The Cancer Genome Atlas (TCGA) is a large data repository of multi-omics and clinical data of cancers. The Cancer Genome Atlas (TCGA) is a large data repository of multi-omics and clinical data of cancers.
This demonstration shows how to extract differentially expressed genes (DEGs) between normal and tumor samples (part 1) and potential controller miRNAs (part 2). The operation of importing TCGA miRNA-Seq data or importing RNA-Seq data becomes much simpler than what you see on the following movies after v1.20.5031.
We extracted the following miRNAs as potential controller miRNAs of Prostate Adenocarcinoma from this tutorial. You can download the list of potential gene-miRNA pairs for more details.
hsa-mir-10a, hsa-mir-15b, hsa-mir-17, hsa-mir-20a, hsa-mir-20b, hsa-mir-25, hsa-mir-30b, hsa-mir-32, hsa-mir-93, hsa-mir-96, hsa-mir-106a, hsa-mir-130b, hsa-mir-141, hsa-mir-148a, hsa-mir-182, hsa-mir-183, hsa-mir-191, hsa-mir-200c, hsa-mir-203, hsa-mir-204, hsa-mir-363, hsa-mir-375, hsa-mir-451, hsa-mir-484, hsa-mir-573, hsa-mir-629, hsa-mir-708, hsa-mir-888, hsa-mir-890, hsa-mir-891b, hsa-mir-892a, hsa-mir-892b
https://www.dropbox.com/s/8a2aa8rn74lt6rw/TCGA-PRAD_Correlations_between_miRNAs_and_targets.txt?dl=1
Tutorial Movie
This movie tutorial shows how to get RNA-seq data and analyze with Subio Platform on your computer. Preparation in part1, and extracting potential controller miRNAs in part2. "Find miRNA Targets" tool is included in Advanced Plug-in. It supports miRecords, mirTarbase, TargetScan, PITA and miRanda databases of miRNA and target gene pairs.
Part 1
Analyzing TCGA PRAD RNA-Seq
The import process becomes much easier than this movie. You can skip until 9min 20sec.
9:20 editing parameter to bring information about tumor condition.
10:30 editing DataSet to group patients.
11:20 checking data quality with scatter plot and histogram.
11:45 filtering to remove too-low and too-stable genes.
13:00 PCA to overview all samples.
14:25 extracting DEGs between normal and tumor.
15:00 creating region lists of the DEGs.
15:40 preparing for combining miRNA data. Make a list of the order of samples in barcode.
Please take an Online Training for a full instruction of the data analysis.
Part 2
Analyzing TCGA PRAD miRNA-Seq Integratively with Gene Expression Data
The import process becomes much easier than this movie. You can skip until 5min 45sec.
5:45 viewing signal values and editing normalization.
6:25 editing a DataSet to group samples.
6:45 editing parameters again to clean up.
7:10 editing parameters again to import the orders of samples of RNA-Seq data.
8:15 creating new DataSets in which samples are ordered as RNA-Seq DataSets.
9:00 applying "Find miRNA Target" tool to search potential controllers of the DEGs.
10:10 browsing the result (comparing the distributions of correlation coefficient between "all samples" and "normal-tumor paired sampels")
11:45 viewing expression patterns of miRNA-gene pairs.
12:10 exporting the table of correlation coefficients of miRNA-gene pairs.
Please take an Online Training for a full instruction of the data analysis.
Related Topics:
- Find miRNA Targets
- Importing miRNA-Seq data of TCGA
- Be careful of using microRNA expression datasets.
Data Source:
The Cancer Genome Atlas
Gene Expression Omnibus
"MicroRNA expression data for human primary and metastatic prostate cancer samples and control normal adjacent benign prostate"