Suggestions(1)
Exact(3)
Africa: 399 African HIV-1 subtype C samples downloaded from Los Alamos HIV Sequence Database [ 18- 20].
Further, we evaluated the performance of ADTEx on publicly available 18 paired ovarian cancer/normal samples downloaded from the TCGA project.
As a case study, we applied Amalgam to merge three publicly available human breast cancer samples downloaded from the TCGA data portal, that is, an Agilent gene expression microarray (G4502A) sample, an Illumina HiSeq RNA-Seq (V2), and a copy number variant data sample from Affymetrix Genome wide SNP 6.0 array.
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miRNA expression data and the corresponding clinical data for glioblastoma samples were downloaded from The Cancer Genome Atlas (TCGA) data portal.
Additionally, miRNA expression data from 436 samples were downloaded from The Cancer Genome Atlas (TCGA) stomach adenocarcinoma track.
26 mRNA expression and miRNA expression data for hepatocellular carcinoma patient samples were downloaded from The Cancer Genome Atlas (TCGA) Data Portal (https://tcga-data.nci.nih.gov/tcga/) in May 2014.
Thus, in an effort to explore the extent to which this class of SVs was being expressed in our cancer samples, we downloaded from the TCGA data portal the results of RNA sequencing (RNA-Seq) and microarray (Affymetrix) profiling studies carried out on these same samples.
Discriminant analysis was performed using a multi-sample classifier downloaded from Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/).msu.edu/
The second dataset with HM-27K information consisted of 241 glioblastoma samples (TCGA-GBM, survival information available for 239 samples) and was downloaded from The Cancer Genome Atlas (TCGA) website (http://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp) [ 29, 40].
Samples have been downloaded from the cDNA Stanford Microarray database [ 39].
Also, expression tables of all the epigenetic factors in all samples can be downloaded from the Download section of the database.
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