Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.16.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0272	0.932
27DAP/17DAP	1.12092	0.859
39DAP/27DAP	0.83134	0.392
41DAP/39DAP	1.10318	0.772
42DAP/41DAP	1.1864	0.894
43DAP/42DAP	0.84418	0.554
47DAP/43DAP	0.96707	0.828
52DAP/47DAP	1.49474	0.31
57DAP/52DAP	0.9856	0.976

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96073	0.3
17DAP/reference	0.9988	1
27DAP/reference	1.01485	0.794
39DAP/reference	0.99211	0.855
41DAP/reference	0.93126	0.267
42DAP/reference	0.96668	0.091
43DAP/reference	1.02309	0.425
47DAP/reference	1.00194	1
52DAP/reference	1.02735	0.498
57DAP/reference	0.92556	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01266	1
27DAP/17DAP	0.99962	1
39DAP/27DAP	0.98545	0.887
41DAP/39DAP	0.97036	0.959
42DAP/41DAP	1.05108	0.81
43DAP/42DAP	0.99014	0.928
47DAP/43DAP	1.00968	0.973
52DAP/47DAP	0.98684	0.93
57DAP/52DAP	1.01389	0.963
57DAP/7DAP	1.01751	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91215	0.108
17DAP/reference	0.91227	0.028
27DAP/reference	0.9172	0.031
39DAP/reference	1.02887	0.511
41DAP/reference	1.19569	0.375
42DAP/reference	0.9674	0.189
43DAP/reference	0.95098	0.066
47DAP/reference	0.94615	0.293
52DAP/reference	0.99362	0.679
57DAP/reference	1.046	0.746

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01688	0.802
17DAP/reference	0.98629	0.594
27DAP/reference	0.94507	0.366
39DAP/reference	0.91682	0.113
41DAP/reference	0.9735	0.441
42DAP/reference	0.93552	0.055
43DAP/reference	1.0201	0.777
47DAP/reference	0.97935	0.194
52DAP/reference	0.94551	0.029
57DAP/reference	0.97644	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97883	0.249
17DAP/reference	0.97897	0.571
27DAP/reference	0.94963	0.051
39DAP/reference	0.96456	0.111
41DAP/reference	0.98482	0.56
42DAP/reference	0.89806	0.041
43DAP/reference	0.91916	0.106
47DAP/reference	0.94091	0.306
52DAP/reference	0.90296	0.177
57DAP/reference	0.80791	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97823	1
26DAP/20DAP	0.92315	1
34DAP/26DAP	0.90193	0.488
51DAP/34DAP	0.97848	0.816
52DAP/51DAP	0.99752	1
53DAP/52DAP	1.06003	0.783
55DAP/53DAP	0.92027	0.515
57DAP/55DAP	0.96544	0.819
62DAP/57DAP	1.022	1
68DAP/62DAP	0.90643	0.641
68DAP/14DAP	1.05261	0.578

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.909	0.186

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	10.5479	0.058
Mature Green Tomato/Ripe Tomato	0.83332	0.036
Immature Eggplant/Mature Eggplant	0.74863	0.063
Ripe Pepper/Ripe Tomato	1.31333	1
Mature Eggplant/Ripe Tomato	3.92262	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97157	0.961
1-1-2/M82	0.82779	1
12-2/M82	0.97212	1
12-4/M82	0.95497	1
1-3/M82	0.97415	1
2-1-1/M82	0.97031	1
2-1/M82	N/A	N/A
2-6/M82	0.9745	1
3-2/M82	1.09764
4-1-1/M82	1.1644	1
4-1/M82	0.88195	1
4-3-2/M82	0.91983	1
4-3/M82	1.12995	1
5-3/M82	1.0574	1
6-2/M82	0.95085	0.481
6-3/M82	0.9882	1
7-1/M82	N/A	N/A
7-2/M82	1.08578	1
9-3-2/M82	0.7421	0.355

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	0.90792	1
IL12-4/WTpooled	2.12601	0.52
IL1-4/WTpooled	0.81494	0.834
WT/WTpooled	0.80031	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	0.84224	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0086	0.921
DC3000/delta hrp 6h	0.94202	0.95
DC3000/delta hrp 12h	1.01631	1
DC3000/delta hrp 24h	1.05026	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04855	0.441
DC3000 delta B/DC3000 delta AB	1.01637	0.726

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88248	0.265
Exp 36h	1.16261	1
Exp 60h	0.94077	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00362
Var 0h	0.89352	0.933
Var 12h I row2-row1	1.16243	0.204
Var 12h NI row2-row1	1.03318	1
Var 36h I row2-row1	1.02011	1
Var 36h NI row2-row1	0.89701	0.584
Var 60h I row2-row1	1.16411	0.562
Var 60h NI row2-row1	0.92638	0.932
Time course 0hI-0hNI	1.05539	0.852
Time course 12hI-12hNI	0.97869	0.87
Time course 36hI-36hNI	0.95509	0.36
Time course 60hI-60hNI	0.98373	1

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)	1.12732	0.267
transgenic ySAMdc/azygous control (breaker)	0.91976	0.49
transgenic ySAMdc/azygous control (red)	1.01537	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00503	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.62228	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77421	0.172
Manapal/WT (break)	0.72967	0.333
Manapal/WT (red)	0.42035	0.199