Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.8.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85571	0.29
27DAP/17DAP	1.1106	0.849
39DAP/27DAP	1.24084	0.539
41DAP/39DAP	0.90562	0.561
42DAP/41DAP	2.51055	0.018
43DAP/42DAP	1.10682	1
47DAP/43DAP	1.14937	0.689
52DAP/47DAP	0.69158	0.28
57DAP/52DAP	1.30689	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9631	0.371
17DAP/reference	1.0977	0.172
27DAP/reference	1.0932	0.216
39DAP/reference	1.0222	0.92
41DAP/reference	1.08017	0.516
42DAP/reference	0.93615	0.069
43DAP/reference	0.98869	0.785
47DAP/reference	0.97139	0.392
52DAP/reference	0.95961	0.382
57DAP/reference	1.05246	0.419

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01591	1
27DAP/17DAP	1.06902	0.805
39DAP/27DAP	1.08759	0.581
41DAP/39DAP	0.97851	0.98
42DAP/41DAP	0.99326	0.87
43DAP/42DAP	1.19989	0.134
47DAP/43DAP	1.10129	0.182
52DAP/47DAP	0.99914	0.962
57DAP/52DAP	1.12493	0.407
57DAP/7DAP	0.99511	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86195	0.183
17DAP/reference	1.13339	0.147
27DAP/reference	0.93785	0.264
39DAP/reference	0.80963	0.031
41DAP/reference	1.08381	0.593
42DAP/reference	1.00592	0.751
43DAP/reference	1.04189	1
47DAP/reference	0.95664	0.504
52DAP/reference	0.98585	0.571
57DAP/reference	0.88524	0.215

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00386	0.884
17DAP/reference	1.00166	0.805
27DAP/reference	0.95606	0.366
39DAP/reference	1.09397	0.355
41DAP/reference	1.14817	0.285
42DAP/reference	0.98487	0.534
43DAP/reference	1.2439	0.124
47DAP/reference	1.05461	0.413
52DAP/reference	1.20634	0.02
57DAP/reference	1.08357	0.26

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92968	0.391
17DAP/reference	1.16788	0.321
27DAP/reference	1.05251	0.967
39DAP/reference	0.89871	0.299
41DAP/reference	1.70842	0.637
42DAP/reference	0.92002	0.552
43DAP/reference	0.72569	0.092
47DAP/reference	1.22807	0.019
52DAP/reference	0.76776	0.172
57DAP/reference	1.25297	0.111

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11711	0.966
26DAP/20DAP	1.29434	0.481
34DAP/26DAP	0.95763	0.94
51DAP/34DAP	0.80528	0.213
52DAP/51DAP	1.03867	0.842
53DAP/52DAP	1.05108	0.868
55DAP/53DAP	1.04464	0.982
57DAP/55DAP	0.6642	0.118
62DAP/57DAP	1.28024	0.069
68DAP/62DAP	1.39561	0.455
68DAP/14DAP	1.16821	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.2786	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.24202	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.75136

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	2.61536
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	1.94953	0.401
4-3-2/M82	1.58529	0.241
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	1.98466

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	0.97707
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.57281
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	0.95373	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06921	0.921
DC3000/delta hrp 6h	1.7857	1
DC3000/delta hrp 12h	1.06867	1
DC3000/delta hrp 24h	0.99644	0.84

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	1.38771	0.208

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.99113	1
Exp 60h	1.25858	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03827	1
Var 0h	1.28423	0.98
Var 12h I row2-row1	1.02924	1
Var 12h NI row2-row1	1.15772	1
Var 36h I row2-row1	1.09151	0.489
Var 36h NI row2-row1	0.89251	0.61
Var 60h I row2-row1	0.91338	0.832
Var 60h NI row2-row1	0.9488	1
Time course 0hI-0hNI	0.90317	0.233
Time course 12hI-12hNI	1.00108	1
Time course 36hI-36hNI	1.33599	0.114
Time course 60hI-60hNI	1.48933	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)	0.99527	0.931
transgenic ySAMdc/azygous control (breaker)	0.66441	0.139
transgenic ySAMdc/azygous control (red)	1.02017	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05938	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.06521	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11101	0.307
Manapal/WT (break)	1.29885	0.183
Manapal/WT (red)	1.39258	0.142