Figures:
Supplementary Figure 1. Comparison of microarray results with quantitative polymerase chain reaction (QPCR). A scatter plot of the log2 ratio from microarrays verses ratios calculated from QPCR measurements for 13 targets in seven different mutants. A table of microarray and QPCR values for each primer set in each mutant are provided in Supplementary Table 1. Key: mex67-6 (light blue), spt6-14 (pink), rrp6D (red), prp11-1 (green) prp19-1 (orange), prp20-1 (brown), ded1-120 (dark blue).
Supplementary Figure 2. A plot of intron vs. exon log2 ratios reveals distinct transcript accumulation phenotypes. A plot of the log2 ratio for the exon feature of an mRNA against the log2 ratio for the intron signal from the same gene is shown. X coordinate values are exon log ratios and Y coordinates are intron log ratios for the corresponding mRNA feature. The values for three unique yeast mutations are shown: dbr1Æ, an intron decay mutant, (green); prp4-1, a splicing mutant, (orange); and rbp1-1, a transcription mutant (blue).
Supplementary Figure 3. The ceg1-250 mutation causes widespread intron accumulation. A plot of the log2 ratio for the exon feature of an mRNA against the log2 ratio for the intron signal from the same gene is shown. X coordinate values are exon log ratios and Y coordinates are intron log ratios for the corresponding mRNA feature. The values for the ceg1-250 and prp4-1 mutations are shown: ceg1-250, an mRNA capping mutant, (purple); prp4-1, a splicing mutant, (orange).
Supplementary Figure 4. ROC plots for the individual classifiers of the multi-class SVM. See methods for explanation of ROC curve.
Tables:
Supplementary Table 1. Values for individual points represented in Supplementary Figure 1.
|
mex67-6 |
|
spt6-14 |
|
rrp6D |
|
prp11-1 |
|
prp19-1 |
|
prp20-1 |
|
ded1-120 |
|
Gene |
QPCR |
array |
QPCR |
array |
QPCR |
array |
QPCR |
array |
QPCR |
array |
QPCR |
array |
QPCR |
array |
YRA1
EX2 |
0.525 |
1.500 |
-0.175 |
-0.954 |
1.025 |
0.710 |
-0.575 |
-0.580 |
0.925 |
1.230 |
2.825 |
2.090 |
-0.833 |
-0.050 |
RPL39 INT |
0.725 |
-0.470 |
1.125 |
-0.830 |
2.075 |
0.460 |
1.100 |
0.880 |
2.250 |
1.660 |
2.275 |
1.090 |
2.400 |
1.540 |
RPL39 EX2 |
-0.700 |
-1.190 |
-1.075 |
-1.590 |
0.300 |
0.490 |
-1.500 |
-0.930 |
-1.400 |
-0.360 |
0.700 |
1.060 |
0.433 |
0.840 |
RPS13 INT |
1.050 |
0.460 |
1.175 |
0.290 |
2.750 |
0.952 |
-0.100 |
0.230 |
-0.700 |
0.830 |
0.475 |
0.760 |
1.800 |
