Redundant Probe Set Pairs on the ATH1 Affymetrix array
The ATH1 array from Affymetrix includes the following pairs of redundant probe sets annotated as interrogating different regions of the same gene. If the annotations are correct, then expression measurements from redundant probe sets ought to be correlated. We tested this assumption using a large collection ofexpression data from the ATH1 array. The results appear below.
We found that many redundant probe set pairs exhibit little or no correlation. Investigating these probe sets and their putative targets in more detail revealed that many were simply mis-annotated. Others may in fact interrogate differentially-regulated alternative mRNA transcripts arising from the same gene. The following table lists some of these, along with results from the statistical analysis.
View probe set and their targets
To view the probe sets and their targets, launch the Integrated Genome Browser by visiting the IGB download page.
Next, set up your data loading in IGB as follows:
- After IGB starts, click Data Access tab.
- Choose species: Arabidopsis thaliana.
- Choose genome version: A_thaliana_Jan_2004.
- Open Bioviz Quickload folder
- Click TAIR7_protein_coding_gene (TAIR7 gene models) data set checkbox (make sure you click the square). The data set should move into the Loaded Data Sets table in the middle of the tab and load mode will be set automatically to Don't Load.
- Under Load Mode, choose Whole Genome for the TAIR7_protein_coding_gene data set.
- Open NetAffx DAS2/affy folder
- Click the ath1-121501 netaffx consensus (ATH1 probe sets) data set checkbox (make sure you click the square). The data should then appear in the Loaded Data Sets table, with Load Mode set by default to Region in View.
- Open Bioviz DAS2 folder
- Click cDNA_TAIR7sm data set checkbox (make sure you click the square). The data set should move into the Loaded Data Sets Loaded table in the middle of the tab and load mode will be set automatically to Region in View.
Now that your data loading preferences are set up, click any of the IGB links below. When you click an IGB link, the viewer should show you the region specified in the link. To see the probe sets and cDNAs:
- Click an IGB link (see links column)
- Click the Refresh Data button to load probe sets and cDNAs.
Note: Some of the probe sets you see in the viewer might not be listed in the table below; this is because our analysis removed all probe sets that are promiscuous, i.e., map onto multiple gene targets according to the TAIR probe set-to-gene mappings we used.
To see an example screen capture from IGB version 5.4, view this file.
| gene | probe sets | links | Ave tr len | Rsquared | p | r | notes | |
|---|---|---|---|---|---|---|---|---|
| 1 | AT5G04440 |
250886_at
250887_at |
IGB: chr5:1254848-1257054 | 1.11e+03 | 0.0598 | 0.0903 | -0.245 | Full cDNA support, but probe sets are on opposite strands. |
