Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.18.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05509	0.912
27DAP/17DAP	1.09678	0.88
39DAP/27DAP	0.91693	0.641
41DAP/39DAP	0.97207	0.897
42DAP/41DAP	0.92386	1
43DAP/42DAP	1.2692	0.58
47DAP/43DAP	1.18973	0.733
52DAP/47DAP	1.21347	0.821
57DAP/52DAP	1.15242	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94144	0.3
17DAP/reference	0.86056	0.065
27DAP/reference	0.95749	0.514
39DAP/reference	0.86464	0.021
41DAP/reference	0.84035	0.085
42DAP/reference	0.89156	0.004
43DAP/reference	0.91414	0.17
47DAP/reference	0.93261	0.127
52DAP/reference	0.96093	0.461
57DAP/reference	1.11076	0.114

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00304	0.732
27DAP/17DAP	1.06064	0.881
39DAP/27DAP	1.14018	0.751
41DAP/39DAP	0.79216	0.662
42DAP/41DAP	1.10908	0.861
43DAP/42DAP	0.81324	0.383
47DAP/43DAP	1.09486	0.798
52DAP/47DAP	1.28084	0.586
57DAP/52DAP	1.36657	0.657
57DAP/7DAP	0.95443	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04743	1
17DAP/reference	1.06333	0.297
27DAP/reference	0.92854	0.109
39DAP/reference	1.12009	0.267
41DAP/reference	1.17846	0.475
42DAP/reference	1.14635	0.308
43DAP/reference	1.1624	0.132
47DAP/reference	0.8562	0.222
52DAP/reference	1.1739	0.328
57DAP/reference	1.06858	0.536

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06306	0.787
17DAP/reference	0.83294	0.008
27DAP/reference	0.92604	0.188
39DAP/reference	1.01292	1
41DAP/reference	1.03125	0.718
42DAP/reference	0.78775	0.02
43DAP/reference	1.02858	0.977
47DAP/reference	0.85934	0.032
52DAP/reference	0.9533	0.171
57DAP/reference	0.85894	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90954	0.119
17DAP/reference	0.92745	0.313
27DAP/reference	1.00775	1
39DAP/reference	1.07936	0.496
41DAP/reference	1.15625	0.357
42DAP/reference	0.94934	0.445
43DAP/reference	0.93863	0.348
47DAP/reference	0.97249	0.494
52DAP/reference	0.79517	0.121
57DAP/reference	0.90141	0.092

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.81022	0.585
26DAP/20DAP	0.91844	1
34DAP/26DAP	1.21416	1
51DAP/34DAP	1.22976	0.925
52DAP/51DAP	1.44813	0.335
53DAP/52DAP	1.15862	0.944
55DAP/53DAP	0.99023	0.917
57DAP/55DAP	0.93193	0.757
62DAP/57DAP	0.93685	0.994
68DAP/62DAP	3.0555	0.523
68DAP/14DAP	0.91112	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04219	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.13516
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.04078
12-2/M82	N/A	N/A
12-4/M82	0.96148
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	1.00156
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	1.10649
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	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	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	1.05555	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98808	1
DC3000/delta hrp 6h	1.67334	1
DC3000/delta hrp 12h	0.96364	1
DC3000/delta hrp 24h	0.71136	0.087

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.87654	0.943
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	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	0.36049
Time course 60hI-60hNI	1.34207

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)	1.29346	0.36
transgenic ySAMdc/azygous control (breaker)	1.39549	0.166
transgenic ySAMdc/azygous control (red)	0.97321	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9534	0.126

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95284	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.43852	0.172
Manapal/WT (break)	1.10725	1
Manapal/WT (red)	0.94609	0.728