Data Analysis

Original data are:

PC9

##           SHMT1     SHMT2      PSAT     PHGDH      GLDC    MTHFD1
## 1 MYC 1.0567164 0.5932203 0.8737113 0.7126600 1.1563636 0.9505188
## 2 MYC 1.2268657 0.4839925 0.5489691 0.6571835 1.3418182 0.8200319
## 3 MYC 1.1820896 0.5536723 0.5319588 0.5675676 1.1563636 0.6823623
## 4  NT 1.0746269 1.2975518 1.2603093 1.1692745 0.8629091 1.1085395
## 5  NT 1.0119403 0.8644068 0.8814433 1.0113798 1.5054545 1.0642458
## 6  NT 0.9134328 0.8380414 0.8582474 0.8193457 0.6316364 0.8272147
##     MTHFD1L    MTHFD2       MYC
## 1 0.6658960 0.3518732 0.2489001
## 2 0.7005780 0.5014409 0.4280327
## 3 0.6936416 0.4841499 0.3488372
## 4 1.2069364 1.2233429 1.0747957
## 5 1.0005780 0.8429395 0.9842866
## 6 0.7924855 0.9337176 0.9409177

A549

##           SHMT1     SHMT2      PSAT     PHGDH      GLDC    MTHFD1
## 1 MYC 0.7463415 0.6012365 0.5226244 0.7603211 0.5988909 0.6268478
## 2 MYC 0.7439024 0.6136012 0.7194570 0.7224771 0.7208872 0.8449860
## 3 MYC 0.9097561 0.8825348 0.6787330 0.7500000 0.9648799 0.8593688
## 4  NT 0.9487805 1.1514683 0.9977376 1.1043578 1.3918669 1.0307631
## 5  NT 0.9634146 1.0788253 1.0588235 0.9254587 0.9038817 0.9804235
## 6  NT 1.0878049 0.7697063 0.9434389 0.9701835 0.7042514 0.9888134
##     MTHFD1L    MTHFD2       MYC
## 1 0.8402310 0.5533537 0.5088339
## 2 0.7911453 0.9054878 0.6996466
## 3 0.7536092 0.8780488 0.6042403
## 4 1.1665063 0.9054878 1.3886926
## 5 1.0365736 0.9512195 0.8657244
## 6 0.7969201 1.1432927 0.7455830

Calculate the difference between combination of test and control samples

Subset the data into two group: control and test: for each of the subset there will be 3 observations
Calculate the difference for the combination of control and test subset, which will give 9 differences total.
Do this for another cell-line

PC9 Cell Line Difference

## $SHMT1
## [1] -0.01791045  0.04477612  0.14328358  0.15223881  0.21492537  0.31343284
## [7]  0.10746269  0.17014925  0.26865672
## 
## $SHMT2
## [1] -0.7043315 -0.2711864 -0.2448211 -0.8135593 -0.3804143 -0.3540490
## [7] -0.7438795 -0.3107345 -0.2843691
## 
## $PSAT
## [1] -0.386597938 -0.007731959  0.015463918 -0.711340206 -0.332474227
## [6] -0.309278351 -0.728350515 -0.349484536 -0.326288660
## 
## $PHGDH
## [1] -0.4566145 -0.2987198 -0.1066856 -0.5120910 -0.3541963 -0.1621622
## [7] -0.6017070 -0.4438122 -0.2517781
## 
## $GLDC
## [1]  0.2934545 -0.3490909  0.5247273  0.4789091 -0.1636364  0.7101818
## [7]  0.2934545 -0.3490909  0.5247273
## 
## $MTHFD1
## [1] -0.158020750 -0.113727055  0.123304070 -0.288507582 -0.244213887
## [6] -0.007182761 -0.426177175 -0.381883480 -0.144852354
## 
## $MTHFD1L
## [1] -0.54104046 -0.33468208 -0.12658960 -0.50635838 -0.30000000 -0.09190751
## [7] -0.51329480 -0.30693642 -0.09884393
## 
## $MTHFD2
## [1] -0.8714697 -0.4910663 -0.5818444 -0.7219020 -0.3414986 -0.4322767
## [7] -0.7391931 -0.3587896 -0.4495677
## 
## $MYC
## [1] -0.8258957 -0.7353865 -0.6920176 -0.6467630 -0.5562539 -0.5128850
## [7] -0.7259585 -0.6354494 -0.5920805

A549 Cell Line Difference

## $SHMT1
## [1] -0.20243902 -0.21707317 -0.34146341 -0.20487805 -0.21951220 -0.34390244
## [7] -0.03902439 -0.05365854 -0.17804878
## 
## $SHMT2
## [1] -0.5502318 -0.4775889 -0.1684699 -0.5378671 -0.4652241 -0.1561051
## [7] -0.2689335 -0.1962906  0.1128284
## 
## $PSAT
## [1] -0.4751131 -0.5361991 -0.4208145 -0.2782805 -0.3393665 -0.2239819
## [7] -0.3190045 -0.3800905 -0.2647059
## 
## $PHGDH
## [1] -0.3440367 -0.1651376 -0.2098624 -0.3818807 -0.2029817 -0.2477064
## [7] -0.3543578 -0.1754587 -0.2201835
## 
## $GLDC
## [1] -0.79297597 -0.30499076 -0.10536044 -0.67097967 -0.18299445  0.01663586
## [7] -0.42698706  0.06099815  0.26062847
## 
## $MTHFD1
## [1] -0.4039153 -0.3535757 -0.3619656 -0.1857771 -0.1354375 -0.1438274
## [7] -0.1713943 -0.1210547 -0.1294447
## 
## $MTHFD1L
## [1] -0.326275265 -0.196342637  0.043310876 -0.375360924 -0.245428296
## [6] -0.005774783 -0.412897016 -0.282964389 -0.043310876
## 
## $MTHFD2
## [1] -0.35213415 -0.39786585 -0.58993902  0.00000000 -0.04573171 -0.23780488
## [7] -0.02743902 -0.07317073 -0.26524390
## 
## $MYC
## [1] -0.8798587 -0.3568905 -0.2367491 -0.6890459 -0.1660777 -0.0459364
## [7] -0.7844523 -0.2614841 -0.1413428

T-test p values:

Compare the two cell-line gene-wise.

## $SHMT1
## [1] 2.139095e-06
## 
## $SHMT2
## [1] 0.1634846
## 
## $PSAT
## [1] 0.9050551
## 
## $PHGDH
## [1] 0.134795
## 
## $GLDC
## [1] 0.02046114
## 
## $MTHFD1
## [1] 0.5707619
## 
## $MTHFD1L
## [1] 0.2043328
## 
## $MTHFD2
## [1] 0.002219787
## 
## $MYC
## [1] 0.03581783