Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.1.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85713	0.357
27DAP/17DAP	0.52244	0.034
39DAP/27DAP	0.53235	0.221
41DAP/39DAP	0.49523	0.041
42DAP/41DAP	0.71442	0.774
43DAP/42DAP	1.11375	1
47DAP/43DAP	0.73337	0.26
52DAP/47DAP	0.96626	0.789
57DAP/52DAP	1.55182	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37939	0.034
17DAP/reference	0.84386	0.053
27DAP/reference	0.76354	0.018
39DAP/reference	0.75327	0.021
41DAP/reference	0.74576	0.021
42DAP/reference	0.76428	0.011
43DAP/reference	0.80176	0.051
47DAP/reference	0.74403	0.007
52DAP/reference	0.60069	0.016
57DAP/reference	0.90213	0.036

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10295	1
27DAP/17DAP	0.79506	0.312
39DAP/27DAP	0.36196	0.028
41DAP/39DAP	1.28119	0.014
42DAP/41DAP	0.84202	0.046
43DAP/42DAP	0.58017	0.022
47DAP/43DAP	0.84902	0.28
52DAP/47DAP	1.21508	0.749
57DAP/52DAP	1.0717	0.8
57DAP/7DAP	0.52184	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.50808	0.031
17DAP/reference	0.90773	0.124
27DAP/reference	0.7157	0.017
39DAP/reference	0.68093	0.023
41DAP/reference	0.54191	0.012
42DAP/reference	0.53883	0.01
43DAP/reference	0.45094	0.011
47DAP/reference	0.41096	0.03
52DAP/reference	0.45659	0.01
57DAP/reference	0.46081	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23063	0.325
17DAP/reference	0.96947	0.474
27DAP/reference	1.00938	0.735
39DAP/reference	0.75061	0.144
41DAP/reference	0.59098	0.007
42DAP/reference	0.61375	0.014
43DAP/reference	0.45585	0.002
47DAP/reference	0.55341	0.01
52DAP/reference	0.54524	0.004
57DAP/reference	0.63463	0.107

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.78409	0.015
17DAP/reference	1.97206	0.084
27DAP/reference	1.31208	0.027
39DAP/reference	1.15854	0.211
41DAP/reference	0.76581	0.07
42DAP/reference	0.59581	0.018
43DAP/reference	0.71871	0.061
47DAP/reference	0.47555	0.004
52DAP/reference	0.47576	0.047
57DAP/reference	1.10923	0.771

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.53377	0.966
26DAP/20DAP	0.60307	0.512
34DAP/26DAP	1.09901	1
51DAP/34DAP	0.74194	0.333
52DAP/51DAP	0.86824	1
53DAP/52DAP	1.2189	0.319
55DAP/53DAP	1.00762	0.964
57DAP/55DAP	0.95044	0.831
62DAP/57DAP	0.71529	0.871
68DAP/62DAP	2.73271	0.151
68DAP/14DAP	0.87884

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.66702	0.079

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.90186	0.058
Mature Green Tomato/Ripe Tomato	14.71	0.015
Immature Eggplant/Mature Eggplant	0.30442	0.059
Ripe Pepper/Ripe Tomato	6.62557	0.258
Mature Eggplant/Ripe Tomato	33.932	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92104	0.907
1-1-2/M82	0.94736	1
12-2/M82	N/A	N/A
12-4/M82	1.12943	0.611
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	1.13239	0.452
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	1.18272	1
6-2/M82	0.71801	1
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.89229
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.70455	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.1342	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.84694
IL1-4/WTpooled	1.18832	1
WT/WTpooled	1.03848	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	0.87996	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90465
DC3000/delta hrp 6h	1.15856
DC3000/delta hrp 12h	1.37019	1
DC3000/delta hrp 24h	N/A	N/A

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.34403	0.024
DC3000 delta B/DC3000 delta AB	0.31692	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9357	1
Exp 36h	0.73767	0.426
Exp 60h	0.56938	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	1.09742	1
Var 0h	1.10627	0.594
Var 12h I row2-row1	0.72465	0.363
Var 12h NI row2-row1	0.92425	0.713
Var 36h I row2-row1	0.891	1
Var 36h NI row2-row1	1.65431	1
Var 60h I row2-row1	1.4471	0.543
Var 60h NI row2-row1	0.95454	1
Time course 0hI-0hNI	0.98805	0.973
Time course 12hI-12hNI	0.97428	0.864
Time course 36hI-36hNI	0.8943	0.171
Time course 60hI-60hNI	0.10108	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)	1.00261	1
transgenic ySAMdc/azygous control (breaker)	2.00531	0.166
transgenic ySAMdc/azygous control (red)	0.92577	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.66328	0.075

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.04675	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.85717	0.083
Manapal/WT (break)	5.59797	0.123
Manapal/WT (red)	6.09243	0.164