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frankchang91
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@frankchang91-12833
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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 |
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.
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.