Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.11.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99068	0.779
27DAP/17DAP	1.10603	0.859
39DAP/27DAP	1.05574	1
41DAP/39DAP	1.15926	0.38
42DAP/41DAP	0.97781	1
43DAP/42DAP	1.11136	0.91
47DAP/43DAP	1.00861	0.966
52DAP/47DAP	0.78783	0.461
57DAP/52DAP	1.06689	0.72

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91114	0.601
17DAP/reference	0.79927
27DAP/reference	0.97711	0.822
39DAP/reference	0.81148	0.412
41DAP/reference	0.92309
42DAP/reference	1.09172	0.842
43DAP/reference	0.53458
47DAP/reference	1.01936	0.72
52DAP/reference	0.79341	0.33
57DAP/reference	0.57641	0.21

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79578	0.121
27DAP/17DAP	0.95457	0.878
39DAP/27DAP	1.43803	0.056
41DAP/39DAP	1.14308	0.817
42DAP/41DAP	0.9067	0.434
43DAP/42DAP	1.38577	0.021
47DAP/43DAP	1.07467	0.772
52DAP/47DAP	1.00361	0.982
57DAP/52DAP	1.04087	0.891
57DAP/7DAP	1.02199	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.70187	0.025
17DAP/reference	1.46699	0.008
27DAP/reference	1.30819	0.008
39DAP/reference	1.79907	0.006
41DAP/reference	1.73264	0.01
42DAP/reference	1.76751	0.024
43DAP/reference	1.99501	0.007
47DAP/reference	1.85721	0.017
52DAP/reference	1.63725	0.007
57DAP/reference	1.74239	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39583	0.384
17DAP/reference	0.96326	0.474
27DAP/reference	0.966	0.537
39DAP/reference	0.92876	0.339
41DAP/reference	0.96678	0.459
42DAP/reference	0.90453	0.392
43DAP/reference	0.82443	0.152
47DAP/reference	1.36001	0.054
52DAP/reference	0.95942	0.156
57DAP/reference	1.04401	0.705

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40594	0.019
17DAP/reference	1.15757	0.488
27DAP/reference	1.68351	0.019
39DAP/reference	1.35512	1
41DAP/reference	1.28978	0.013
42DAP/reference	1.08424	0.327
43DAP/reference	1.45467	0.027
47DAP/reference	N/A	N/A
52DAP/reference	1.65273	0.04
57DAP/reference	N/A	N/A

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04832	0.945
26DAP/20DAP	0.83814	0.512
34DAP/26DAP	1.16002	0.542
51DAP/34DAP	0.9621	0.747
52DAP/51DAP	0.94906	1
53DAP/52DAP	1.20396	0.343
55DAP/53DAP	1.24478	0.312
57DAP/55DAP	1.14295	0.969
62DAP/57DAP	1.20274	0.868
68DAP/62DAP	1.0907	0.962
68DAP/14DAP	1.06246	0.889

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93198	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.73979	0.223
Mature Green Tomato/Ripe Tomato	0.95779	0.569
Immature Eggplant/Mature Eggplant	1.2341	0.288
Ripe Pepper/Ripe Tomato	1.92841	1
Mature Eggplant/Ripe Tomato	1.78342	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05129	1
1-1-2/M82	1.01278	1
12-2/M82	0.96574	0.955
12-4/M82	0.90523	0.619
1-3/M82	0.9198	0.378
2-1-1/M82	1.00031	1
2-1/M82	1.16642	1
2-6/M82	0.91806	1
3-2/M82	1.05271	0.84
4-1-1/M82	1.07457	1
4-1/M82	0.83588	0.737
4-3-2/M82	0.9882	1
4-3/M82	0.95349	1
5-3/M82	1.0348	0.572
6-2/M82	1.03197	1
6-3/M82	1.01055	1
7-1/M82	0.95983	0.803
7-2/M82	0.92458	0.578
9-3-2/M82	0.79638	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.76835	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.68963	0.362
IL12-4/WTpooled	1.12571	0.785
IL1-4/WTpooled	1.13997	0.395
WT/WTpooled	1.01449	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.71651	0.853

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00503	1
DC3000/delta hrp 6h	1.16812	1
DC3000/delta hrp 12h	1.00229	1
DC3000/delta hrp 24h	0.98252	0.934

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9842
DC3000 delta B/DC3000 delta AB	1.07696	0.524

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.95283	1
Var 0h	0.97003	1
Var 12h I row2-row1	0.99873	1
Var 12h NI row2-row1	0.79982	0.438
Var 36h I row2-row1	1.19801	0.908
Var 36h NI row2-row1	1.18928	0.482
Var 60h I row2-row1	1.18427	0.562
Var 60h NI row2-row1	1.26156	0.904
Time course 0hI-0hNI	0.97513	0.898
Time course 12hI-12hNI	1.0674	0.741
Time course 36hI-36hNI	0.98958	0.654
Time course 60hI-60hNI	1.29358	0.042

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.83289	0.314
transgenic ySAMdc/azygous control (breaker)	1.42446	1
transgenic ySAMdc/azygous control (red)	1.22227	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.16696	1
Manapal/WT (break)	1.11608	1
Manapal/WT (red)	0.96589	0.728