1.540 |
RPS13 EX2 |
-1.375 |
-1.600 |
-1.525 |
-1.620 |
-0.675 |
0.163 |
-1.850 |
-1.500 |
-1.300 |
-0.270 |
0.150 |
-0.270 |
0.233 |
0.560 |
RPL30 INT |
1.025 |
0.220 |
0.100 |
-0.710 |
1.150 |
1.240 |
0.050 |
0.200 |
-0.400 |
0.540 |
-0.400 |
1.110 |
2.300 |
1.880 |
PBN1 |
-0.475 |
0.140 |
0.250 |
0.035 |
0.450 |
-0.180 |
-0.675 |
-0.081 |
0.225 |
0.330 |
0.400 |
-0.070 |
-0.400 |
0.000 |
RPS2 |
-1.500 |
-1.560 |
-1.550 |
-1.700 |
-1.050 |
-0.450 |
-0.750 |
-0.600 |
-1.525 |
-0.570 |
-0.200 |
-0.398 |
0.100 |
0.450 |
U2 snRNA |
2.725 |
1.940 |
2.075 |
1.710 |
0.650 |
0.634 |
0.800 |
0.439 |
4.008 |
2.479 |
3.000 |
1.795 |
-1.225 |
0.320 |
U4 snRNA |
2.075 |
1.580 |
n/a |
n/a |
5.700 |
2.850 |
-0.825 |
-0.506 |
0.450 |
0.553 |
1.200 |
0.510 |
-0.550 |
-0.090 |
U5 snRNA |
2.250 |
1.660 |
3.075 |
1.520 |
4.475 |
2.510 |
-0.725 |
-0.182 |
1.675 |
1.711 |
0.750 |
1.459 |
-1.350 |
-0.430 |
U6 snRNA |
2.150 |
1.980 |
3.650 |
1.460 |
8.925 |
4.570 |
n/a |
n/a |
-0.775 |
0.714 |
0.050 |
0.934 |
-1.625 |
-0.090 |
pre-EFB1 |
1.075 |
1.580 |
2.350 |
1.680 |
6.575 |
1.350 |
2.200 |
0.058 |
2.975 |
3.300 |
n/a |
n/a |
-0.500 |
0.080 |
Supplementary Table 2.
Oligonucleotides used for QPCR analysis.
Gene |
Name |
Target |
Forward oligo (5Õ-3Õ) |
Reverse oligo (5Õ-3Õ) |
YRA1 |
YDR381W |
Exon 2 |
GTAGGTGGTGTTCAAAGAGT |
ATTGGAGAGCCCGTTAAA |
RPL39 |
YJL189W |
Intron |
TTCGTATGTGCACGATATG |
CATCTTGGTTCTTCTCCAG |
PPL39 |
YJL189W |
Exon 2 |
AAAGTCTTTCAGAATCAAGCA |
CATCTTGGTTCTTCTCCAG |
RPS13 |
YDR064W |
Intron |
ATTCCACTAAATATTACTTTAAACAG |
GGATTTCTGGAGCCAAA |
RPS13 |
YDR064W |
Exon 2 |
CTGCTATTCCATACTCTAGAAATG |
GGATTTCTGGAGCCAAA |
RPL30 |
YGL030W |
Intron |
TTTATCGTTTACATTTCAAGAG |
AATCCCAAGAATCTATCAACC |
PBN1 |
YCL052C |
ORF |
CTGCGACACAGGTGACAA |
GGTACCATTTTTGATCTTGGA |
RPS2 |
YL123W |
ORF |
CCCAAGAGGTTCTGGA |
TGGAGAAACTGGCAATG |
LSR1 |
LSR1 |
U2 snRNA |
ATAGTAGGTTGGGAGATAATATTTATGG |
GAAGGAGAACGTCGCGGTGGTC |
SNR14 |
SNR14 |
U4 snRNA |
CGCATATCAGTGAGGATTCGTCCGAG |
GGGATGTATCAGAACTTC |
SNR7 |
SNR7 |
U5 snRNA |
TTACAGATCAATGGCGGAGGGAGGTC |
ACACCCGGATGGTTCTGGTA |
SNR6 |
SNR6 |
U6 snRNA |
GTTCGCGAAGTAACCCTTCGTGGAC |
TTGCTTTATTTAGAGAAACATTTTG |
EFB1 |
YAL003W |
pre-EFB1 |
ACAGTATCTGACGATAGCACA |
GACGTCAGCTTGAGAAAC |
Supplementary
Table 3. Filtered IA data used to create the cluster of Fig 1.
Supplementary
Table 4. SVM scores used for the heat map in Fig. 2.
Supplementary
Table 5. Experimental details and strain genotypes.