Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.14.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9115	0.596
27DAP/17DAP	1.40862	0.742
39DAP/27DAP	1.26795	0.779
41DAP/39DAP	1.12391	1
42DAP/41DAP	1.16134	0.843
43DAP/42DAP	0.95258	0.888
47DAP/43DAP	0.73303	0.251
52DAP/47DAP	1.51652	0.639
57DAP/52DAP	0.92879	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0277	1
17DAP/reference	1.12824	0.092
27DAP/reference	0.99792	0.797
39DAP/reference	1.18086	0.209
41DAP/reference	1.32068	0.022
42DAP/reference	0.93416	0.176
43DAP/reference	1.01024	1
47DAP/reference	1.01145	1
52DAP/reference	1.02229	1
57DAP/reference	1.02867	0.853

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90468	0.277
27DAP/17DAP	1.00433	1
39DAP/27DAP	1.11225	0.532
41DAP/39DAP	1.0622	0.914
42DAP/41DAP	0.85895	0.111
43DAP/42DAP	1.09399	0.04
47DAP/43DAP	1.05831	0.713
52DAP/47DAP	0.9858	0.917
57DAP/52DAP	1.05075	0.856
57DAP/7DAP	1.20585	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93911	0.402
17DAP/reference	1.04507	1
27DAP/reference	0.9287	0.135
39DAP/reference	0.96812	0.411
41DAP/reference	0.89081	0.146
42DAP/reference	1.00745	0.436
43DAP/reference	0.87263	0.1
47DAP/reference	0.81913	0.168
52DAP/reference	0.63815	0.012
57DAP/reference	0.81913	0.056

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15403	0.495
17DAP/reference	1.09145	0.357
27DAP/reference	1.0269	1
39DAP/reference	1.00421	0.702
41DAP/reference	1.01915	0.702
42DAP/reference	0.91534	0.135
43DAP/reference	1.09222	0.373
47DAP/reference	0.90554	0.173
52DAP/reference	0.96182	0.407
57DAP/reference	1.02297	0.737

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05319	0.903
17DAP/reference	0.93741	0.348
27DAP/reference	1.10407	0.357
39DAP/reference	0.90583	0.101
41DAP/reference	0.9282	0.148
42DAP/reference	0.84577	0.028
43DAP/reference	0.8665	0.081
47DAP/reference	0.83326	0.084
52DAP/reference	0.97936	0.718
57DAP/reference	0.94775	0.38

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06783	0.966
26DAP/20DAP	0.96522	1
34DAP/26DAP	1.01186	1
51DAP/34DAP	0.98037	0.835
52DAP/51DAP	1.03784	0.808
53DAP/52DAP	1.09757	0.444
55DAP/53DAP	1.10285	0.614
57DAP/55DAP	1.08936	0.793
62DAP/57DAP	1.28	0.133
68DAP/62DAP	0.78626	0.464
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88536	0.137

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.40324	0.029
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.45113
Mature Eggplant/Ripe Tomato	0.74098	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.24882
12-2/M82	N/A	N/A
12-4/M82	1.06402	1
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	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.09128	0.378
6-2/M82	N/A	N/A
6-3/M82	0.75373
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	3.22377	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.1557	0.365
IL2-6/WTpooled	0.85282	0.473
IL7-5/WTpooled	1.25431	0.75
IL7-3/WTpooled	1.20519	1
IL12-4/WTpooled	0.93791	1
IL1-4/WTpooled	1.00949	1
WT/WTpooled	1.02546	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	1.04353	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.74544	0.95
DC3000/delta hrp 12h	0.90441	1
DC3000/delta hrp 24h	1.33251	0.062

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.77245
DC3000 delta B/DC3000 delta AB	0.94256	0.445

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89329	1
Exp 36h	0.59074	0.449
Exp 60h	0.88487	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98254	1
Var 0h	1.02582	0.936
Var 12h I row2-row1	0.9463	0.705
Var 12h NI row2-row1	0.94638	0.627
Var 36h I row2-row1	1.00916	1
Var 36h NI row2-row1	1.99763	1
Var 60h I row2-row1	1.30499	0.562
Var 60h NI row2-row1	1.09301	0.904
Time course 0hI-0hNI	1.07912	0.719
Time course 12hI-12hNI	0.98127	0.893
Time course 36hI-36hNI	0.92173	0.323
Time course 60hI-60hNI	1.22704	0.012

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)	1.50973	0.408
transgenic ySAMdc/azygous control (breaker)	0.58812	0.142
transgenic ySAMdc/azygous control (red)	1.05014	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01521	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87302	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97928	1
Manapal/WT (break)	0.78527	0.333
Manapal/WT (red)	0.58551	0.181