Journal: The Journal of Biological Chemistry

Article Title: O -Linked β- N -Acetylglucosaminylation ( O -GlcNAcylation) in Primary and Metastatic Colorectal Cancer Clones and Effect of N -Acetyl-β- d -glucosaminidase Silencing on Cell Phenotype and Transcriptome *

doi: 10.1074/jbc.M112.345546

Figure Lengend Snippet: Summary of IPA performed for cDNA microarray analysis of the siOGA-SW620 and pS-SW620 clones

Article Snippet: Microarray CEL files were read into Partek and preprocessed by Robust Multiarray Averaging ( 23 ) using default parameters, followed by quantile normalization and probe summarization using median polish.

Techniques: Microarray, Clone Assay

Journal: The Journal of Biological Chemistry

Article Title: O -Linked β- N -Acetylglucosaminylation ( O -GlcNAcylation) in Primary and Metastatic Colorectal Cancer Clones and Effect of N -Acetyl-β- d -glucosaminidase Silencing on Cell Phenotype and Transcriptome *

doi: 10.1074/jbc.M112.345546

Figure Lengend Snippet: OGA silencing affects the transcriptome of SW620 metastatic CRC clone. Control pS-SW620 cells and OGA-silenced SW620 cells were subjected to cDNA microarray analysis. Gene Ontology-based over-representation for the microarray dataset was performed with the IPA software. Over-represented genes were categorized according to their functions (A), and canonical pathways were annotated using the KEGG database (B).

Article Snippet: Microarray CEL files were read into Partek and preprocessed by Robust Multiarray Averaging ( 23 ) using default parameters, followed by quantile normalization and probe summarization using median polish.

Techniques: Control, Microarray, Software

Journal: The Journal of Biological Chemistry

Article Title: O -Linked β- N -Acetylglucosaminylation ( O -GlcNAcylation) in Primary and Metastatic Colorectal Cancer Clones and Effect of N -Acetyl-β- d -glucosaminidase Silencing on Cell Phenotype and Transcriptome *

doi: 10.1074/jbc.M112.345546

Figure Lengend Snippet: Experimental validation of microarray data for four selected proteins. Total proteins were extracted from pS-SW620 and siOGA-SW620 cells and analyzed for the levels of four proteins that showed altered regulation by cDNA microarray assay. A, left panel, representative Western blots using anti-E-cadherin, β-catenin, caveolin-1, IκB-β, and actin antibodies. Right panel, quantitative analysis of the protein levels in the two cell lines. B, total proteins were extracted from SW620 cells (control) and from SW620 cells treated with 25 μm TMG for 24 h (TMG) and analyzed for the level of the above-mentioned proteins. Left panel, representative Western blots. Right panel, quantitative analysis of the relative protein levels in the two samples. All quantitative results (A.U., arbitrary units) are expressed as the mean ± S.E. of at least three repeats. Asterisks indicate significant difference between clones (p ≤ 0.05).

Article Snippet: Microarray CEL files were read into Partek and preprocessed by Robust Multiarray Averaging ( 23 ) using default parameters, followed by quantile normalization and probe summarization using median polish.

Techniques: Biomarker Discovery, Microarray, Western Blot, Control, Clone Assay

Journal: PLoS ONE

Article Title: Long-term ethanol exposure: Temporal pattern of microRNA expression and associated mRNA gene networks in mouse brain

doi: 10.1371/journal.pone.0190841

Figure Lengend Snippet: DE microRNAs common to all 3 brain regions.

Article Snippet: All microRNA microarray data files are available from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO, https://www.ncbi.nlm.nih.gov/geo/ ), accession number GSE90608.

Techniques:

Journal: PLoS ONE

Article Title: Long-term ethanol exposure: Temporal pattern of microRNA expression and associated mRNA gene networks in mouse brain

doi: 10.1371/journal.pone.0190841

Figure Lengend Snippet: 0h DE microRNA targets dysregulated at multiple time points in each brain region.

Article Snippet: All microRNA microarray data files are available from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO, https://www.ncbi.nlm.nih.gov/geo/ ), accession number GSE90608.

Techniques:

Journal: PLoS ONE

Article Title: Long-term ethanol exposure: Temporal pattern of microRNA expression and associated mRNA gene networks in mouse brain

doi: 10.1371/journal.pone.0190841

Figure Lengend Snippet: Profiles are based on hierarchical clustering of centered and scaled expression log ratios of microRNAs DE in at least one time point. Average expression is plotted in red, and each individual microRNA is plotted in gray. Blue text indicates the total number of microRNAs in each cluster.

Article Snippet: All microRNA microarray data files are available from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO, https://www.ncbi.nlm.nih.gov/geo/ ), accession number GSE90608.

Techniques: Expressing

Journal: PLoS ONE

Article Title: Long-term ethanol exposure: Temporal pattern of microRNA expression and associated mRNA gene networks in mouse brain

doi: 10.1371/journal.pone.0190841

Figure Lengend Snippet: Profiles are based on hierarchical clustering of centered and scaled expression log ratios of microRNAs DE in at least one time point. Average expression is plotted in red, and each individual microRNA is plotted in gray. Blue text indicates the total number of microRNAs in each cluster.

Article Snippet: All microRNA microarray data files are available from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO, https://www.ncbi.nlm.nih.gov/geo/ ), accession number GSE90608.

