mRNA summary¶
The mRNA summary report builder provides expression sequencing data information for supplied samples. If the supplied tumor sample has expression data for its corresponding normal sample and information about the TCGA project and the availablility of other data types (i.e., WES, CNV, miRNA, and methylation) for the same individual, this report builder also provides a rough estimation of the fold change of each gene.
mRNA summary module in Sequence Miner¶
The expression value can be viewed in one of the following three normalized or non-normalized formats, depending on user input.
Expression value format |
Description |
|---|---|
HTSeq |
Raw read counts of the expression data at individual gene level, calculated using the HTSeq tool 1 |
FPKM |
FPKM, or fragments per kilobase of transcript per million mapped reads, is a normalized format of the expression value that normalizes read count based on gene length and the total number of mapped reads 2. It is calculated as follows:
|
FPKM UQ (default) |
FPKM UQ, or fragments per kilobase of transcript per million mapped reads upper quartile, is a modified version of the FPKM normalization method 3. It is calculated as follows:
|
Interpreting the output¶
Output columns can be viewed in different Perspectives (see also Column descriptions).
The Default view perspective shows the expression value of each gene per supplied sample, whereas the Candidate genes perspective shows only the genes provided in the candidate_gene_report_grid or candidate_gene_report_file fields.
If available, expression values are provided for both the tumor sample and its corresponding normal sample. A fold change in the expression of the gene in the tumor sample is also calculated relative to the normal sample. A positive value indicates higher expression in the tumor and vice versa. The fold change value can provide insight about the most highly expressed or least expressed genes at the individual sample level or the group level.
The PN and Flag output columns can provide insight about the presence of other data types that are available for both the tumor sample and its corresponding normal sample, which can be useful for a multi-omic study.
Column descriptions¶
Group |
Column |
Description |
|---|---|---|
FPKM |
These columns are displayed only when either FPKM or FPKM UQ is selected in the expression_value field. |
|
normal |
FPKM normalized expression value of the corresponding normal sample |
|
tumor |
FPKM normalized expression value of the tumor sample |
|
UQ_normal |
FPKM (upper quartile) normalized expression value of the corresponding normal sample |
|
UQ_tumor |
FPKM (upper quartile) normalized expression value of the tumor sample |
|
read |
These columns are displayed only when HTSeq is selected in the expression_value field. |
|
count_normal |
Raw (non-normalized) read counts from HTSeq of the corresponding normal sample |
|
count_tumor |
Raw (non-normalized) read counts from HTSeq of the tumor sample |
|
Other columns |
candidate_gene |
A binary value (0 or 1) indicating whether the gene is one of the candidate genes selected in the candidate_gene_report_grid or candidate_gene_report_file; 1 indicates TRUE and 0 indicates FALSE |
Expr_value_log2_fold_change |
The log2 fold change in expression in tumor relative to normal; a positive values indicates higher expression in the tumor and vice versa; the formula for calculation is as follows: log2((expression value in tumor + 1)/(expression value in normal + 1)) |
|
cdsStart |
Start of the protein coding sequence (CDS) of the gene |
|
cdsEnd |
End of the protein coding sequence (CDS) of the gene |
|
Biotype |
The biological type of the gene (protein coding, lincRNA, miRNA, etc.) |
|
Description |
The name of the gene and other information about the gene, in a longer format |
|
SubjectID |
The TCGA ID of the individual (TCGA--**) |
|
Disease_type |
The type of cancer |
|
Primary_site |
The primary site or organ of the cancer type |
|
TCGA_project |
A four letter code for the project of the cancer type |
|
PN |
CNV_normal |
Sample name/ID of the CNV data of the tumor sample’s corresponding normal sample |
CNV_tumor |
Sample name/ID of the CNV data of the same tumor sample |
|
Methyl_normal |
Sample name/ID of the methylation sequencing data of the tumor sample’s corresponding normal sample |
|
Methyl_tumor |
Sample name/ID of methylation sequencing data of the same tumor sample |
|
miRNA_normal |
Sample name/ID of miRNA sequencing data of corresponding normal sample for the same tumor sample |
|
miRNA_tumor |
Sample name/ID of miRNA sequencing data of the same tumor sample |
|
RNASeq_normal |
Sample name/ID of mRNA sequencing data of corresponding normal sample for the same tumor sample |
|
RNASeq_tumor |
Sample name/ID of mRNA sequencing data of the same tumor sample |
|
WES |
Sample name/ID of WES data of the same tumor sample |
|
Flag |
CNV_normal |
A logical value (true/false) indicating whether the CNV data of the corresponding normal sample is available for the same tumor sample |
CNV_tumor |
A logical value (true/false) indicating whether CNV data of the same tumor sample is available |
|
Methyl_normal |
A logical value (true/false) indicating whether methylation sequencing data of corresponding normal sample is available for the same tumor sample |
|
Methyl_tumor |
A logical value (true/false) indicating whether methylation sequencing data of the same tumor sample is available |
|
miRNA_normal |
A logical value (true/false) indicating whether miRNA sequencing data of corresponding normal sample is available for the same tumor sample |
|
miRNA_tumor |
A logical value (true/false) indicating whether miRNA sequencing data of the same tumor sample is available |
|
RNASeq_normal |
A logical value (true/false) indicating whether mRNA sequencing data of corresponding normal sample is available for the same tumor sample |
|
RNASeq_tumor |
A logical value (true/false) indicating whether mRNA sequencing data of the same tumor sample is available |
|
WES |
A logical value (true/false) indicating whether WES data of the same tumor sample is available |
Perspective views¶
Perspectives subtabs focus on subsets of the columns in the Default view.
Perspective |
Description |
|---|---|
Candidate genes |
Displays only the genes selected in the candidate_gene_report_grid or candidate_gene_report_file fields. |
Default view |
Displays all genes |