Table 1 Summary of Type III secretion system (T3SS) hrp cluster genes detected by RNA-seq and microarray
From: RNA-seq and microarray complement each other in transcriptome profiling
Locus Tag | Gene Symbol | RNA-seq | Microarray | Detected by | ||||
|---|---|---|---|---|---|---|---|---|
| Â | Â | log2FC | p-value | FDR | log2FC | p-value | FDR | Â |
XAC0412 | hrcN | −2.2355 | 7.66E-09 | 1.27E-06 | −0.8217 | 0.00E+00 | 0.00E+00 | †|
XAC0409 | hrcJ | −3.1488 | 4.20E-15 | 1.40E-12 | −2.1840 | 0.00E+00 | 0.00E+00 | †|
XAC0406 | hrcU | −2.6729 | 1.01E-13 | 2.56E-11 | −1.0507 | 0.00E+00 | 0.00E+00 | †|
XAC0405 | hrcV | −1.5755 | 3.27E-08 | 4.88E-06 | −0.8427 | 4.00E-05 | 2.58E-03 | †|
XAC0407 | hrpB1 | −3.9638 | 7.53E-28 | 3.61E-25 | −2.8603 | 0.00E+00 | 0.00E+00 | †|
XAC0408 | hrpB2 | −2.8155 | 2.48E-09 | 4.67E-07 | −1.9507 | 0.00E+00 | 0.00E+00 | †|
XAC0410 | hrpB4 | −1.9274 | 7.42E-05 | 6.05E-03 | −1.5237 | 0.00E+00 | 0.00E+00 | †|
XAC0403 | hrcQ | −2.0615 | 6.36E-07 | 7.64E-05 | −0.8647 | 0.00E+00 | 0.00E+00 | †|
XAC0402 | hrcR | −1.7123 | 4.73E-06 | 5.53E-04 | −0.8677 | 0.00E+00 | 0.00E+00 | †|
XAC0399 | hrpD5 | −1.7287 | 2.67E-10 | 5.50E-08 | −1.5487 | 0.00E+00 | 0.00E+00 | †|
XAC0398 | hrpD6 | −1.5446 | 5.85E-07 | 7.43E-05 | −1.6347 | 0.00E+00 | 0.00E+00 | †|
XAC0397 | hrpE | −2.1535 | 7.67E-16 | 2.76E-13 | −1.8163 | 0.00E+00 | 0.00E+00 | †|
XAC0394 | hrpF | −2.0517 | 7.04E-15 | 2.17E-12 | −1.2113 | 0.00E+00 | 0.00E+00 | †|
XAC0416 | hpa1 | −5.0096 | 1.49E-51 | 1.29E-48 | −4.2917 | 0.00E+00 | 0.00E+00 | †|
XAC0396 | hpaB | −1.5429 | 1.56E-07 | 2.11E-05 | −1.2527 | 0.00E+00 | 0.00E+00 | †|
XAC0393 | hpaF | −0.9235 | 1.96E-04 | 1.34E-02 | −0.6083 | 1.00E-05 | 8.10E-04 | †|
XAC0411 | hrpB5 | −1.9690 | 3.92E-03 | 1.38E-01 | −0.8457 | 0.00E+00 | 0.00E+00 | ψ |
XAC0401 | hrcS | −1.0156 | 4.00E-02 | 4.71E-01 | −1.0837 | 0.00E+00 | 0.00E+00 | ψ |
XAC0404 | hpaP | −1.2673 | 1.10E-02 | 2.74E-01 | −1.1110 | 0.00E+00 | 0.00E+00 | ψ |
XAC0395 | XAC0395 | −1.0817 | 4.73E-02 | 5.08E-01 | −0.8640 | 0.00E+00 | 0.00E+00 | ψ |
XAC0415 | hrcC | −0.2713 | 2.49E-01 | 8.27E-01 | −0.4053 | 4.75E-03 | 1.78E-01 | $ |
XAC0413 | hrpB7 | −1.2107 | 1.08E-02 | 2.74E-01 | −0.6590 | 0.00E+00 | 0.00E+00 | ψ |
XAC0417 | hpa2 | −1.4130 | 8.33E-03 | 2.31E-01 | −0.4610 | 4.40E-04 | 2.64E-02 | $ |
XAC0400 | hpaA | −1.0585 | 2.76E-03 | 1.10E-01 | −0.7763 | 9.74E-03 | 2.05E-01 | $ |
XAC0414 | hrcT | −1.0474 | 1.10E-02 | 2.74E-01 | −0.6800 | 0.00E+00 | 0.00E+00 | ψ |