Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.15.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19011	0.485
27DAP/17DAP	0.94822	0.939
39DAP/27DAP	0.94963	0.7
41DAP/39DAP	0.93063	0.735
42DAP/41DAP	1.39276	0.786
43DAP/42DAP	0.89591	0.721
47DAP/43DAP	1.01098	0.953
52DAP/47DAP	1.70943	0.635
57DAP/52DAP	0.92999	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25299	0.068
17DAP/reference	1.53694	0.049
27DAP/reference	1.2776	0.014
39DAP/reference	1.19363	0.318
41DAP/reference	1.13833	0.552
42DAP/reference	1.03421	0.628
43DAP/reference	1.10551	0.596
47DAP/reference	0.99509	0.636
52DAP/reference	1.23007	0.217
57DAP/reference	0.98488	0.61

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01673	1
27DAP/17DAP	1.04648	0.872
39DAP/27DAP	1.04722	0.677
41DAP/39DAP	0.91395	0.586
42DAP/41DAP	0.94864	0.599
43DAP/42DAP	1.3401	0.019
47DAP/43DAP	1.01083	0.973
52DAP/47DAP	0.98799	0.925
57DAP/52DAP	0.86648	0.12
57DAP/7DAP	1.24082	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.75776	0.032
17DAP/reference	1.15875	0.269
27DAP/reference	0.99555	0.614
39DAP/reference	0.91204	0.17
41DAP/reference	0.93665	0.341
42DAP/reference	1.13998	0.405
43DAP/reference	0.99128	0.608
47DAP/reference	0.84213	0.383
52DAP/reference	0.86624	0.097
57DAP/reference	0.91338	0.25

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81405	0.353
17DAP/reference	1.02198	0.786
27DAP/reference	1.16624	0.682
39DAP/reference	1.1877	0.502
41DAP/reference	1.13956	0.471
42DAP/reference	1.03044	1
43DAP/reference	0.88064	0.314
47DAP/reference	1.05502	0.639
52DAP/reference	0.90061	0.5
57DAP/reference	0.90401	0.107

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.79662	0.028
17DAP/reference	0.89426	0.56
27DAP/reference	1.42974	0.052
39DAP/reference	1.07788	0.752
41DAP/reference	0.87138	0.237
42DAP/reference	1.00825	1
43DAP/reference	1.0402	0.858
47DAP/reference	0.99202	0.593
52DAP/reference	0.62205	0.088
57DAP/reference	0.96841	0.491

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.34875	0.966
26DAP/20DAP	1.19356	0.361
34DAP/26DAP	1.11619	1
51DAP/34DAP	1.13501	0.677
52DAP/51DAP	0.99881	1
53DAP/52DAP	1.04549	0.91
55DAP/53DAP	0.93194	0.698
57DAP/55DAP	1.08796	0.997
62DAP/57DAP	1.2502	0.257
68DAP/62DAP	1.20615	0.792
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.8551	0.239

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.81869	0.132
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.82215	1

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	1.12603	0.694
1-3/M82	0.71708
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	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.96218
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	1.28674	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.83339	0.321
IL2-6/WTpooled	3.11405	0.395
IL7-5/WTpooled	0.91184	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.59319	0.673
IL1-4/WTpooled	0.90954	0.834
WT/WTpooled	0.99734	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	1.15097	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.21251	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.31121	0.054

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.50592	0.068
DC3000 delta B/DC3000 delta AB	0.89912	0.511

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91023	1
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99715	1
Var 0h	0.97561	1
Var 12h I row2-row1	0.96982	0.948
Var 12h NI row2-row1	0.98838	1
Var 36h I row2-row1	0.82874	0.805
Var 36h NI row2-row1	3.00375	1
Var 60h I row2-row1	1.12662	0.543
Var 60h NI row2-row1	1.16448	0.904
Time course 0hI-0hNI	0.9792	0.935
Time course 12hI-12hNI	0.99532	1
Time course 36hI-36hNI	0.86631	0.078
Time course 60hI-60hNI	0.50062	0.005

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)	0.98909	0.862
transgenic ySAMdc/azygous control (breaker)	0.66568	0.134
transgenic ySAMdc/azygous control (red)	0.94451	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89422	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92933	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.80694	0.274