GSEA output interpretation

Question

[1769mkc]

I have done the diffrential gene expression for stages , i did the GSEA for the same as one of my comparison i had made is Normal Stem cell vs leukemic stem cells ,so i have few doubts ,one of them is about the core enrichment which i see in the excel output ..what does that mean when it says "YES" while other set of genes says "NO"

one of the pathway from HALLMARK used for my analysis GSEA

NAME    PROBE   GENE SYMBOL GENE_TITLE  RANK IN GENE LIST   RANK METRIC SCORE   RUNNING ES  CORE ENRICHMENT
row_0   NMI null    null    48  13.3946952819824    0.062136382 Yes
row_1   CASP8   null    null    101 10.8794260025024    0.11161677  Yes
row_2   TDRD7   null    null    137 9.82681369781494    0.15721846  Yes
row_3   PSMA3   null    null    138 9.80134296417236    0.20535222  Yes
row_4   CASP1   null    null    175 8.84163761138916    0.24603985  Yes
row_5   B2M null    null    258 7.59345960617065    0.2771055   Yes
row_6   ELF1    null    null    300 7.04479360580444    0.30858937  Yes
row_7   TXNIP   null    null    406 6.27002573013306    0.3314096   Yes
row_8   FAM46A  null    null    449 5.92081880569458    0.35729778  Yes
row_9   CD47    null    null    840 4.13194370269775    0.34798124  Yes
row_10  IFIT2   null    null    918 3.85698509216309    0.3610769   Yes
row_11  GBP2    null    null    1462    2.69929122924805    0.33310914  No
row_12  SAMD9L  null    null    1810    2.12585210800171    0.3172053   No
row_13  SAMD9   null    null    1854    2.08373498916626    0.3241739   No
row_14  WARS    null    null    1936    1.96378028392792    0.3276685   No
row_15  CCRL2   null    null    1977    1.92678117752075    0.33409402  No
row_16  IFIH1   null    null    2332    1.57100236415863    0.31493393  No
row_17  PARP9   null    null    2485    1.43167436122894    0.31042516  No
row_18  PARP14  null    null    2537    1.39259052276611    0.31339222  No
row_19  SP110   null    null    2581    1.35366022586823    0.31677547  No

How do i interpret here? I have gone through various tutorial with gsea data but im not still not sure about it, in this case my control is HSC and test is LSC so I ranked the gene based on logfold and adjpvalue and ran a preranked GSEA ..

A clear explanation would be really helpful

Answer 1

[h.mon]

GSEA User Guide has a table explaining each column of the output, here is the explanation for "Core Enrichment":

Genes with a Yes value in this column contribute to the leading-edge subset within the gene set. This is the subset of genes that contributes most to the enrichment result. Use the Leading Edge analysis to analyze the overlap between multiple leading-edge subsets.

[1769mkc]

as you can see the figure..where i see the red portion vs blue portion...so since in this comparison i have HSC vs LSC where HSC is my control and LSC my test..so can you tell me what i read is the red one show high enrichment ,the can i tell that the genes that are in the red portion are enriched and regulated in HSC as compared to LSC or vice versa ?