyte growth with nutrient synthesis. Hub lncRNAs and key ceRNA networks (e.g., MSTRG.28669.5-miR-221-ccnb2) were identified. This study provides the first comprehensive characterization of ncRNA-mediated regulation and ceRNA networks during ovarian development in Qihe gibel carp, establishing a foundation for understanding ovarian differentiation in this species.

Animals↗
PubMed2000

[Study of differential expressed genes in vascular endothelial cell line ECV304 induced by low density lipoprotein].

OBJECTIVE: To isolate and clone the differential expressed genes induced by atherogenic factors on vascular endothelium and to understand the molecular mechanism of atherosclerosis. METHODS: The differential display reverse transcription PCR method (DDRT-PCR) was used to analyze the differential expressed cDNA in ECV304 induced by low density lipoprotein (LDL). After sequencing and homology research, the differential expressed cDNA fragments were confirmed by northern blot analysis. RESULTS: Up-regulated and down-regulated cDNAs fragments were isolated in ECV304. It was found that some cDNAs fragments were highly homologous to the known human genes, while others were fragments of novel genes. The known up-regulated genes included human 10 kD protein, FGFR1 oncogene partner, intercellular adhesion molecular-1, FK506 binding protein and rTS beta genes. The known down-regulated genes included human fb19, Apobec1-binding protein 1 and RBP2. The expression levels of different genes varied by 70%-200%. CONCLUSION: By DDRT-PCR method, our results showed that LDL could change the expression of many genes in endothelial cells. The high expression level of ICAM-1 in the endothelial cells stimulated by LDL suggested that ICAM-1 is an important adhesion molecular in atherogenesis. The down-regulated expression of Apobec 1-binding protein 1 may affect the cellular synthesis of apolipoprotein. The high expression level of FGFR1 oncogene partner is likely related to the differentiation of ECV304. The function of other differential expressed genes remains to be elucidated.

Cells, Cultured↗
PubMed2001

The Drosophila gene twister, an orthologue of the yeast helicase SKI2, is differentially expressed during development.

We have identified and characterized a Drosophila orthologue of SKI2, which, in Saccharomyces cerevisiae, is one of the key components in the cytoplasmic 3'-5' decay of mRNA. The Drosophila orthologue (twister, tst), is expressed as two transcripts which differ in the lengths of their 3'-UTRs, with the smaller transcript being particularly abundant in 0-2 h embryos and the larger transcript reaching its highest levels in 6-8 h embryos. TST protein is expressed in two forms which are differentially expressed in adult tissues and throughout development. Differential expression of TST may modulate activity of the mRNA turnover pathway and could have a major impact on the expression of target RNAs.

Animals↗
PubMed2001

Analysis of genes differentially expressed in astrocytes stimulated with lipopolysaccharide using cDNA arrays.

We used cDNA arrays to investigate differentially expressed genes in astrocytes challenged with lipopolysaccharide (LPS). Astrocyte cultures were prepared from 1-day-old rat brains. Purified astrocytes were treated with LPS (1 microg/ml) for 2, 8 and 48 h. Differentially expressed genes in these astrocytes were examined with Atlas rat cDNA arrays. At all the three time points studied, three genes were found consistently up-regulated: I-kappaB alpha chain, NF-kappaB, and interferon induced protein. In addition to these three, six other genes were also up-regulated at 2 and 8 h. They were genes encoding vascular cell adhesion protein 1 (VCAM-1), interferon regulatory factor 1 (IRF-1), mitochondrial hydroxymethylglutaryl-CoA synthase (HMG-CoA synthase), aldehyde dehydrogenase 2, macrophage inflammatory protein 1 (MIP-1) and neurotensin receptor 2. At these two time points, three genes were down-regulated: copper-zinc-containing superoxide dismutase 1 (SOD-1), insulin-like growth factor binding protein 1 (IGFBP-1), and insulin-like growth factor binding protein 3 (IGFBP-3). Expression of several differentially expressed genes in cDNA array (I-kappaB, VCAM-1 and MIP-3) were further confirmed by reverse transcription polymerase chain reaction study. The prominently modulated genes could be classified into three categories: nuclear transcription factors, pro-inflammatory cytokines/chemokines and metabolic enzymes. Application of pyrrolidine dithiocarbamate, an inhibitor of nuclear factor-kB (NF-kappaB), prior to LPS stimulation not only prevented up-regulation of NF-kappaB gene expression, but also completely blocked up-regulation of pro-inflammatory cytokine genes (TNF-alpha and interleukin-1beta) and two chemokine genes: CXC chemokine LIX and CC chemokine MIP-3 alpha. These results indicate that both up-regulation of inflammatory cytokine expression and down-regulation of growth factor expression are probably involved in the response of astrocytes upon exposure to LPS.

Animals↗
PubMedDate not supplied

Isolation of differentially expressed cDNAs during ferret tracheal development: application of differential display PCR.