Techniques: Expressing

Journal: PLoS ONE

Article Title: Long-term ethanol exposure: Temporal pattern of microRNA expression and associated mRNA gene networks in mouse brain

doi: 10.1371/journal.pone.0190841

Figure Lengend Snippet: Profiles are based on hierarchical clustering of centered and scaled expression log ratios of microRNAs DE in at least one time point. Average expression is plotted in red, and each individual microRNA is plotted in gray. Blue text indicates the total number of microRNAs in each cluster.

Article Snippet: All microRNA microarray data files are available from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO, https://www.ncbi.nlm.nih.gov/geo/ ), accession number GSE90608.

Techniques: Expressing

Journal: PLoS ONE

Article Title: Long-term ethanol exposure: Temporal pattern of microRNA expression and associated mRNA gene networks in mouse brain

doi: 10.1371/journal.pone.0190841

Figure Lengend Snippet: Only genes with an associated microRNA are listed. Critical network genes were dysregulated at 120hr and present in at least one of the top three IPA networks derived from the time-point based network analysis. Blue text indicates that RNAs were also identified in the cluster sharing the greatest overlap with the list of critical network genes: AMY—cluster 4; NAC—cluster 3; PFC: cluster 4. Inset shows temporal expression pattern for the designated cluster. See for a full version of the inset figures. Red upward pointing arrow indicates up-regulation; Green downward pointing arrow indicates down-regulation. Bracketed letters denote membership in cell-type specific gene lists (See ) enriched in the analyzed datasets [a = astrocyte, i = immune related, m = microglia, n = neuron, o = oligodendrocyte.] (Cell specific gene lists were pre-loaded into IPA and automatically scored against all datasets submitted to Core Analysis. Significant enrichment was determined by p value < 0.05 using Fisher’s exact test.) A single asterisk (*) indicates the microRNA was uniquely detected in the indicated brain-region.

Article Snippet: All microRNA microarray data files are available from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO, https://www.ncbi.nlm.nih.gov/geo/ ), accession number GSE90608.

Techniques: Derivative Assay, Expressing

Journal: PLoS ONE

Article Title: Long-term ethanol exposure: Temporal pattern of microRNA expression and associated mRNA gene networks in mouse brain

doi: 10.1371/journal.pone.0190841

Figure Lengend Snippet: Hub genes identified in the cluster-based networks and their associated microRNAs.

Article Snippet: All microRNA microarray data files are available from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO, https://www.ncbi.nlm.nih.gov/geo/ ), accession number GSE90608.

Techniques: Expressing

Journal: PLoS ONE

Article Title: Dynamic Gene Expression in the Human Cerebral Cortex Distinguishes Children from Adults

doi: 10.1371/journal.pone.0037714

Figure Lengend Snippet: Y-axis shows mRNA expression levels [–DCt values (Ct reference–Ct target)] derived from qPCR experiments whereas the X-axis shows the log2 normalized microarray expression signal intensities. Correlations were considered significant when p<0.05. ρ = correlation coefficient.

Article Snippet: Microarray image files collected for this project are MIAME (Minimum Information about a Microarray Experiment ) compliant and have been deposited in the National Center for Biotechnology Information's Gene Expression Omnibus (GEO) data repository under the series accession number GSE37721.

Techniques: Expressing, Derivative Assay, Microarray

Journal: Carcinogenesis

Article Title: Genetic deletion of sphingosine kinase 1 suppresses mouse breast tumor development in an HER2 transgenic model

doi: 10.1093/carcin/bgx097

Figure Lengend Snippet: Genetic deletion of SphK1 reduced CLDN2 in HER2/neu-induced mice breast tumors. (A) Whole genome expression profile evaluated by microarray analysis assessed the expression of 39000 gene transcripts. Gene expression microarray heatmap (n = 2 per group) of dysregulated genes. (B) Twenty molecules with the most significant expression changes (10 up-regulation and 20 down-regulation) between SphK1+/+ and SphK1−/− tumors are shown. (C) CLDN2 mRNA expression in tumors from SphK1+/+ and SphK1−/− mice was confirmed by qRT-PCR analysis and analyzed by unpaired t-test. ****P ≤ 0.0001 vs. SphK1+/+. (D) Representative paraffin-tumor sections immunostained for CLDN2 in tumors from SphK1+/+ and SphK1−/− mice (P = 0.1339).

Article Snippet: Partek pre-processes raw intensity files from microarray experiment using GCRMA’s background subtraction and uses quantile normalization as the normalization technique.

Techniques: Expressing, Microarray, Gene Expression, Quantitative RT-PCR

Journal: Carcinogenesis

Article Title: Genetic deletion of sphingosine kinase 1 suppresses mouse breast tumor development in an HER2 transgenic model

doi: 10.1093/carcin/bgx097

Figure Lengend Snippet: SphK1 and CLDN2 levels are increased in HER2-positive breast cancers in humans. Tissue microarray containing breast cancer samples from 92 HER2-positive breast cancer patients and matched adjacent normal breast tissues (n = 34) are stained for SphK1 and CLDN2. Staining were scored based on the intensity (0–3) and proportion (0–3), and the total scores were used for the analysis. [(A) and (B)] SphK1 and CLDN2 expressions were compared with pathological features including grade, stage and hormone receptor status. [(C) and (D)] Representative image of high, moderate and low SphK1 and CLDN2 expressing tumors.

Article Snippet: Partek pre-processes raw intensity files from microarray experiment using GCRMA’s background subtraction and uses quantile normalization as the normalization technique.

Techniques: Microarray, Staining, Expressing