Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.3.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9522	0.722
27DAP/17DAP	1.08865	0.91
39DAP/27DAP	0.94099	0.641
41DAP/39DAP	1.16209	0.624
42DAP/41DAP	1.11639	0.843
43DAP/42DAP	0.94342	0.877
47DAP/43DAP	1.84346	0.415
52DAP/47DAP	0.95389	0.842
57DAP/52DAP	1.21273	0.96

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22047	0.065
17DAP/reference	1.25537	0.017
27DAP/reference	1.08233	0.365
39DAP/reference	0.96171	0.734
41DAP/reference	1.36991	0.012
42DAP/reference	1.0417	0.812
43DAP/reference	0.87286	0.691
47DAP/reference	1.07786	0.046
52DAP/reference	1.12927	0.335
57DAP/reference	1.66706

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9502	0.595
27DAP/17DAP	1.00289	0.969
39DAP/27DAP	1.09085	0.596
41DAP/39DAP	0.97583	0.986
42DAP/41DAP	0.93955	0.595
43DAP/42DAP	0.82399	0.089
47DAP/43DAP	0.94051	0.734
52DAP/47DAP	1.29824	0.408
57DAP/52DAP	1.28075	0.238
57DAP/7DAP	1.38399	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98509	0.445
17DAP/reference	1.20693	0.399
27DAP/reference	1.40754	0.011
39DAP/reference	1.06249	1
41DAP/reference	0.99168	0.646
42DAP/reference	0.95576	0.436
43DAP/reference	1.11438	0.511
47DAP/reference	1.00765	1
52DAP/reference	0.90976	0.278
57DAP/reference	0.92589	0.28

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01187	1
17DAP/reference	1.07882	0.496
27DAP/reference	1.04919	0.988
39DAP/reference	0.9266	0.416
41DAP/reference	1.01274	0.735
42DAP/reference	0.88898	0.189
43DAP/reference	1.11126	0.655
47DAP/reference	0.85468	0.019
52DAP/reference	1.06248	0.629
57DAP/reference	0.89148	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15561	0.408
17DAP/reference	0.93651	0.488
27DAP/reference	0.98212	0.657
39DAP/reference	1.026	1
41DAP/reference	1.0483	1
42DAP/reference	0.9646	0.552
43DAP/reference	0.91118	0.305
47DAP/reference	0.89513	0.174
52DAP/reference	1.39764	0.908
57DAP/reference	1.24364	0.354

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98656	1
26DAP/20DAP	0.92852	1
34DAP/26DAP	0.77542	0.35
51DAP/34DAP	0.85123	0.22
52DAP/51DAP	1.04418	0.915
53DAP/52DAP	0.87835	0.484
55DAP/53DAP	1.05182	1
57DAP/55DAP	1.03534	0.94
62DAP/57DAP	1.60171
68DAP/62DAP	1.49864	0.626
68DAP/14DAP	1.21393

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04871	0.865

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.2991	0.478
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.24823
Mature Eggplant/Ripe Tomato	1.02335

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.07908
12-2/M82	N/A	N/A
12-4/M82	0.88384
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	0.9169
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	1.04619	0.496
6-2/M82	N/A	N/A
6-3/M82	0.57897
7-1/M82	N/A	N/A
7-2/M82	1.29614
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.83961	0.321
IL2-6/WTpooled	1.06634
IL7-5/WTpooled	0.94814	1
IL7-3/WTpooled	0.98318
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.00813	1
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	0.73666	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.82317
DC3000/delta hrp 6h	1.13482	1
DC3000/delta hrp 12h	1.03301	1
DC3000/delta hrp 24h	1.06282	0.673

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	3.0253

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	0.8029	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93618
Var 0h	1.18375	0.936
Var 12h I row2-row1	1.43582	0.473
Var 12h NI row2-row1	1.40812	0.649
Var 36h I row2-row1	1.36243	0.489
Var 36h NI row2-row1	0.94059	0.706
Var 60h I row2-row1	0.79506	0.306
Var 60h NI row2-row1	0.9274	1
Time course 0hI-0hNI	1.09378	0.603
Time course 12hI-12hNI	0.90256	0.377
Time course 36hI-36hNI	1.15938	0.248
Time course 60hI-60hNI	2.43338	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)	1.05805	0.305
transgenic ySAMdc/azygous control (breaker)	1.11893	1
transgenic ySAMdc/azygous control (red)	0.85432	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0684	0.046

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)	0.86438	1
Manapal/WT (break)	1.07342	1
Manapal/WT (red)	1.18842	0.413