| 2 | AT3G09410 |
259033_at
259034_at |
IGB: chr3:2894914-2901106 | 1.55e+03 | 0.0427 | 4.66e-06 | -0.207 | Two gene models have the same locus id, but do not overlap. |
| 3 | AT1G55310 |
259666_at
259648_at |
IGB: chr1:20633631-20636664 | 1.11e+03 | 0.00844 | 0.123 | -0.0919 | Nearly full cDNA support, but probe sets are on opposite strands. |
| 4 | AT4G12640 |
254825_at
254826_at |
IGB: chr4:7462497-7467959 | 2.8e+03 | 0.00669 | 0.312 | 0.0818 | No cDNA support for full gene model and probe sets interrogate exons separated by a large intron. Good candidate for split. |
| 5 | AT3G09470 |
258705_at
258699_at |
IGB: chr3:2910278-2914606 | 1.67e+03 | 0.0111 | 0.135 | 0.105 | cDNA support for larger, 3-prime extended gene model. Discordance may be due to differential regulation of alternative polyadenylation/transcriptional stop site choice. |
| 6 | AT3G50590 |
252162_at
252171_at |
IGB: chr3:18781899-18790583 | 5.21e+03 | 0.0283 | 0.00886 | 0.168 | No cDNA support for full gene model. Good candidate for split. |
| 7 | AT5G35980 |
249679_at
249678_at |
IGB: chr5:14145113-14153654 | 3.4e+03 | 0.0305 | 0.000131 | 0.175 | Full cDNA support for larger 3-prime extended variant. Discordance may be due to differential regulation of alternative polyadenylation/transcriptional stop site choice. 249678_at would detect both variants, but 249679_at would detect only the larger 3-prime extended variant. |
| 8 | AT2G37840 |
266080_at
266081_at |
IGB: chr2:15858780-15863479 | 2.77e+03 | 0.0327 | 0.000205 | 0.181 | Full cDNA support for one variant (AT2G37840.1), partial cDNA support for the other variant (AT2G37840.2). Variant .2 could be a candidate for early transcriptional termination relative to the other. Both probe sets would detect each variant, provided the gene models are accurate. If variant .2 terminates early, 266080_AT would not detect it. |
| 9 | AT3G52640 |
252062_at
252028_at |
IGB: chr3:19525752-19531622 | 2.55e+03 | 0.0803 | 3.67e-10 | 0.283 | No cDNA support for full gene model. Variants differ in 3-prime exons, but probe sets would detect all. |
| 10 | AT4G11830 |
254846_at
254893_at |
IGB: chr4:7115629-7121339 | 3.84e+03 | 0.0997 | 7.93e-11 | 0.316 | Full cDNA support for one variant AT4G11830.1. Variants differ in 5-prime exons 2 and 3. Retained intron in variant AT4G11830.2 merges exons 2 and 3. Probe sets would detect all known variants. |
| 11 | AT5G24710 |
246960_at
246961_at |
IGB: chr5:8459050-8468276 | 4.48e+03 | 0.108 | 1.52e-07 | 0.329 | No cDNA support for full model. No variants. Good split candidate. |
| 12 | AT5G53480 |
248272_at
248268_at |
IGB: chr5:21730491-21735108 | 3.81e+03 | 0.117 | 1.75e-14 | 0.343 | cDNA support for full model. No variants. |
| 13 | AT4G01290 |
255616_at
255615_at |
