Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.11.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8019	0.31
27DAP/17DAP	1.47527	0.629
39DAP/27DAP	1.25866	0.752
41DAP/39DAP	1.04807	0.978
42DAP/41DAP	1.11224	0.941
43DAP/42DAP	0.88246	0.801
47DAP/43DAP	0.94784	0.729
52DAP/47DAP	0.85498	0.626
57DAP/52DAP	1.22024	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01588	0.872
17DAP/reference	1.01985	0.764
27DAP/reference	1.00494	1
39DAP/reference	1.08726	0.174
41DAP/reference	1.04383	0.312
42DAP/reference	0.95785	0.163
43DAP/reference	1.05252	0.152
47DAP/reference	0.93202	0.032
52DAP/reference	0.84303	0.043
57DAP/reference	0.96586	0.503

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90383	0.542
27DAP/17DAP	1.11611	0.887
39DAP/27DAP	1.08292	0.615
41DAP/39DAP	2.04704	0.011
42DAP/41DAP	0.62198	0.009
43DAP/42DAP	1.03321	1
47DAP/43DAP	1.12446	0.601
52DAP/47DAP	1.04569	0.973
57DAP/52DAP	1.09675	0.632
57DAP/7DAP	1.16786	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96718	0.183
17DAP/reference	1.22047	0.035
27DAP/reference	1.05621	0.664
39DAP/reference	1.16428	0.186
41DAP/reference	1.07863	0.812
42DAP/reference	1.10153	0.405
43DAP/reference	1.31991	0.048
47DAP/reference	1.21295	0.272
52DAP/reference	1.28109	0.139
57DAP/reference	1.79835	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01989	0.885
17DAP/reference	0.98312	0.594
27DAP/reference	0.87586	0.15
39DAP/reference	0.97106	0.485
41DAP/reference	1.003	0.601
42DAP/reference	0.93988	0.289
43DAP/reference	1.34152	0.087
47DAP/reference	1.05415	0.556
52DAP/reference	1.04958	0.498
57DAP/reference	1.44215	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96981	0.526
17DAP/reference	1.08467	0.354
27DAP/reference	1.23831	0.057
39DAP/reference	1.23928	0.02
41DAP/reference	1.2082	0.086
42DAP/reference	1.04442	0.789
43DAP/reference	0.84958	0.064
47DAP/reference	0.88494	0.231
52DAP/reference	0.94421	0.493
57DAP/reference	0.78545	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02196	1
26DAP/20DAP	1.07227	1
34DAP/26DAP	1.14332	1
51DAP/34DAP	1.1236	0.719
52DAP/51DAP	0.9461
53DAP/52DAP	1.05906	0.921
55DAP/53DAP	1.80349	0.33
57DAP/55DAP	6.64389	0.805
62DAP/57DAP	0.78563	0.681
68DAP/62DAP	0.7652	0.543
68DAP/14DAP	0.3559	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.44548	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.64193
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.59668

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02816	1
1-1-2/M82	0.93066	1
12-2/M82	1.1159
12-4/M82	1.43674
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	0.85359	0.752
4-1-1/M82	1.06732
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	2.56799
5-3/M82	0.97191	1
6-2/M82	0.86192
6-3/M82	0.95346
7-1/M82	N/A	N/A
7-2/M82	0.84706
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	1.12253
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.73156
IL1-4/WTpooled	1.07778	1
WT/WTpooled	0.96203	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	1.39713	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02718	0.921
DC3000/delta hrp 6h	1.23991	1
DC3000/delta hrp 12h	1.08054	1
DC3000/delta hrp 24h	1.01255	0.797

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	0.56042

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24879	1
Exp 36h	N/A	N/A
Exp 60h	1.51702	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03475	1
Var 0h	0.84347	0.933
Var 12h I row2-row1	1.26169	0.473
Var 12h NI row2-row1	1.03057	1
Var 36h I row2-row1	1.40924	0.309
Var 36h NI row2-row1	1.00141	1
Var 60h I row2-row1	1.3503	0.487
Var 60h NI row2-row1	1.01063	1
Time course 0hI-0hNI	1.15363	0.413
Time course 12hI-12hNI	1.02244	0.85
Time course 36hI-36hNI	2.38681	0.004
Time course 60hI-60hNI	4.58933	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	0.57169	0.251
transgenic ySAMdc/azygous control (red)	1.68792	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96529	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.13821	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73433	1
Manapal/WT (break)	0.94616	1
Manapal/WT (red)	N/A	N/A