Project description:To characterize lncRNA expression in breast tumors and identify lncRNAs specifically expressed in the basal-like subtype of breast tumors
Project description:Lung cancer is a heterogeneous disease with high mortality rate globally. Lung adenocarcinoma (ADC) is the most common histological subtype of lung cancer. Multiple studies indicate that lncRNAs emerge as a novel class of critical regulators of cancer. However, the expression of lncRNAs has not been comprehensively surveyed in ADC at a genome-wide scale. Herein we examined landscapes of the lncRNAs and their potential target genes in an integrative fashion in ADC. The differences expression level of lncRNAs and mRNA were determined by microarray. qRT-PCR was performed to validate the lncRNAs expression level in a cohort of 42 tumor tissues and adjacent normal lung tissues. R and Bioconductor were used for data analysis. TF-lncRNAs-gene networks were generated by Cytoscape software. A total of 3045 lncRNAs were differentially expressed between tumor and normal tissues (1048 up and 1997 down). The qRT-PCR of 9 lncRNAs results showed that the expression patterns of these lncRNAs were consistent with the microarray data. Meanwhile, we find NONHSAT077036 expression was associated with N classification and clinical stage. Further, we analyzed the potential co-regulatory relationship between the lncRNAs and target genes using the ‘cis’ and ‘trans’ model. In the 25 related transcription factors (TFs), our analysis in TCGA database found that patients with lower expression of POU2F2 and higher expression of TRIM28 had a shorter overall survival time, suggesting that POU2F2 and TRIM28 could be biomarkers for poor prognosis of ADC. Hence, “POU2F2-lncRNAs” “TRIM28-lncRNAs” two element networks and “POU2F2-lncRNAs-mRNAs” “TRIM28-lncRNAs-mRNAs” there element relationship tables were generated.
Project description:LncRNA expression profiling for liver tissues of mice fed for NFD, LSF and HSF groups Summary: An abstract of the experiment and the data analysis. Experiment Workflow: A workflow of the experiment and the data analysis. Project Description: Sample and experiment information. Array Information: Mouse 8 x 60K LncRNA expression array information. Summary Table of Files for Data Delivery: Contains summary table of files for data delivery and the recommended software programs for viewing the data. Data Analysis for LncRNAs 1. Raw LncRNA data normalization and low intensity filtering: Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity LncRNAs were filtered (LncRNAs that at least 6 out of 9 samples have flags in Present or Marginal were chosen for further analysis, these LncRNAs can be found from the LncRNA Expression Profiling Data.xls file). 2. Quality assessment of LncRNA data after filtering: Contains Box Plot and Scatter Plot for LncRNAs after filtering (This data can be found from the LncRNA Expression Profiling Data.xls file). 3. Differentially expressed LncRNAs screening: Contains differentially expressed genes with statistical significance that passed Volcano Plot filtering (Fold Change >= 2.0, P-value <= 0.05) (This data can be found from the Differentially Expressed LncRNAs.xls file). 4. Heat Map and Hierarchical Clustering: Hierarchical Clustering of Differentially Expressed LncRNAs (The heat map can be found from the LncRNA Expression Profiling Data.xls file). Data Analysis for mRNAs 1. Raw mRNA data normalization and low intensity filtering: Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity mRNAs were filtered (mRNAs that at least 6 out of 9 samples have flags in Present or Marginal were chosen for further analysis, these mRNAs can be found from the mRNA Expression Profiling Data.xls file). 2. Quality assessment of mRNA data after filtering: Contains Box Plot and Scatter Plot for mRNAs after filtering (This data can be found from the mRNA Expression Profiling Data.xls file). 3. Differentially expressed mRNAs screening: Contains differentially expressed genes with statistical significance that passed Volcano Plot filtering (Fold Change >= 2.0, P-value <= 0.05) (This data can be found from the Differentially Expressed mRNAs.xls file). 4. Heat Map and Hierarchical Clustering: Hierarchical Clustering of Differentially Expressed mRNAs (The heat map can be found from the mRNA Expression Profiling Data.xls file). 5. Pathway analysis: Pathway analysis of the differentially expressed mRNAs. 6. GO analysis: GO term analysis of the differentially expressed mRNAs. LncRNA Classification and Subgroup Analysis 1. Rinn lincRNAs profiling: Contains profiling data of all lincRNAs based on John Rinn's papers (This data can be found from the Rinn lincRNAs profiling.xls file). 2. LincRNAs nearby coding gene data table: Contains the differentially expressed lincRNAs and nearby coding gene pairs (distance < 300 kb) (This data can be found from the LincRNAs nearby coding gene data table.xls file). Sample RNA Quality Control: Sample quality control data file from NanoDrop ND-1000 spectrophotometer and standard denaturing agarose gel electrophoresis. Methods: A brief introduction of methods for sample preparation, microarray design, experiment, and data analysis.