Expression of GAL1 (06051) and GAl10/UDP-glucose 4-epimerase (06050)
#> Joining, by = "fastqFileName"
CPM and rank for TEF1 (CNAG_06125) in YPD or DMEM CO2 37 90 min
| gene | medium | median_log2cpm | quantile |
|---|---|---|---|
| CKF44_06125 | DMEM | 15.21845 | 0.9984211 |
| CKF44_06125 | YPD | 14.71931 | 0.9982776 |
highly expressed crypto genes – 75th to 95th percentile
I tried many intervals, and widening to top 75 netted the most genes whose expression was consistently high across ALL conditions. narrowing the interval decreased the number of genes in that range across ALL conditions down to 5 or less (though most of the genes were highly expressed in, say, 142 / 146 of the unique concat conditions)
| gene | treatment_tally | median_log2cpm | mean_quantile | quantile_sd |
|---|---|---|---|---|
| CKF44_00006 | 146 | 10.30493 | 0.8751453 | 0.0255795 |
| CKF44_00402 | 146 | 10.38472 | 0.8817586 | 0.0281594 |
| CKF44_00509 | 146 | 10.56398 | 0.8965574 | 0.0311383 |
| CKF44_00602 | 146 | 10.51135 | 0.8952115 | 0.0270342 |
| CKF44_01018 | 146 | 10.48432 | 0.8922041 | 0.0290333 |
| CKF44_01083 | 146 | 10.40630 | 0.8787208 | 0.0349441 |
| CKF44_01106 | 146 | 10.33366 | 0.8701196 | 0.0322008 |
| CKF44_01278 | 146 | 10.26794 | 0.8730660 | 0.0352172 |
| CKF44_01475 | 146 | 10.48109 | 0.8862681 | 0.0337783 |
| CKF44_01568 | 146 | 10.39724 | 0.8840611 | 0.0278882 |
| CKF44_01655 | 146 | 10.20040 | 0.8614053 | 0.0286747 |
| CKF44_01722 | 146 | 10.85759 | 0.9204695 | 0.0219071 |
| CKF44_02134 | 146 | 9.88108 | 0.8274114 | 0.0310610 |
| CKF44_02177 | 146 | 10.54762 | 0.8901652 | 0.0317665 |
| CKF44_02486 | 146 | 10.23253 | 0.8722982 | 0.0277540 |
| CKF44_02671 | 146 | 10.78905 | 0.9169755 | 0.0142576 |
| CKF44_02948 | 146 | 10.50731 | 0.8968837 | 0.0286800 |
| CKF44_03439 | 146 | 10.61384 | 0.9030351 | 0.0209172 |
| CKF44_03706 | 146 | 10.56189 | 0.8924391 | 0.0317257 |
| CKF44_03931 | 146 | 10.67367 | 0.9024806 | 0.0280053 |
MSA of the promoters (100bp upstream) of genes shown above
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.
NOTE: there if a pwm/pfm that goes along with this image of course
MSA of 10 bp upstream of all introns
#> [1] 0.1919815 0.1923186 0.1895406 0.1908105 0.1931301 0.1843017 0.1826488
#> [8] 0.1702303 0.1452700 0.1110761
| A | 0.0385005 | 0.0512811 | 0.0524815 | 0.0330705 | 0.0508494 | 0.0853854 | 0.0896944 | 0.1284762 | 0.1574426 | -0.0029644 |
| C | 0.0291867 | 0.0252927 | 0.0361979 | 0.0385244 | 0.0404272 | 0.0219504 | 0.0640099 | 0.0455409 | -0.0081061 | -0.0846052 |
| G | 0.0569385 | 0.0609691 | 0.0192342 | 0.0387392 | 0.0401427 | 0.0025708 | -0.0135594 | 0.0024607 | -0.0450855 | 0.1868622 |
| T | 0.0673558 | 0.0547757 | 0.0816270 | 0.0804764 | 0.0617109 | 0.0743951 | 0.0425039 | -0.0062476 | 0.0410189 | 0.0117834 |