IGB: chr4:537996-543969 | 3.68e+03 | 0.128 | 4.08e-14 | 0.357 | No cDNA support for full model. No variants, but there is an adjacent gene upstream interrogated by probe set 255623_at. Should check for correlation with this probe set, since it may be a part of this transcriptional unit. To get lots of expression data for all three probe sets, use the cressexpress.org ReST-style Web service. |
| 14 | AT3G18930 |
256917_at
256948_at |
IGB: chr3:6523380-6525649 | 1.94e+03 | 0.136 | 0.00289 | 0.369 | -- |
| 15 | AT4G33180 |
253367_at
253366_at |
IGB: chr4:16000143-16002372 | 1.18e+03 | 0.144 | 1.63e-07 | 0.379 | -- |
| 16 | AT4G33520 |
253339_at
253342_at |
IGB: chr4:16118798-16126253 | 2.52e+03 | 0.16 | 4.01e-19 | 0.4 | -- |
| 17 | AT5G46470 |
248875_at
248845_at |
IGB: chr5:18859827-18867068 | 4.85e+03 | 0.166 | 1.06e-09 | 0.407 | -- |
| 18 | AT2G01220 |
265793_at
265760_at |
IGB: chr2:123174-126526 | 1.39e+03 | 0.168 | 5.43e-21 | 0.41 | -- |
| 19 | AT4G16980 |
245459_at
245318_at |
IGB: chr4:9556896-9557931 | 835 | 0.174 | 2.31e-09 | 0.417 | -- |
| 20 | AT3G22620 |
256937_at
256929_at |
IGB: chr3:8008440-8010124 | 1.3e+03 | 0.177 | 0.000399 | 0.42 | -- |
| 21 | AT1G31710 |
246601_at
246602_at |
IGB: chr1:11349720-11355567 | 2.21e+03 | 0.185 | 8.63e-06 | 0.431 | -- |
| 22 | AT1G11130 |
262479_at
262451_at |
IGB: chr1:3722756-3727543 | 2.85e+03 | 0.193 | 2.48e-19 | 0.44 | -- |
| 23 | AT5G14620 |
250140_at
250139_at |
IGB: chr5:4715155-4718807 | 2.18e+03 | 0.215 | 1.78e-22 | 0.463 | -- |
| 24 | AT1G77080 |
264945_at
264949_at |
IGB: chr1:28960430-28965091 | 854 | 0.22 | 1.32e-12 | 0.469 | -- |
| 25 | AT2G25760 |
266652_at
266651_at |
IGB: chr2:10991785-10996102 | 2.61e+03 | 0.223 | 6.03e-26 | 0.472 | -- |
| 26 | AT2G32560 |
267117_at
267116_at |
IGB: chr2:13831770-13834163 | 1.37e+03 | 0.224 | 6.56e-07 | 0.473 | -- |
| 27 | AT2G17410 |
264876_at
264878_at |
IGB: chr2:7565979-7570934 | 2.82e+03 | 0.25 | 1.28e-26 | 0.5 | -- |
| 28 | AT4G05050 |
255257_at
AFFX-Athal-Ubq_5_f_at |
IGB: chr4:2587901-2589460 | 1.08e+03 | 0.258 | 1.3e-32 | 0.508 | -- |
| 29 | AT3G17880 |
258219_at
258187_at |
IGB: chr3:6123351-6126376 | 1.39e+03 | 0.267 | 8.59e-30 | 0.517 | -- |
| 30 | AT2G46020 |
266909_at
266605_at |
IGB: chr2:18930276-18938942 | 6.58e+03 | 0.276 | 0.0012 | 0.525 | -- |
| 31 | AT4G38600 |
252947_at
252948_at |
IGB: chr4:18040924-18049386 | 6.05e+03 | 0.283 | 2.23e-11 | 0.532 | -- |
| 32 | AT5G35430 |
249723_at
249722_at |
IGB: chr5:13679070-13683345 | 2.78e+03 | 0.285 | 2.01e-21 | 0.534 | -- |
| 33 | AT3G03380 |
259047_at
259048_at |
IGB: chr3:799521-808629 | 3.6e+03 | 0.297 | 1.81e-37 | 0.545 | -- |
| 34 | AT3G54380 |
251893_at
251894_at |
IGB: chr3:20144771-20147869 | 1.36e+03 | 0.315 | 1.35e-32 | 0.561 | -- |
| 35 | AT1G26300 |
245870_at
245872_at |
IGB: chr1:9095786-9099841 | 956 | 0.316 | 3.9e-14 | 0.562 | -- |
| 36 | AT5G13030 |
250275_at
250276_at |
IGB: chr5:4133118-4137021 | 2.36e+03 | 0.34 | 1.1e-43 | 0.583 | -- |
