Selection for Feature Gene Subset in Microarray Expression Profiles Based on a Hybrid Algorithm Using SVM and GA

2006 ◽  
pp. 637-647 ◽  
Author(s):  
Wei Xiong ◽  
Chen Zhang ◽  
Chunguang Zhou ◽  
Yanchun Liang
Keyword(s):  
Hybrid Algorithm ◽  
Expression Profiles ◽  
Gene Subset ◽  
Selection For ◽  
Microarray Expression

Profiling and bioinformatics analysis of differentially expressed circular RNAs in human intervertebral disc degeneration

2019 ◽  
Vol 51 (6) ◽  
pp. 571-579 ◽  
Author(s):  
Shunmin Wang ◽  
Jingchuan Sun ◽  
Haisong Yang ◽  
Weiguo Zou ◽  
Bing Zheng ◽  
...  
Keyword(s):  
Intervertebral Disc ◽  
Disc Degeneration ◽  
Intervertebral Disc Degeneration ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Functional Changes ◽  
Qrt Pcr ◽  
Reverse Transcription Pcr ◽  
Microarray Expression

AbstractThe functional changes of nucleus pulposus (NP) cells are considered to be the initiating factors of intervertebral disc degeneration (IDD), and the differentially expressed circRNAs in NP cells may play an important role in the process of IDD. To identify circular RNAs (circRNAs) associated with human IDD, we isolated the NP cells from human degenerated and non-degenerated intervertebral disc and identified NP cells by microscopy and cell proliferation. CircRNA microarray expression profiles were obtained from NP cells of degenerated and non-degenerated intervertebral disc and further validated by quantitative reverse transcription PCR (qRT-PCR). The expression data were analyzed by bioinformatics. Microarray analysis identified 7294 circRNAs differentially expressed in degenerated human IDD NP cells. Among them, 3724 circRNAs were up-regulated and 3570 circRNAs were down-regulated by more than 2 folds. After validating by qRT-PCR, we predicted the possible miRNAs of the top dysregulated circRNAs using TargetScan, and miRanda. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the most modulated circRNAs regulate the viability, degradation, apoptosis and oxidative stress in NP cells, and the possible mechanism underlying IDD was discussed. These results revealed that circRNAs may play a role in IDD and might be a promising candidate molecular target for gene therapy.

scholarly journals Microarray Expression Profiles and Bioinformatics Analyses Reveal Aberrant Circular RNAs Expression in Bladder Cancer

2020 ◽  
Vol Volume 13 ◽  
pp. 10889-10899
Author(s):  
Jun Yang ◽  
Junwen Chen ◽  
Si Wu ◽  
Xiang Fei ◽  
Xia Wang ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Expression Profiles ◽  
Circular Rnas ◽  
Bioinformatics Analyses ◽  
Microarray Expression

scholarly journals Expression Profiles of Long Noncoding RNAs in Intranasal LPS-Mediated Alzheimer’s Disease Model in Mice

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Liang Tang ◽  
Lan Liu ◽  
Guangyi Li ◽  
Pengcheng Jiang ◽  
Yan Wang ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Network Analysis ◽  
Expression Profiles ◽  
Disease Model ◽  
Noncoding Rnas ◽  
Memory Loss ◽  
Long Noncoding Rnas ◽  
Specific Effects ◽  
Microarray Expression

Alzheimer’s disease (AD), characterized by memory loss, cognitive decline, and dementia, is a progressive neurodegenerative disease. Although the long noncoding RNAs (lncRNAs) have recently been identified to play a role in the pathogenesis of AD, the specific effects of lncRNAs in AD remain unclear. In present study, we have investigated the expression profiles of lncRNAs in hippocampal of intranasal LPS-mediated Alzheimer’s disease models in mice by microarray method. A total of 395 lncRNAs and 123 mRNAs was detected to express differently in AD models and controls (>2.0 folds,p<0.05). The microarray expression was validated by Quantitative Real-Time-PCR (qRT-PCR). The pathway analysis showed the mRNAs that correlated with lncRNAs were involved in inflammation, apoptosis, and nervous system related pathways. The lncRNA-TFs network analysis suggested the lncRNAs were mostly regulated by HMGA2, ONECUT2, FOXO1, and CDC5L. Additionally, lncRNA-target-TFs network analysis indicated the FOXL1, CDC5L, ONECUT2, and CDX1 to be the TFs most likely to regulate the production of these lncRNAs. This is the first study to investigate lncRNAs expression pattern in intranasal LPS-mediated Alzheimer’s disease model in mice. And these results may facilitate the understanding of the pathogenesis of AD targeting lncRNAs.

scholarly journals Comparison of microarray expression profiles between follicular variant of papillary thyroid carcinomas and follicular adenomas of the thyroid

BMC Genomics ◽  
2015 ◽  
Vol 16 (S1) ◽  
Author(s):  
Hans-Juergen Schulten ◽  
Zuhoor Al-Mansouri ◽  
Ibtisam Baghallab ◽  
Nadia Bagatian ◽  
Ohoud Subhi ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Papillary Thyroid ◽  
Follicular Variant ◽  
Thyroid Carcinomas ◽  
Microarray Expression

Gene Expression Profiles of Hydroxyurea Tolerant Cell Lines Identify Genetic Mechanisms That Influence Hydroxyurea Maximum Tolerated Dose

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1005-1005
Author(s):  
Rosa Diaz ◽  
Jonathan M Flanagan ◽  
Thad A Howard ◽  
Russell E. Ware
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Cell Lines ◽  
Expression Profiles ◽  
K562 Cells ◽  
Maximum Tolerated Dose ◽  
False Discovery ◽  
Microarray Expression ◽  
Tolerant Cell

