miRNA summary¶
The miRNA summar report builder provides miRNA 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 availability 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 for each miRNA gene.
miRNA summary module in Sequence Miner¶
The expression value can be viewed for gene (expression for all reads aligned to known miRNAs in the miRbase reference) or individual isoforms of the miRNA, depending on user input 1. For both outputs, the expression is shown in the following formats:
Expression value format |
Description |
|---|---|
read_count |
The raw read counts of the expression data at the individual gene or isoform level |
reads_per_million_miRNA_mapped |
Read counts normalized to reads per million mapped reads (RPM) |
Example use case¶
A user is interested in knowing the overall miRNA expression pattern of the tumor samples in a particular TCGA cohort or project (e.g., ACC). Using this report builder, it is possible to identify the most active miRNA genes and the fold change of each gene (for tumor samples with corresponding normal samples) in the entire TCGA project.
Interpreting the output¶
Output columns can be viewed in different Perspectives (see also Column descriptions).
The Default view perspective shows the miRNA expression value of each gene or miRNA isoform per supplied sample, whereas the Candidate genes perspective shows only the genes provided in the candidate_gene_report_grid or candidate_gene_report_file input fields.
If available, expression values are displayed for both the tumor sample and its corresponding normal sample. A fold change in the expression of the miRNA 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 active miRNA 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 multi-omic studies.
Column descriptions¶
Group |
Column |
Description |
|---|---|---|
tumor |
cross_mapped |
A logical value (Y = Yes, N = No) indicating whether reads to the miRNA are cross-mapped to another miRNA (in the miRBase) or to different regions of the same miRNA in the tumor sample |
read_count |
The raw (non-normalized) read counts of the tumor sample |
|
reads_per_million_miRNA_mapped |
Read counts of the tumor sample normalized to reads per million mapped reads (RPM) |
|
normal |
cross_mapped |
A logical value (Y = Yes, N = No) indicating whether reads to the miRNA are cross-mapped to another miRNA (in the miRBase) or to different regions of the same miRNA in the corresponding normal sample |
read_count |
The raw (non-normalized) read counts of the corresponding normal sample |
|
reads_per_million_miRNA_mapped |
Read counts of the corresponding normal sample normalized to reads per million mapped reads (RPM) |
|
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 fields; 1 indicates TRUE and 0 indicates FALSE |
Expr_value_log2_fold_change |
The log2 fold change in miRNA expression in tumor relative to normal; a positive value indicates higher expression in the tumor and vice versa; the formula for calculation is log2((expression value in tumor + 1)/(expression value in normal + 1)) |
|
miRNA_ID |
The ID of the miRNA (both stem-loop and mature form) in miRBase |
|
miRNA_region |
The type of miRNA region (mature, precursor, etc.) and the miRBase unique identifier of the region |
|
isoform_coords |
The genomic location of the observed isoform of the miRNA |
|
Biotype |
The biological type of the gene (lincRNA, miRNA, etc.) |
|
Description |
The name of the gene and 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 |
The sample name/ID of the CNV data of the tumor sample’s corresponding normal sample |
CNV_tumor |
The sample name/ID of the CNV data of the same tumor sample |
|
Methyl_normal |
The sample name/ID of the methylation sequencing data of the tumor sample’s corresponding normal sample |
|
Methyl_tumor |
The sample name/ID of the methylation sequencing data of the same tumor sample |
|
miRNA_normal |
The sample name/ID of the miRNA sequencing data of the tumor sample’s corresponding normal sample |
|
miRNA_tumor |
The sample name/ID of the miRNA sequencing data of the same tumor sample |
|
RNASeq_normal |
The sample name/ID of the mRNA sequencing data of the tumor sample’s corresponding normal sample |
|
RNASeq_tumor |
The sample name/ID of the mRNA sequencing data of the same tumor sample |
|
WES |
The sample name/ID of the 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 the CNV data of the same tumor sample is available |
|
Methyl_normal |
A logical value (true/false) indicating whether the methylation sequencing data of the corresponding normal sample is available for the same tumor sample |
|
Methyl_tumor |
A logical value (true/false) indicating whether the methylation sequencing data of the same tumor sample is available |
|
miRNA_normal |
A logical value (true/false) indicating whether the miRNA sequencing data of corresponding normal sample is available for the same tumor sample |
|
miRNA_tumor |
A logical value (true/false) indicating whether the miRNA sequencing data of the same tumor sample is available |
|
RNASeq_normal |
A logical value (true/false) indicating whether the mRNA sequencing data of corresponding normal sample is available for the same tumor sample |
|
RNASeq_tumor |
A logical value (true/false) indicating whether the mRNA sequencing data of the same tumor sample is available |
|
WES |
A logical value (true/false) indicating whether the 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 |