| 37 | AT5G63200 |
247364_at
247363_at |
IGB: chr5:25366136-25370328 | 2.08e+03 | 0.341 | 1.06e-05 | 0.584 | -- |
| 38 | AT3G54320 |
251892_at
251891_at |
IGB: chr3:20125607-20129717 | 1.48e+03 | 0.351 | 8.8e-05 | 0.593 | -- |
| 39 | AT2G07360 |
265779_at
265778_at |
IGB: chr2:3047202-3057274 | 3.99e+03 | 0.371 | 7.64e-34 | 0.609 | -- |
| 40 | AT2G02410 |
266204_at
266173_at |
IGB: chr2:632538-634931 | 1.22e+03 | 0.374 | 6.53e-10 | 0.611 | -- |
| 41 | AT2G39140 |
267018_at
267017_at |
IGB: chr2:16337160-16340538 | 1.5e+03 | 0.387 | 3.34e-42 | 0.622 | -- |
| 42 | AT3G53670 |
251954_at
251953_at |
IGB: chr3:19901298-19903480 | 1.4e+03 | 0.406 | 3.25e-54 | 0.637 | -- |
| 43 | AT2G43160 |
266436_at
266437_at |
IGB: chr2:17955038-17960898 | 3.32e+03 | 0.42 | 5.04e-44 | 0.648 | -- |
| 44 | AT3G06810 |
258524_at
258525_at |
IGB: chr3:2146297-2150937 | 2.79e+03 | 0.423 | 0.000325 | 0.65 | -- |
| 45 | AT2G46340 |
263779_at
263780_at |
IGB: chr2:19029316-19034540 | 3.58e+03 | 0.428 | 1.18e-25 | 0.654 | -- |
| 46 | AT1G21830 |
262488_at
262489_at |
IGB: chr1:7661048-7662695 | 975 | 0.431 | 2.23e-59 | 0.656 | -- |
| 47 | AT5G62000 |
247468_at
247508_at |
IGB: chr5:24927483-24932531 | 3.43e+03 | 0.443 | 3.33e-55 | 0.666 | -- |
| 48 | AT2G35450 |
266620_at
266621_at |
IGB: chr2:14910023-14912551 | 1.21e+03 | 0.445 | 1.5e-33 | 0.667 | -- |
| 49 | AT5G56180 |
247997_at
248002_at |
IGB: chr5:22754450-22758342 | 1.73e+03 | 0.458 | 1.04e-39 | 0.677 | -- |
| 50 | AT2G34555 |
266907_at
266952_at |
IGB: chr2:14563966-14565876 | 1.14e+03 | 0.473 | 9.69e-06 | 0.688 | -- |
| 51 | AT2G39080 |
266192_at
266193_at |
IGB: chr2:16316806-16319687 | 1.24e+03 | 0.479 | 4.36e-70 | 0.692 | -- |
| 52 | AT1G10090 |
264515_at
264516_at |
IGB: chr1:3289958-3296281 | 3.14e+03 | 0.482 | 2.27e-27 | 0.694 | -- |
| 53 | AT1G63900 |
260322_at
260321_at |
IGB: chr1:23720281-23723023 | 1.54e+03 | 0.487 | 1.08e-39 | 0.698 | -- |
| 54 | AT1G09660 |
264664_at
264665_at |
IGB: chr1:3127672-3131174 | 1.38e+03 | 0.504 | 3.74e-72 | 0.71 | -- |
| 55 | AT3G19720 |
257044_at
257045_at |
IGB: chr3:6850276-6855619 | 2.62e+03 | 0.514 | 1.53e-47 | 0.717 | -- |
| 56 | AT1G01320 |
261054_at
261053_at |
IGB: chr1:121033-130199 | 5.76e+03 | 0.548 | 2.17e-59 | 0.74 | -- |
| 57 | AT1G02205 |
264146_at
264147_at |
IGB: chr1:418677-422538 | 2.24e+03 | 0.549 | 1.84e-37 | 0.741 | -- |
| 58 | AT2G44950 |
266817_at
266818_at |
IGB: chr2:18549268-18555766 | 3.29e+03 | 0.551 | 7.13e-15 | 0.743 | -- |
| 59 | AT2G31010 |
267201_at
267200_at |
IGB: chr2:13201187-13207305 | 3.02e+03 | 0.552 | 2.92e-15 | 0.743 | -- |
| 60 | AT3G12800 |
257686_at
257687_at |
IGB: chr3:4063230-4064895 | 1.07e+03 | 0.561 | 1.1e-85 | 0.749 | -- |
| 61 | AT5G24690 |
246959_at
246958_at |
IGB: chr5:8455359-8458841 | 2.12e+03 | 0.564 | 3.01e-80 | 0.751 | -- |
| 62 | AT2G28540 |
264076_at
264081_at |
