Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.3.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13642	0.912
27DAP/17DAP	0.808	0.5
39DAP/27DAP	0.98775	0.82
41DAP/39DAP	1.87609	0.504
42DAP/41DAP	1.2906	0.806
43DAP/42DAP	1.50797	0.213
47DAP/43DAP	0.96594	0.794
52DAP/47DAP	1.19937	0.895
57DAP/52DAP	0.72446	0.729

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21024	0.018
17DAP/reference	1.40676	0.282
27DAP/reference	1.08227	0.587
39DAP/reference	1.20798	0.026
41DAP/reference	1.12139	0.265
42DAP/reference	1.15675	0.469
43DAP/reference	1.36837
47DAP/reference	1.40746	0.448
52DAP/reference	1.67882	0.007
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98784	0.763
27DAP/17DAP	0.86947	0.648
39DAP/27DAP	1.3666	0.12
41DAP/39DAP	0.77112	0.321
42DAP/41DAP	1.59869	0.378
43DAP/42DAP	6.73235	0.013
47DAP/43DAP	0.72131	0.01
52DAP/47DAP	0.58781	0.064
57DAP/52DAP	0.78166	0.264
57DAP/7DAP	1.48535	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93341	0.402
17DAP/reference	0.93657	0.144
27DAP/reference	1.10371	0.246
39DAP/reference	0.74043	0.011
41DAP/reference	0.75338	0.047
42DAP/reference	0.67356	0.01
43DAP/reference	0.71749	0.022
47DAP/reference	0.88069	0.293
52DAP/reference	0.61455	0.012
57DAP/reference	0.66701	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20518	0.049
17DAP/reference	1.20917	0.197
27DAP/reference	1.30377	0.062
39DAP/reference	1.29356	0.099
41DAP/reference	1.35719	0.02
42DAP/reference	1.55167	0.007
43DAP/reference	1.68852	0.04
47DAP/reference	1.46287	0.012
52DAP/reference	1.43928	0.012
57DAP/reference	1.13025	0.552

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98768	0.489
17DAP/reference	1.10235	0.578
27DAP/reference	0.81299	0.05
39DAP/reference	0.85516	0.111
41DAP/reference	1.06643	0.537
42DAP/reference	1.14566	0.49
43DAP/reference	0.90787	0.319
47DAP/reference	1.4088	0.006
52DAP/reference	1.14903	0.19
57DAP/reference	1.71346	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.2441	0.966
26DAP/20DAP	2.46371	0.099
34DAP/26DAP	1.35283	0.304
51DAP/34DAP	1.12606	0.898
52DAP/51DAP	0.75215	0.151
53DAP/52DAP	0.75328	0.106
55DAP/53DAP	0.92348	0.686
57DAP/55DAP	0.75664	0.165
62DAP/57DAP	1.10325
68DAP/62DAP	1.45398	0.162
68DAP/14DAP	1.93371

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.6279	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	7.08312	0.058
Mature Green Tomato/Ripe Tomato	0.17823	0.029
Immature Eggplant/Mature Eggplant	2.73023	0.05
Ripe Pepper/Ripe Tomato	2.24648	1
Mature Eggplant/Ripe Tomato	3.00122	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00527	1
1-1-2/M82	0.95479	1
12-2/M82	1.04002	1
12-4/M82	0.9571	1
1-3/M82	0.88839	0.501
2-1-1/M82	1.24705
2-1/M82	1.39343	1
2-6/M82	1.09786	0.695
3-2/M82	0.82683
4-1-1/M82	1.06831	1
4-1/M82	1.15971
4-3-2/M82	1.1589	1
4-3/M82	0.89003	1
5-3/M82	1.03759	1
6-2/M82	1.04282
6-3/M82	0.95959	1
7-1/M82	1.04566
7-2/M82	1.01738	1
9-3-2/M82	0.75463	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91989	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.10792	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.08135
IL1-4/WTpooled	0.91395	0.834
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	1.56646	0.154

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01254	0.921
DC3000/delta hrp 6h	0.47171	0.706
DC3000/delta hrp 12h	1.15523	1
DC3000/delta hrp 24h	1.11035	0.158

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	0.80698

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13992	0.254
Exp 36h	1.53977	1
Exp 60h	0.93783	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.92968
Var 0h	0.8909	0.226
Var 12h I row2-row1	1.03724	0.58
Var 12h NI row2-row1	0.56023	0.494
Var 36h I row2-row1	0.86516	0.34
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.98576
Var 60h NI row2-row1	1.13898	0.904
Time course 0hI-0hNI	1.08635	0.833
Time course 12hI-12hNI	0.91223	0.738
Time course 36hI-36hNI	1.31585	0.722
Time course 60hI-60hNI	0.4213	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)	1.21421	0.271
transgenic ySAMdc/azygous control (breaker)	0.91579	0.49
transgenic ySAMdc/azygous control (red)	0.8657	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03927	0.556

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.69511	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04695	1
Manapal/WT (break)	0.7923	1
Manapal/WT (red)	1.099	1