Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.14.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80129	0.221
27DAP/17DAP	1.95244	0.24
39DAP/27DAP	1.10808	0.949
41DAP/39DAP	1.17374	0.522
42DAP/41DAP	0.97843	1
43DAP/42DAP	1.07159	1
47DAP/43DAP	1.13214	0.442
52DAP/47DAP	2.19506	0.119
57DAP/52DAP	0.9186	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81964	0.078
17DAP/reference	0.66535	0.007
27DAP/reference	0.87158	0.061
39DAP/reference	0.67171	0.027
41DAP/reference	0.77938	0.011
42DAP/reference	1.31711	0.002
43DAP/reference	0.87162	0.025
47DAP/reference	1.07961	0.885
52DAP/reference	1.35389	0.027
57DAP/reference	1.11923	0.141

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78609	0.105
27DAP/17DAP	1.05691	0.938
39DAP/27DAP	1.05931	0.643
41DAP/39DAP	1.29589	0.115
42DAP/41DAP	0.83037	0.075
43DAP/42DAP	1.42337	0.026
47DAP/43DAP	1.04773	0.779
52DAP/47DAP	1.40226	0.205
57DAP/52DAP	1.51767	0.073
57DAP/7DAP	1.09431	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03721	0.676
17DAP/reference	1.17557	0.038
27DAP/reference	1.24602	0.014
39DAP/reference	1.34829	0.007
41DAP/reference	1.28819	0.045
42DAP/reference	1.33681	0.132
43DAP/reference	1.47272	0.006
47DAP/reference	1.24897	0.127
52DAP/reference	1.3157	0.034
57DAP/reference	1.46529	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90088	0.222
17DAP/reference	0.88362	0.176
27DAP/reference	0.91261	0.139
39DAP/reference	0.97816	0.509
41DAP/reference	1.11272	0.248
42DAP/reference	1.20077	0.455
43DAP/reference	0.92135	0.394
47DAP/reference	1.25093	0.022
52DAP/reference	0.70604	0.004
57DAP/reference	0.88411	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02627	1
17DAP/reference	0.97389	0.636
27DAP/reference	1.31003	0.027
39DAP/reference	1.19795	0.046
41DAP/reference	1.1768	0.1
42DAP/reference	1.12737	0.327
43DAP/reference	1.19989	0.071
47DAP/reference	1.24956	0.934
52DAP/reference	1.4211	0.055
57DAP/reference	2.06442	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95646	1
26DAP/20DAP	0.9437	1
34DAP/26DAP	0.92736	0.735
51DAP/34DAP	1.26556	0.473
52DAP/51DAP	1.22991	0.121
53DAP/52DAP	1.14351	0.594
55DAP/53DAP	0.86296	0.252
57DAP/55DAP	1.12067	0.644
62DAP/57DAP	4.52203	0.303
68DAP/62DAP	1.44163	0.225
68DAP/14DAP	2.78895	0.08

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.40836	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.24527	0.068
Mature Green Tomato/Ripe Tomato	0.26846	0.021
Immature Eggplant/Mature Eggplant	0.68324	0.096
Ripe Pepper/Ripe Tomato	0.34831	0.224
Mature Eggplant/Ripe Tomato	0.22099	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06558	1
1-1-2/M82	0.87466	1
12-2/M82	1.65168	1
12-4/M82	0.92874	1
1-3/M82	0.95974	1
2-1-1/M82	0.95471	1
2-1/M82	1.13217	1
2-6/M82	1.28014	0.505
3-2/M82	0.85034
4-1-1/M82	1.09252	1
4-1/M82	0.76119	1
4-3-2/M82	1.07811	1
4-3/M82	1.00485	1
5-3/M82	0.64009	0.364
6-2/M82	1.23133	1
6-3/M82	0.96261	1
7-1/M82	0.49225	0.429
7-2/M82	0.95819	1
9-3-2/M82	0.88828	1

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	1.06472	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89153
DC3000/delta hrp 6h	0.97505	0.95
DC3000/delta hrp 12h	1.34963	1
DC3000/delta hrp 24h	1.20415	0.079

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02968
DC3000 delta B/DC3000 delta AB	1.06327	0.491

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	1.90416	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97356	1
Var 0h	0.867	1
Var 12h I row2-row1	1.13921	0.189
Var 12h NI row2-row1	0.99449	1
Var 36h I row2-row1	1.06528	1
Var 36h NI row2-row1	1.02744	1
Var 60h I row2-row1	0.85272	0.285
Var 60h NI row2-row1	0.9948	1
Time course 0hI-0hNI	1.10909	0.662
Time course 12hI-12hNI	1.24161	0.02
Time course 36hI-36hNI	1.73956	0.004
Time course 60hI-60hNI	2.02926	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)	1.05717	0.748
transgenic ySAMdc/azygous control (breaker)	0.48802	0.124
transgenic ySAMdc/azygous control (red)	1.10725	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99107	0.757

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71082	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.75046	0.172
Manapal/WT (break)	0.52788	0.299
Manapal/WT (red)	0.57945	0.181