IGB: chr2:12225059-12231005 | 2.71e+03 | 0.567 | 1.78e-17 | 0.753 | -- |
| 63 | AT3G16857 |
256790_at
257649_at |
IGB: chr3:5755829-5759476 | 2.42e+03 | 0.574 | 4.13e-09 | 0.757 | -- |
| 64 | AT5G60410 |
247630_at
247629_at |
IGB: chr5:24312015-24318472 | 3.17e+03 | 0.586 | 5.4e-08 | 0.765 | -- |
| 65 | AT4G09900 |
255026_at
255025_at |
IGB: chr4:6221560-6224230 | 1.36e+03 | 0.589 | 2.05e-67 | 0.767 | -- |
| 66 | AT2G20740 |
265427_at
265426_at |
IGB: chr2:8942587-8944691 | 883 | 0.597 | 2.26e-95 | 0.773 | -- |
| 67 | AT5G63420 |
247385_at
247386_at |
IGB: chr5:25417511-25423294 | 3.03e+03 | 0.599 | 1.81e-67 | 0.774 | -- |
| 68 | AT1G08680 |
264795_at
264796_at |
IGB: chr1:2762508-2769070 | 2.68e+03 | 0.62 | 1.38e-05 | 0.787 | -- |
| 69 | AT2G37480 |
265953_at
265952_at |
IGB: chr2:15744860-15747026 | 1.41e+03 | 0.625 | 1.5e-104 | 0.791 | -- |
| 70 | AT1G56500 |
259603_at
259633_at |
IGB: chr1:21163308-21171086 | 3.43e+03 | 0.672 | 1.96e-109 | 0.82 | -- |
| 71 | AT4G00400 |
255692_at
255662_at |
IGB: chr4:173971-176937 | 1.85e+03 | 0.677 | 4.6e-103 | 0.823 | -- |
| 72 | AT3G18000 |
258217_at
258218_at |
IGB: chr3:6154268-6157658 | 1.91e+03 | 0.677 | 1.68e-87 | 0.823 | -- |
| 73 | AT1G51110 |
245744_at
245745_at |
IGB: chr1:18938915-18941427 | 1.44e+03 | 0.689 | 3.44e-98 | 0.83 | -- |
| 74 | AT3G17970 |
258215_at
258214_at |
IGB: chr3:6147867-6152081 | 2.02e+03 | 0.702 | 9.18e-104 | 0.838 | -- |
| 75 | AT3G09600 |
258723_at
258724_at |
IGB: chr3:2946319-2949100 | 1.14e+03 | 0.713 | 2.87e-58 | 0.844 | -- |
| 76 | AT5G39785 |
249423_at
249418_at |
IGB: chr5:15946315-15949604 | 1.95e+03 | 0.722 | 1.78e-61 | 0.85 | -- |
| 77 | AT5G14180 |
250219_at
250199_at |
IGB: chr5:4571240-4574564 | 1.41e+03 | 0.724 | 2.51e-11 | 0.851 | -- |
| 78 | AT3G48570 |
252324_at
252328_at |
IGB: chr3:18014797-18016059 | 490 | 0.751 | 2.34e-146 | 0.867 | -- |
| 79 | AT2G30600 |
267524_at
267523_at |
IGB: chr2:13043852-13048861 | 2.71e+03 | 0.767 | 6.67e-134 | 0.876 | -- |
| 80 | AT2G03390 |
265706_at
265707_at |
IGB: chr2:1030298-1032719 | 1.36e+03 | 0.776 | 1.46e-156 | 0.881 | -- |
| 81 | AT5G44820 |
249021_at
254521_at |
IGB: chr5:18112839-18114912 | 1.21e+03 | 0.795 | 5.33e-81 | 0.891 | -- |
| 82 | AT2G07340 |
265777_at
265776_at |
IGB: chr2:3045455-3046816 | 584 | 0.807 | 3.91e-174 | 0.899 | -- |
| 83 | AT2G30520 |
267516_at
267517_at |
IGB: chr2:13009718-13012772 | 2.08e+03 | 0.817 | 6.49e-165 | 0.904 | -- |
| 84 | AT4G20130 |
254501_at
254502_at |
IGB: chr4:10878815-10882039 | 1.69e+03 | 0.819 | 1.44e-167 | 0.905 | -- |
| 85 | AT3G26980 |
257784_at
257785_at |
IGB: chr3:9947302-9949377 | 985 | 0.85 | 2.45e-196 | 0.922 | -- |
| 86 | AT5G62440 |
247454_at
247453_at |
IGB: chr5:25089608-25091315 | 818 | 0.857 | 9.09e-206 | 0.925 | -- |
| 87 | AT1G65390 |
264153_at
264213_at |
IGB: chr1:24296052-24298393 | 1.32e+03 | 0.91 | 3.51e-44 | 0.954 | -- |