Abstract Abstract 1005 Hydroxyurea has emerged over the past decade as an effective therapeutic agent for patients with sickle cell anemia (SCA). However, drug dosing and hematological responses can be highly variable; both %HbF response and maximum tolerated dose (MTD) vary widely among patients with SCA who receive hydroxyurea treatment. To obtain further insight into the cellular and molecular pathways, as well as genetic factors that might influence the hydroxyurea MTD, K562 erythroleukemia cells were exposed to hydroxyurea in vitro, to create cell lines that were highly drug tolerant to doses ranging from 250μM to 1500μM. Cell lines had dose-response curves that exhibited clear drug tolerance; naïve K562 showed 50% proliferation in the presence of 250μM hydroxyurea, while tolerant cell lines showed >90% proliferation at the same dose as measured by the BrdU Cell Proliferation Assay. In addition, the tolerant lines showed normal and equivalent progression through cell cycle by flow cytometry cell cycle analysis. After 15 weeks of continuous exposure, cells were harvested and mRNA microarray expression profiles were analyzed for naïve K562 (no hydroxyurea exposure) and cell lines tolerant to 500, 1000, or 1500μM hydroxyurea. Gene expression was measured on Affymetrix U133 Plus 2.0 chips. Differential expression between sample groups was determined using ANOVA, and p-values were corrected for multiple testing using the Benjamin-Hochberg false discovery rate (FDR) method to identify genetic profiles and genes consistently increased or decreased compared to naïve K562 cells. Using a threshold of 2-fold change compared to untreated cells and a false discovery rate <5%, a total of 864 genes were significantly altered in hydroxyurea tolerant cells, including 337 genes whose expression consistently correlated with increasing hydroxyurea dose (Pearson correlation p<.001). The PANTHER classification system was used to group genes into categories based on molecular functions. Of the genes that correlated significantly with increasing hydroxyurea dosing (n=337), there were 181 up-regulated genes and 156 down-regulated genes that had molecular functions including catalytic activity, binding, transcription regulator activity and transporter activity. Genes with transporter activity included SLC6A19, ATP6VOD1, ABCG2, ATP6V1B2 and KCNN4. Other genes of interest based on function included RRM2, PLS3, KCNAB2, UBE2A and SRI. Real-time quantitative reverse transcription (RT)-PCR then quantified the expression of 20 candidate genes to verify the accuracy of the microarray expression data. The next steps will include correlation of these findings with clinical data, specifically early reticulocyte mRNA expression and hydroxyurea MTD values obtained from children with SCA enrolled in the prospective Hydroxyurea Study of Long-term Effects (HUSTLE, NCT00305175). These data document that continuous in vitro exposure of K562 cells to hydroxyurea leads to tolerant cell lines that feature substantial changes in gene expression. Altered expression of certain genes present in erythroid cells including RRM2 and membrane transporters represent compensatory changes in response to hydroxyurea exposure, and may help explain the variability in hydroxyurea MTD observed among patients with SCA. Disclosures: Off Label Use: Hydroxyurea is not FDA approved for pediatric sickle cell patients. Howard:Baylor College of Medicine: Employment.

scholarly journals Pla2g2a Attenuates Colon Tumorigenesis in Azoxymethane-Treated C57BL/6 Mice; Expression Studies Reveal Pla2g2a Target Genes and Pathways

2009 ◽  
Vol 31 (5) ◽  
pp. 345-356
Author(s):  
Remond J. A. Fijneman ◽  
Lindsey K. Bade ◽  
Johannes R. Peham ◽  
Mark A. van de Wiel ◽  
Victor W. M. van Hinsbergh ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Wnt Signaling Pathway ◽  
Enrichment Analysis ◽  
Germline Mutations ◽  
Gene Set Enrichment Analysis ◽  
Colon Tumorigenesis ◽  
Expression Studies ◽  
Microbial Defense ◽  
Microarray Expression

Background: The group IIA secretory phospholipase A2 gene, Pla2g2a, confers resistance to intestinal tumorigenesis in the ApcMin/+ mouse model. However, it is unclear how Pla2g2a exerts its tumor-suppressive effects and whether its mode of action depends on Apc-germline mutations.Methods: We tested whether expression of a Pla2g2a transgene provides protection against carcinogen-induced colon tumors, and examined whether the normal colon microenvironment is modulated by Pla2g2a expression.Results: Pla2g2a strongly inhibited colon tumorigenesis in mice following treatment with the DNA alkylating agent azoxymethane (AOM). Moreover, AOM-induced duodenal tumors were also attenuated by Pla2g2a expression. These tumors demonstrated upregulation of β-catenin, indicative of involvement of the Wnt signaling pathway. Comparison of genome-wide microarray expression profiles of healthy (non-pathologic) colon tissues from Pla2g2a-transgenic to non-transgenic mice revealed 382 genes that were differentially expressed, comprising clusters of genes involved in inflammation and microbial defense, cell signaling and cell cycle, transactivation, apoptosis and mitochondrial function, DNA repair, and lipid and energy metabolism. Pathway analysis using Gene Set Enrichment Analysis (GSEA) indicated that Pla2g2a suppresses the expression of interferon-induced genes.Conclusion: Our results demonstrate that Pla2g2a attenuates colon tumorigenesis independent of Apc-germline mutations, and reveal Pla2g2a target genes and pathways in non-pathologic colon microenvironment that influence conditions for colorectal cancer development.

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