Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.15.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	16.6123	0.065
27DAP/17DAP	1.13673	0.847
39DAP/27DAP	1.1175	1
41DAP/39DAP	0.44315	0.041
42DAP/41DAP	0.58086	0.262
43DAP/42DAP	0.66952	0.456
47DAP/43DAP	0.98009	0.902
52DAP/47DAP	1.10378	0.932
57DAP/52DAP	1.32537	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24453	0.081
17DAP/reference	1.19011	0.026
27DAP/reference	1.15459	0.258
39DAP/reference	1.09845	0.534
41DAP/reference	1.39587	0.187
42DAP/reference	1.3752	0.001
43DAP/reference	1.11854	0.569
47DAP/reference	1.4106	0.001
52DAP/reference	1.496	0.015
57DAP/reference	1.19072	0.195

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	5.77525	0.036
27DAP/17DAP	1.30706	0.061
39DAP/27DAP	0.55544	0.028
41DAP/39DAP	1.25413	0.945
42DAP/41DAP	1.074	1
43DAP/42DAP	0.39946	0.02
47DAP/43DAP	0.72538	0.01
52DAP/47DAP	1.44683	0.16
57DAP/52DAP	0.9677	0.709
57DAP/7DAP	0.83895	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01567	0.758
17DAP/reference	0.80593	0.021
27DAP/reference	0.94139	0.325
39DAP/reference	0.92228	0.126
41DAP/reference	0.85741	0.122
42DAP/reference	0.82091	0.034
43DAP/reference	0.8581	0.145
47DAP/reference	0.97437	0.671
52DAP/reference	0.76357	0.012
57DAP/reference	0.76962	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99554	0.756
17DAP/reference	1.25997	0.081
27DAP/reference	1.3093	0.072
39DAP/reference	1.0431	1
41DAP/reference	1.28235	0.022
42DAP/reference	1.40176	0.025
43DAP/reference	1.42565	0.011
47DAP/reference	1.26537	0.012
52DAP/reference	1.30605	0.181
57DAP/reference	1.13874	0.277

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96561	0.489
17DAP/reference	0.91539	0.452
27DAP/reference	0.82675	0.051
39DAP/reference	0.86774	0.122
41DAP/reference	0.89747	0.185
42DAP/reference	1.02557	0.816
43DAP/reference	1.09363	0.961
47DAP/reference	1.539	0.032
52DAP/reference	0.99051	0.704
57DAP/reference	0.89887	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.33579	0.966
26DAP/20DAP	0.98473	1
34DAP/26DAP	0.93259	0.927
51DAP/34DAP	1.17	0.377
52DAP/51DAP	0.85086	1
53DAP/52DAP	2.39318	0.024
55DAP/53DAP	1.0803	0.696
57DAP/55DAP	1.27216	0.764
62DAP/57DAP	1.02796	1
68DAP/62DAP	1.07447	1
68DAP/14DAP	0.94585	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.95576	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	3.15766	0.016
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.09819

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00747	1
1-1-2/M82	0.75429	0.958
12-2/M82	1.52443	0.2
12-4/M82	0.99477	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.15377	0.452
3-2/M82	1.21532	0.717
4-1-1/M82	0.90136	1
4-1/M82	1.38193	0.372
4-3-2/M82	0.75915	0.698
4-3/M82	1.29262	1
5-3/M82	0.90528	0.642
6-2/M82	0.81203
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.96496	1
9-3-2/M82	0.79491	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.78314	0.321
IL2-6/WTpooled	1.1664	0.456
IL7-5/WTpooled	1.52026	1
IL7-3/WTpooled	0.92275	0.293
IL12-4/WTpooled	0.88779	1
IL1-4/WTpooled	1.02844	1
WT/WTpooled	0.99324	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	1.19508	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03827	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.25804	1
DC3000/delta hrp 24h	1.0129	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.24027	0.648
DC3000 delta B/DC3000 delta AB	0.94949	0.589

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	1.03156	1
Var 0h	0.98079	1
Var 12h I row2-row1	1.02941	0.613
Var 12h NI row2-row1	0.84098	0.713
Var 36h I row2-row1	0.9236	1
Var 36h NI row2-row1	1.43609	0.482
Var 60h I row2-row1	1.05905	1
Var 60h NI row2-row1	1.03276	1
Time course 0hI-0hNI	1.05737	0.852
Time course 12hI-12hNI	0.90382	0.275
Time course 36hI-36hNI	0.78612	0.023
Time course 60hI-60hNI	0.29353	0.006

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)	1.04598	0.571
transgenic ySAMdc/azygous control (breaker)	1.18869	1
transgenic ySAMdc/azygous control (red)	0.98376	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94497	0.126

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.57711	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.95171	1
Manapal/WT (red)	0.75067	0.36