How to do gene set enrichment analysis on a ranked list of genes expressing leukemia?
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@frankchang91-12833
Last seen 7.0 years ago

 There is a Bioconductor package named GCAR which does gene set enrichment analysis on a ranked list of the important genes affected in leukemia.  Also, there is a Excel csv file containing the low high SAL4 expressors of leukemia shown below. How does a R programmer do gene set enrichment analysis taking into the ranked list of important genes affected in leukemia?

Gene Symbol GSM564657 GSM564658 GSM564664 GSM564669 GSM564684 GSM564686 GSM564708 GSM564709 GSM564718 GSM564737 GSM564613 GSM564638 GSM564659 GSM564660 GSM564661 GSM564663 GSM564674 GSM564698 GSM564743 GSM564757
DDR1 /// MIR4640 0.86292 -1.2231 0.85521 0.98346 -1.3606 -0.91181 0.59042 -1.3425 -0.8703 -0.10628 -1.7599 0.31686 0.91914 0.66079 0.82625 0.6512 -2.5206 1.0449 0.10255 0.72291
RFC2 0.71972 -0.19024 0.11766 -0.70879 0.020472 0.7169 -2.966 -0.26714 -0.21352 -0.7821 0.83578 0.41926 0.37551 0.13589 0.46405 0.36622 0.64407 -0.24098 -0.05438 0.65629
HSPA6 1.8697 -0.26466 0.024394 2.0823 -1.8522 -1.4039 4.1068 0.71796 2.3279 -0.63787 1.2729 2.1889 0.4339 -0.17972 -0.33383 0.68293 -1.7679 0.053254 -0.59556 -2.2927
PAX8 -0.18474 -0.63195 -0.47112 0.32979 -0.07471 -0.2451 0.030715 -0.28209 0.18884 0.26025 -0.11239 0.034533 -0.24915 -0.83818 -0.51669 -0.59721 0.79231 0.60173 -0.20836 0.76962
GUCA1A -0.86138 0.67492 -2.1737 0.1522 0.2704 -0.72968 0.19355 -2.6582 0.895 1.5629 -1.9799 0.51674 0.41464 0.059021 1.4318 0.73677 1.4023 -0.30071 -0.47117 2.198
MIR5193 /// UBA7 0.2295 0.65354 0.54129 -0.25816 -0.53214 -0.07132 0.093214 0.22865 -0.40044 0.93858 -0.24518 -0.82504 -0.30472 -0.66507 -0.82792 0.57332 0.75398 -0.00783 -0.11842 -0.61656
THRA -0.73483 -0.39104 -0.57757 0.10191 -0.29729 -1.7094 1.2908 0.4821 -0.17399 1.1088 -0.2798 -1.2053 -0.78342 -0.75382 0.11174 -0.93046 -1.4827 -0.34829 0.59875 0.7393
PTPN21 0.020656 0.46132 -0.6996 -1.1959 -1.4131 -0.77095 0.67983 -0.6109 0.65418 1.8494 -1.098 -0.69119 -1.3759 -0.76616 -0.75312 -0.89832 -1.1601 -0.75431 2.529 1.1385
CCL5 -0.25198 -0.26877 -0.59057 0.69722 -1.4309 -0.98785 1.542 0.58821 1.424 1.0001 -1.0018 -1.543 -0.44512 0.43954 -2.7618 -0.5176 -0.40649 0.17621 -1.299 0.74179

 

bioconductor gcar • 1.2k views
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Could we use the GSAR enrichment scores to make a hierarchical clustering of the major human leukemia expressors? Please tell me if this question is misguided. Thank you.

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You should read the vignettes of the packages you mention in comments and your own answer. Yes you could do a gene set enrichment with GSAR, fgsea, limma, EGSEA, and others. Each package has its own requirements. So check with the vignette.

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@frankchang91-12833
Last seen 7.0 years ago

Please consult this URL https://github.com/ctlab/fgsea. Thank you.

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