Differential expression data
Wen-Ching Wang
Dear Sir:
I am trying to examine the differential expression profiles between cancer and normal samples across various types of cancer for a few given genes as reported in (Gnad et al. BMC Genomics 2015, 16(Suppl 8):S5 http://www.biomedcentral.com/1471-2164/16/S8/S5). In this paper, they retrieved TCGA RNAseq raw reads and the comparison was made as shown in Figure 5 (below).
In the current cbioportal, there is an expression plot that shows Gene X Expression- RNA Seq V2 (log). Is this plot showing the differential expression profile or only the expression data of the cancer tissues? If it is the latter, could you please kindly suggest how can I perform such an analysis?
Many thanks.
Sincerely yours,
Wen-Ching
Dr. Wen-Ching Wang 王雯靜, Ph.D.
Department of Life Science &
Institute of Molecular and Cellular Biology
National Tsing Hua University, Taiwan
101, Sec. 2, Kuang- Fu Road
Hsinchu, 30013, Taiwan
新竹市光復路二段101號
清華大學生科二館
Tel: 886-3-5742766
Fax: 886-3-5715934
E-mail: wcw...@life.nthu.edu.tw
Materials and methods:
To identify differential gene expression between tumors
and healthy tissues, TCGA RNAseq raw reads were
downloaded for available tumor types (BLCA, BRCA,
COAD, KICH, KIRC, LUAD, LUSC, STAD, TCHA,
UCEC) and processed by our GSNAP [43] based transcriptome
analysis pipeline [44]. RNAseq data for both
tumors and healthy tissues were not available for GBM,
LAML and OV. RNAseq reads were first aligned to ribosomal
RNA sequences to remove ribosomal reads.
Remaining reads were aligned to the human reference
genome (NCBI Build 37) using GSNAP version ‘2012-01-
11’, allowing maximum of 2 mismatches per 75 base
sequence (parameters: “-M 2 -n 10 -B 2 -i 1 -N 1 -w
200000 -E 1 –pairmax-rna = 200000”). Gene expression
was quantified with RPKM values (reads mapping to a
gene per kilobase of transcript per million reads
sequenced) and variance stabilized counts derived from
the number of reads mapped to each RefSeq gene. The
DESeq R package [45] was applied to estimate size factors,
obtain dispersion estimates, and measure differential
gene expression between tumors and healthy tissues
using default parameters. Results were reported as fold
changes and associated adjusted p-values. In addition to
DESeq based negative binomial generalized linear models
for differential expression significance, we defined genes
with tumor exclusive expression (genes that are
expressed in tumors but not in healthy tissues), if their
90% quantile expression levels in all healthy tissues were
equal to the expression levels of pseudo counts, but minimum
1 RPKM in the tumors of at least one cancer type.
Hsiao-Wei Chen
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Hsiao-Wei Chen
Hi Wen-Ching,The gene expression plot (Gene X Expression - RNA Seq V2(log)) on the current portal is only for the tumor samples, not including normal samples. We may add normal data in the future on our portal.
To get the expression plot for certain TCGA cancer types on cBioPortal (https://cbioportal.mskcc.org/), you may search tcga in the "Select Cancer Study" query box, select the TCGA datasets of interest, enter your gene list in the text area below, and submit. You will see the "Expression" tab in the next page, and the expression plot is over there.
Hope this is what you're asking for, if not, please let us know (an example is as attached).Thank you,Annice
On Tue, Aug 9, 2016 at 7:51 AM, Wen-Ching Wang <wcw...@life.nthu.edu.tw> wrote:
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