Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.16.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81877	0.364
27DAP/17DAP	1.31896	0.683
39DAP/27DAP	0.95893	0.719
41DAP/39DAP	0.88698	0.636
42DAP/41DAP	0.8568	1
43DAP/42DAP	0.88988	0.765
47DAP/43DAP	1.32787	0.316
52DAP/47DAP	0.88965	0.643
57DAP/52DAP	1.52673	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81322	0.044
17DAP/reference	0.80481	0.008
27DAP/reference	0.88266	0.03
39DAP/reference	0.8057	0.088
41DAP/reference	0.74977	0.016
42DAP/reference	0.90031	0.027
43DAP/reference	0.88324	0.039
47DAP/reference	0.93485	0.174
52DAP/reference	1.23529	0.079
57DAP/reference	1.20578	0.037

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05071	0.697
27DAP/17DAP	1.13196	0.699
39DAP/27DAP	0.81015	0.215
41DAP/39DAP	1.05548	1
42DAP/41DAP	0.93162	0.579
43DAP/42DAP	0.76994	0.046
47DAP/43DAP	0.87093	0.577
52DAP/47DAP	1.43048	0.362
57DAP/52DAP	0.81058	0.541
57DAP/7DAP	1.5907	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74297	0.043
17DAP/reference	0.96385	0.389
27DAP/reference	0.99148	0.571
39DAP/reference	0.95191	0.354
41DAP/reference	0.88615	0.064
42DAP/reference	1.01106	0.791
43DAP/reference	1.00929	1
47DAP/reference	0.84088	0.128
52DAP/reference	0.93724	0.254
57DAP/reference	0.90499	0.08

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85764	0.14
17DAP/reference	0.83454	0.011
27DAP/reference	0.87797	0.064
39DAP/reference	0.99815	0.586
41DAP/reference	0.94496	0.315
42DAP/reference	0.91197	0.15
43DAP/reference	0.96397	0.516
47DAP/reference	0.84319	0.029
52DAP/reference	0.96535	0.351
57DAP/reference	0.78934	0.017

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90765	0.044
17DAP/reference	0.97684	0.647
27DAP/reference	0.99915	0.843
39DAP/reference	0.98433	0.643
41DAP/reference	0.98817	0.682
42DAP/reference	1.09364	0.635
43DAP/reference	1.29556	0.068
47DAP/reference	0.81778	0.013
52DAP/reference	0.85357	0.2
57DAP/reference	1.24804	0.078

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.81422	0.841
26DAP/20DAP	0.7824	0.223
34DAP/26DAP	1.39637	1
51DAP/34DAP	0.97717	0.863
52DAP/51DAP	1.06531	0.792
53DAP/52DAP	0.95331	0.783
55DAP/53DAP	0.94164	0.709
57DAP/55DAP	1.18916	1
62DAP/57DAP	1.04896	0.902
68DAP/62DAP	1.09685	1
68DAP/14DAP	2.20141	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.25315	0.74

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.01332	0.02
Immature Eggplant/Mature Eggplant	4.27677
Ripe Pepper/Ripe Tomato	0.48166	0.224
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.12086
12-2/M82	N/A	N/A
12-4/M82	1.12333
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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.14631
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.96457

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.59379

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1096	0.894
DC3000/delta hrp 6h	1.17931	1
DC3000/delta hrp 12h	0.99596	1
DC3000/delta hrp 24h	0.89492	0.269

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00979	1
Exp 36h	0.99039	1
Exp 60h	1.02345	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.88039	1
Var 0h	0.8286	1
Var 12h I row2-row1	0.98113	1
Var 12h NI row2-row1	0.64738	1
Var 36h I row2-row1	0.83916
Var 36h NI row2-row1	0.64513	0.706
Var 60h I row2-row1	1.07694	1
Var 60h NI row2-row1	0.52863	0.756
Time course 0hI-0hNI	1.36178	0.799
Time course 12hI-12hNI	0.85271	0.556
Time course 36hI-36hNI	0.58682	0.093
Time course 60hI-60hNI	0.65841	0.015

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)	0.79996	0.362
transgenic ySAMdc/azygous control (breaker)	1.29495	1
transgenic ySAMdc/azygous control (red)	0.8117	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90342	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77063	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85954	0.172
Manapal/WT (break)	0.74927	1
Manapal/WT (red)	1.73248	0.142