The technique of differential display polymerase chain reaction (DD-PCR) was used to identify cDNA sequences, which are temporally expressed during ferret tracheal airway development. Such differentially expressed cDNAs may ultimately prove to be useful markers in elucidating mechanisms of epithelial differentiation and submucosal gland development in the airway. Using two sets of oligonucleotide primers 15 differentially amplified cDNAs were isolated by comparative reverse transcriptase (RT) PCR of 6-h and 3-day postnatal tracheal poly-A mRNA. In situ hybridization was used to assess the reliability of this method and confirm the differential mRNA expression patterns of cloned cDNAs. Results of in situ hybridization analysis demonstrated that 10 of the 15 cDNA sequences gave a temporally regulated pattern of expression, which was concordant with that of the differential display. Furthermore, sequence analysis of the 15 isolated cDNAs revealed that the majority of clones were amplified from two inverted decamer primers. These findings demonstrate the lack of poly-T priming in the differential display reaction, which suggests that this method may yield substantially more information regarding the coding sequence of cloned genes. In support of this observation, 6 of the 15 cDNA sequences contained one complete open reading frame. Although the majority of cDNAs demonstrated no homology to sequence data bases at the DNA or amino acid level, clone FT-4, which demonstrated a differential expression pattern limited to 3-day tracheal time points, was composed of a 10-amino acid repeat domain that was structurally similar to neuropeptide anthoRFamide and barley D hordein seed protein. A second interesting clone, FT-3, demonstrated an infrequent pattern of expression within a subset of epithelial cells limited to early developmental time points (6 h) and was dramatically reduced by 3 days postnatally. Several additional clones with no homologies to previously cloned genes demonstrated expression patterns that were also temporally regulated throughout tracheal development. Although the function of these temporally regulated genes has not been determined, these genes may ultimately prove to be useful markers of cellular differentiation during tracheal development.

Amino Acid Sequence↗
PubMed2006

The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison.

BACKGROUND: Analysis of DNA microarray data takes as input spot intensity measurements from scanner software and returns differential expression of genes between two conditions, together with a statistical significance assessment. This process typically consists of two steps: data normalization and identification of differentially expressed genes through statistical analysis. The Expresso microarray experiment management system implements these steps with a two-stage, log-linear ANOVA mixed model technique, tailored to individual experimental designs. The complement of tools in TM4, on the other hand, is based on a number of preset design choices that limit its flexibility. In the TM4 microarray analysis suite, normalization, filter, and analysis methods form an analysis pipeline. TM4 computes integrated intensity values (IIV) from the average intensities and spot pixel counts returned by the scanner software as input to its normalization steps. By contrast, Expresso can use either IIV data or median intensity values (MIV). Here, we compare Expresso and TM4 analysis of two experiments and assess the results against qRT-PCR data. RESULTS: The Expresso analysis using MIV data consistently identifies more genes as differentially expressed, when compared to Expresso analysis with IIV data. The typical TM4 normalization and filtering pipeline corrects systematic intensity-specific bias on a per microarray basis. Subsequent statistical analysis with Expresso or a TM4 t-test can effectively identify differentially expressed genes. The best agreement with qRT-PCR data is obtained through the use of Expresso analysis and MIV data. CONCLUSION: The results of this research are of practical value to biologists who analyze microarray data sets. The TM4 normalization and filtering pipeline corrects microarray-specific systematic bias and complements the normalization stage in Expresso analysis. The results of Expresso using MIV data have the best agreement with qRT-PCR results. In one experiment, MIV is a better choice than IIV as input to data normalization and statistical analysis methods, as it yields as greater number of statistically significant differentially expressed genes; TM4 does not support the choice of MIV input data. Overall, the more flexible and extensive statistical models of Expresso achieve more accurate analytical results, when judged by the yardstick of qRT-PCR data, in the context of an experimental design of modest complexity.

Algorithms↗
PubMed1995

Isolation of cDNAs that are differentially expressed between androgen-dependent and androgen-independent prostate carcinoma cells using differential display PCR.

In the development of prostate cancer there is an important transition from androgen-dependent growth (which can be treated) to androgen-independent growth (which is beyond medical control). This transition is probably accompanied by genetic changes, resulting in the activation of oncogenes or the inactivation of tumor suppressor genes. In the present manuscript, the isolation of genes that may be involved in advanced, androgen-independent prostate cancer growth is described. Using differential display PCR, 13 cDNAs were isolated representing genes that are differentially expressed between the androgen-dependent prostate carcinoma cell line LN-CaP and the androgen-independent prostate carcinoma cell lines PC-3 and DU 145. These clones were divided into four groups: androgen-responsive genes (TL5, TL25, TL32, and TL35); genes with a marked decreased expression in one of the prostate cancer cell lines (TL27); genes with a marked, increased expression in one or more of the prostate cancer cell lines (TL4, TL16, TL21, and TL22); and genes with minor (but repeatable) changes in expression between prostate cancer cell lines (TL7, TL15, TL18, and TL33). The 13 genes were analyzed for their sequence information, tissue specificity, and androgen responsiveness in order to identify genes of interest. In summary, differential display PCR appears to provide an attractive alternative to existing molecular techniques to screen for differentially expressed genes in prostate cancer cells.

