Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.9.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08474	0.961
27DAP/17DAP	0.60071	0.081
39DAP/27DAP	0.7895	0.583
41DAP/39DAP	1.05428	0.859
42DAP/41DAP	0.81441	0.774
43DAP/42DAP	1.11057	0.937
47DAP/43DAP	1.79943	0.481
52DAP/47DAP	1.14897	0.809
57DAP/52DAP	0.76322	0.737

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0015	0.787
17DAP/reference	1.08887	0.476
27DAP/reference	0.90628	0.064
39DAP/reference	0.91642	0.267
41DAP/reference	1.08586	0.451
42DAP/reference	0.80055	0.003
43DAP/reference	1.05477	0.705
47DAP/reference	0.87086	0.042
52DAP/reference	0.81307	0.069
57DAP/reference	0.92874	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14493	0.899
27DAP/17DAP	0.95057	0.887
39DAP/27DAP	0.89831	0.188
41DAP/39DAP	0.83866	0.599
42DAP/41DAP	0.91824	0.579
43DAP/42DAP	1.12349	0.627
47DAP/43DAP	1.84454	0.234
52DAP/47DAP	0.89449	0.237
57DAP/52DAP	1.10357	0.892
57DAP/7DAP	2.00808	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00556	1
17DAP/reference	1.08345	0.18
27DAP/reference	0.90816	0.051
39DAP/reference	0.99173	0.64
41DAP/reference	0.73764	0.039
42DAP/reference	0.88172	0.13
43DAP/reference	0.81741	0.025
47DAP/reference	0.85287	0.066
52DAP/reference	0.84048	0.057
57DAP/reference	0.91151	0.105

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26135	0.063
17DAP/reference	0.91252	0.195
27DAP/reference	1.16423	0.221
39DAP/reference	0.96804	0.455
41DAP/reference	0.77831	0.016
42DAP/reference	0.8291	0.081
43DAP/reference	1.4402	0.038
47DAP/reference	0.94306	0.246
52DAP/reference	1.10055	0.124
57DAP/reference	1.08312	0.286

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92008	0.197
17DAP/reference	1.02301	0.842
27DAP/reference	1.02289	0.967
39DAP/reference	0.9451	0.179
41DAP/reference	0.9695	0.459
42DAP/reference	0.92613	0.287
43DAP/reference	0.9756	0.59
47DAP/reference	0.93267	0.315
52DAP/reference	1.15839	0.363
57DAP/reference	0.79509	0.122

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13726	0.966
26DAP/20DAP	2.56952	0.493
34DAP/26DAP	2.05709	1
51DAP/34DAP	1.20168	0.785
52DAP/51DAP	1.08307	0.915
53DAP/52DAP	0.9506	0.776
55DAP/53DAP	1.12502	0.898
57DAP/55DAP	0.99187	0.944
62DAP/57DAP	1.09071	0.723
68DAP/62DAP	1.3768	0.936
68DAP/14DAP	0.79393	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73427	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.5369
Mature Eggplant/Ripe Tomato	0.25734

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07395
1-1-2/M82	0.80092
12-2/M82	N/A	N/A
12-4/M82	1.21886
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	1.10965
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	N/A	N/A
IL2-6/WTpooled	1.05122	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.80523	0.418
IL12-4/WTpooled	1.0918	0.737
IL1-4/WTpooled	0.92906
WT/WTpooled	1.01088	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	1.3828

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93911	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.02294	1
DC3000/delta hrp 24h	1.02895	0.728

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	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	0.99929	1
Var 0h	0.9878	1
Var 12h I row2-row1	1.14945	0.379
Var 12h NI row2-row1	0.55704	1
Var 36h I row2-row1	0.86034	1
Var 36h NI row2-row1	0.78548	0.645
Var 60h I row2-row1	1.05131	1
Var 60h NI row2-row1	0.87637	0.359
Time course 0hI-0hNI	0.99046	0.985
Time course 12hI-12hNI	0.97864	0.893
Time course 36hI-36hNI	1.07437	0.651
Time course 60hI-60hNI	6.04339	0.187

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)	0.97718	0.789
transgenic ySAMdc/azygous control (breaker)	1.29762	1
transgenic ySAMdc/azygous control (red)	1.30312	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95243	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84806	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93243	1
Manapal/WT (break)	1.09781	1
Manapal/WT (red)	1.46739	0.413