inst/shiny/interpretation.md

In korkutlab/imogimap: What the Package Does (One Line, Title Case)

Interpret results:

Table:

For each gene pair, a combined action score and three statistical assessments are calculated. Gene1Expr and Gene2Expr columns show expression levels of Gene1 and Gene2 correspondingly. A positive combined action score with both gene expressions marked as "High" indicates a synergistic increase of Immune-associated phenotype (IAP) level in response to high expression of both genes. A negative combined action score with both genes marked as "High" indicates synergistic decrease of IAP level in response to high expression of both genes. The higher the absolute value of a combined action score is, the stronger the two genes co-associate with IAP levels.

Similarly, A positive combined action score with both gene expressions marked as "Low" indicates a synergistic increase of Immune-associated phenotype (IAP) level in response to low expression of both genes. A negative combined action score with both genes marked as "low" means synergistic decrease of IAP level in response to low expression of both genes.

Three statistical measurements include:

• An unpaired Wilcoxon signed-rank pvalue, that evaluates the largest of the three pvalues in the boxplot below.
• A specificity p.value, that measures the probability of finding a score higher than the observed combined action score, by randomly pairing a gene from genome to any of genes in the lists. A lower p.value indicates a more specific results.
• A Sensitivity R coefficient, that measures the sensitivity of the observed combined action score to the exact data configuration. The more robust scores, therefore the least sensitive ones, have lower sensitivityR.

Finally, the last column shows whether the two genes are a known ligand-receptor pair.

Network:

A color coded graphical network of combinatorial associations is shown in the "Network" section. Red (Blue) edges represent synergistic up-regulation (down-regulation) of IAP. Dark red (Dark blue) vertices identify high expression (low expression) of immune checkpoint (ICP) genes, and orange (blue) vertices identify high expression (low expression) of oncogenes. A solid black edge indicates an existing ligand-receptor interaction between two adjacent vertices. The graphics below summarizes network color-codings.

A cutoff parameter is included to subset the list to those pairs with absolute value of combined action scores higher than the cutoff percentile value. For example, a cutoff of 80 will exclude 80% of scores that are lowest in absolute value.

Boxplot

To help user interpret their results, samples are subsetted and stratified to four sub-cohorts according to their gene expression levels. High/low expression levels are determined using the upper/lower quartile of the corresponding gene expression. p.values are calculated using unpaired Wilcoxon signed-rank test. Use the drop-down menu io see boxplot for a different gene-pair.

For more information see https://doi.org/10.1101/2021.10.06.462889 Cite like: ... Contact us at:

korkutlab/imogimap documentation built on March 17, 2023, 8:22 a.m.