Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.18.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.20716	0.054
27DAP/17DAP	0.6306	0.123
39DAP/27DAP	1.07758	0.876
41DAP/39DAP	0.702	0.245
42DAP/41DAP	0.68507	0.259
43DAP/42DAP	0.79044	0.681
47DAP/43DAP	0.99665	0.904
52DAP/47DAP	1.09514	0.903
57DAP/52DAP	1.23127	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8638	0.057
17DAP/reference	0.73047	0.008
27DAP/reference	0.90739	0.194
39DAP/reference	0.67765	0.01
41DAP/reference	0.6765	0.011
42DAP/reference	0.76625	0.001
43DAP/reference	0.73753	0.015
47DAP/reference	0.80314	0.004
52DAP/reference	1.07946	0.991
57DAP/reference	1.03154	0.952

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20264	0.687
27DAP/17DAP	0.80457	0.537
39DAP/27DAP	0.8315	0.4
41DAP/39DAP	1.0817	0.868
42DAP/41DAP	0.80161	0.086
43DAP/42DAP	1.32288	0.513
47DAP/43DAP	1.48624	0.95
52DAP/47DAP	1.33792	0.412
57DAP/52DAP	1.11271	0.818
57DAP/7DAP	1.67513	0.207

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3289	0.129
17DAP/reference	0.9112	0.144
27DAP/reference	0.99959	0.656
39DAP/reference	0.9207	0.17
41DAP/reference	0.96941	0.489
42DAP/reference	1.22924	0.534
43DAP/reference	0.90699	0.23
47DAP/reference	0.87356	0.293
52DAP/reference	0.74413	0.057
57DAP/reference	0.75822	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79644	0.008
17DAP/reference	0.81956	0.029
27DAP/reference	0.87642	0.181
39DAP/reference	0.95063	0.37
41DAP/reference	0.96279	0.393
42DAP/reference	0.88563	0.021
43DAP/reference	0.57326	0.002
47DAP/reference	0.73245	0.019
52DAP/reference	0.95615	0.239
57DAP/reference	0.74552	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87302	0.183
17DAP/reference	0.9845	0.668
27DAP/reference	0.89648	0.174
39DAP/reference	0.88244	0.122
41DAP/reference	0.93161	0.293
42DAP/reference	0.75278	0.028
43DAP/reference	0.96803	0.484
47DAP/reference	0.652	0.005
52DAP/reference	0.74915	0.123
57DAP/reference	1.13955	0.73

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.68172	0.42
26DAP/20DAP	0.79901	0.244
34DAP/26DAP	0.93894	0.94
51DAP/34DAP	0.97298	0.785
52DAP/51DAP	1.38039	0.225
53DAP/52DAP	1.2369	0.723
55DAP/53DAP	1.08514	0.939
57DAP/55DAP	1.25668	0.955
62DAP/57DAP	1.22852	0.622
68DAP/62DAP	1.84095	0.052
68DAP/14DAP	2.00861	0.236

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87254	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	5.91327	0.015
Immature Eggplant/Mature Eggplant	9.20196	0.05
Ripe Pepper/Ripe Tomato	1.48558
Mature Eggplant/Ripe Tomato	40.3414

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.1125
IL2-6/WTpooled	0.98258	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.78422	0.293
IL12-4/WTpooled	0.70875	0.581
IL1-4/WTpooled	1.43855	1
WT/WTpooled	0.96911	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	1.2769

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02969	1
DC3000/delta hrp 6h	0.89454	0.95
DC3000/delta hrp 12h	0.48792	1
DC3000/delta hrp 24h	17.7941	0.023

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.22893	0.042
DC3000 delta B/DC3000 delta AB	2.22629	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98946	1
Exp 36h	0.62837	0.539
Exp 60h	0.89417	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.23339	1
Var 0h	0.95414	1
Var 12h I row2-row1	0.92664	0.77
Var 12h NI row2-row1	0.70334	1
Var 36h I row2-row1	1.68855	0.742
Var 36h NI row2-row1	0.79689	0.743
Var 60h I row2-row1	0.68429	0.292
Var 60h NI row2-row1	0.58976	1
Time course 0hI-0hNI	1.27498	0.764
Time course 12hI-12hNI	1.17166	0.599
Time course 36hI-36hNI	1.47642	0.651
Time course 60hI-60hNI	25.8809	0.008

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)	0.86084	0.299
transgenic ySAMdc/azygous control (breaker)	1.242	0.248
transgenic ySAMdc/azygous control (red)	1.17688	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.86219	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.1106	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.44603	0.093
Manapal/WT (break)	1.16737	1
Manapal/WT (red)	0.87633	0.187