Androgens↗
PubMed2001

[Cloning the differentially expressed genes in the retina of rds mouse during the development of retinitis pigmentosa].

OBJECTIVE: To clone the differentially expressed genes in the retina of rds mouse (the animal model of congenital retinitis pigmentosa) during the disease development. METHODS: The retinal mRNA of rds mouse during the development of retinitis pigmentosa was analyzed by the mRNA differential display. The differentially expressed mRNA fragments were cloned and sequenced. RESULTS: There was obvious difference of gene expression between rds mouse and the control during the development of retinitis pigmentosa. Five differentially expressed bands were cloned and sequenced. One of those had 86% identity (132/154) with the sequence of the human cDNA DKFZp434D1227 from adult testis in GenBank, which was submitted lately (15-Oct-1999) and without much information. The other had lower identity with the sequences in GenBank. A highly expressed clone in the rds mouse on postnatal day 25 had the same length as another clone in the normal on postnatal day 37, which was not expressed in the rds mouse on day 37. The sequences of the two clones were identical in all but two base pairs. CONCLUSION: These results indicate that there are a lot of novel differentially expressed genes in the chronic processing diseases, such as retinitis pigmentosa.

Animals↗
PubMed2004

Differentially expressed genes in pancreatic ductal adenocarcinomas identified through serial analysis of gene expression.

Serial analysis of gene expression (SAGE) is a powerful tool for the discovery of novel tumor markers. The publicly available online SAGE libraries of normal and neoplastic tissues (http://www.ncbi.nlm.nih.gov/SAGE/) have recently been expanded; in addition, a more complete annotation of the human genome and better biocomputational techniques have substantially improved the assignment of differentially expressed SAGE "tags" to human genes. These improvements have provided us with an opportunity to re-evaluate global gene expression in pancreatic cancer using existing SAGE libraries. SAGE libraries generated from six pancreatic cancers were compared to SAGE libraries generated from 11 non-neoplastic tissues. Compared to normal tissue libraries, we identified 453 SAGE tags as differentially expressed in pancreatic cancer, including 395 that mapped to known genes and 58 "uncharacterized" tags. Of the 395 SAGE tags assigned to known genes, 223 were overexpressed in pancreatic cancer, and 172 were underexpressed. In order to map the 58 uncharacterized differentially expressed SAGE tags to genes, we used a newly developed resource called TAGmapper (http://tagmapper.ibioinformatics.org), to identify 16 additional differentially expressed genes. The differential expression of seven genes, involved in multiple cellular processes such as signal transduction (MIC-1), differentiation (DMBT1 and Neugrin), immune response (CD74), inflammation (CXCL2), cell cycle (CEB1) and enzymatic activity (Kallikrein 6), was confirmed by either immunohistochemical labeling of tissue microarrays (Kallikrein 6, CD74 and DMBT1) or by RT-PCR (CEB1, Neugrin, MIC1 and CXCL2). Of note, Neugrin was one of the genes whose previously uncharacterized SAGE tag was correctly assigned using TAGmapper, validating the utility of this program. Novel differentially expressed genes in a cancer type can be identified by revisiting updated and expanded SAGE databases. TAGmapper should prove to be a powerful tool for the discovery of novel tumor markers through assignment of uncharacterized SAGE tags.

Adenocarcinoma↗
PubMed2006

Scanning microarrays at multiple intensities enhances discovery of differentially expressed genes.

MOTIVATION: Scanning parameters are often overlooked when optimizing microarray experiments. A scanning approach that extends the dynamic data range by acquiring multiple scans of different intensities has been developed. RESULTS: Data from each of three scan intensities (low, medium, high) were analyzed separately using multiple scan and linear regression approaches to identify and compare the sets of genes that exhibit statistically significant differential expression. In the multiple scan approach only one-third of the differentially expressed genes were shared among the three intensities, and each scan intensity identified unique sets of differentially expressed genes. The set of differentially expressed genes from any one scan amounted to < 70% of the total number of genes identified in at least one scan. The average signal intensity of genes that exhibited statistically significant changes in expression was highest for the low-intensity scan and lowest for the high-intensity scan, suggesting that low-intensity scans may be best for detecting expression differences in high-signal genes, while high-intensity scans may be best for detecting expression differences in low-signal genes. Comparison of the differentially expressed genes identified in the multiple scan and linear regression approaches revealed that the multiple scan approach effectively identifies a subset of statistically significant genes that linear regression approach is unable to identify. Quantitative RT-PCR (qRT-PCR) tests demonstrated that statistically significant differences identified at all three scan intensities can be verified. AVAILABILITY: The data presented can be viewed at http://www.ncbi.nlm.nih.gov/geo/ under GEO accession no. GSE3017.

Gene Expression Profiling↗