GSEA (Gene Set Enrichment Analysis) for ECU Brease Cancer patients

In this experiment, RNASeq results of differentially expressed (DE) genes
from 129 breast cancer/tumor tissue with matched normal tissue
from various stage of cancer were analyzed.The expression of
TP53BP2 is taken as reference expression for analysis

Analysis

1. Methods

2. Results

Initial Report

Initial report gives the summary of the results that are obtained
by GSEA analysis. The summary will look like the picture on right side.














Enrichment Score for Gene Set

Enrichment score (ES] should be between 100-1000 (Here it is 100-130)
.Normalized Enrichment Score (NES) vs P value of enrichment NES=
Actual ES/Mean ES of all geneset. Nominal p Value(Np)=The nominal p
value estimates the statistical significance of the enrichment score for a
single gene set. Like small np but high FDR-not enough sample, high Np,
small FDR-a single geneset is not significant. If one of many genesets
are enriched, significantVolcano plot present the significantly
differentially expressed (DE) individual genes.The figure can be presented
for exptentof differentially expressed individual genes.








Nikolawski GeneSet shows highest score

Comments: Among 46 breast cancer gene set, Nikolsky gene set
has minimum distance (dotted line) of peak from ES score (Y axis)
Indicating minimum number of genes expression are
needed to achieve the ES score.



















Components of Nikolawski GeneSet

The individual genes in Nikolawski Gene Set are shown with their
expression with fold change, p-valur and FDR.
Both upregulated and downregulated genes are present












Enrichment Scores for individual genes of Nikolawski GeneSet

Individual genes of NIkolawski GeeneSet and their differential expressions






















Gene subset and Set to Set analysis

These analysis shows the relation between Nikolwaski Gene set and
other cancer gene set and subset. Its an way to link other genes also
beyond Nikolawski gene set.































Nikolawski Gene Set Enriched Cellular Pathway

The cellular pathway analysis,presents the results of
expressed genes affects the function of genes that are located
in the genome.

Conclusion

Thus GSEA analysis is very important for identifying genes in
the cellular pathway.Here in this experiments, we identified
the link between breast cancer genes with obesity!