Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.9.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07259	1
27DAP/17DAP	1.18123	0.911
39DAP/27DAP	0.81184	0.544
41DAP/39DAP	1.38595	0.797
42DAP/41DAP	1.15158	0.954
43DAP/42DAP	0.99277	0.906
47DAP/43DAP	1.54961	0.384
52DAP/47DAP	1.08853	0.842
57DAP/52DAP	1.23427	0.958

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87545	0.118
17DAP/reference	1.19092	0.041
27DAP/reference	0.92542	0.163
39DAP/reference	1.05532	0.557
41DAP/reference	1.15476	0.067
42DAP/reference	0.94903	0.233
43DAP/reference	1.04977	0.518
47DAP/reference	0.91188	0.127
52DAP/reference	0.95006	0.341
57DAP/reference	0.97147	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01042	0.75
27DAP/17DAP	1.07249	0.73
39DAP/27DAP	1.20817	0.296
41DAP/39DAP	1.09301	0.876
42DAP/41DAP	0.73292	0.181
43DAP/42DAP	1.06927	0.746
47DAP/43DAP	1.06323	0.892
52DAP/47DAP	1.08271	0.799
57DAP/52DAP	0.97808	0.737
57DAP/7DAP	1.7226	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18373	0.126
17DAP/reference	1.41112	0.022
27DAP/reference	1.32845	0.014
39DAP/reference	1.40881	0.04
41DAP/reference	1.41833	0.039
42DAP/reference	2.08101	0.132
43DAP/reference	1.32122	0.157
47DAP/reference	1.11245	0.745
52DAP/reference	1.03664	0.886
57DAP/reference	1.21774	0.066

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14154	0.246
17DAP/reference	1.20067	0.176
27DAP/reference	0.77826	0.115
39DAP/reference	0.97642	0.539
41DAP/reference	0.95735	0.412
42DAP/reference	0.81221	0.055
43DAP/reference	0.93448	0.37
47DAP/reference	0.93487	0.149
52DAP/reference	0.99714	0.619
57DAP/reference	1.19644	0.363

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07975	0.616
17DAP/reference	1.08882	0.657
27DAP/reference	1.42819	0.031
39DAP/reference	1.17951	0.094
41DAP/reference	1.16066	0.15
42DAP/reference	1.166	0.566
43DAP/reference	1.08128	0.84
47DAP/reference	1.06791	0.704
52DAP/reference	1.41408	0.257
57DAP/reference	1.10787	0.682

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.19573	0.966
26DAP/20DAP	0.69502	0.512
34DAP/26DAP	1.05251	1
51DAP/34DAP	1.06286	0.856
52DAP/51DAP	1.04788	0.954
53DAP/52DAP	0.9042	0.553
55DAP/53DAP	1.02631	0.964
57DAP/55DAP	0.84996	0.234
62DAP/57DAP	1.10702	0.833
68DAP/62DAP	0.99564	0.914
68DAP/14DAP	0.7264	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20652	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.25627
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.19945	0.224
Mature Eggplant/Ripe Tomato	0.11207	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06686	1
1-1-2/M82	0.9242	1
12-2/M82	0.80549	0.862
12-4/M82	1.14858	1
1-3/M82	1.36878	0.248
2-1-1/M82	1.07557	0.689
2-1/M82	0.39825
2-6/M82	1.18746	0.695
3-2/M82	0.76455
4-1-1/M82	1.22433
4-1/M82	N/A	N/A
4-3-2/M82	0.92612	1
4-3/M82	1.1908	1
5-3/M82	1.05835	1
6-2/M82	0.87673
6-3/M82	0.98267	1
7-1/M82	1.06645	0.598
7-2/M82	1.01877	1
9-3-2/M82	0.97457

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15174	1
IL2-6/WTpooled	1.2978	0.395
IL7-5/WTpooled	0.85322	1
IL7-3/WTpooled	0.92148	1
IL12-4/WTpooled	1.08145	0.531
IL1-4/WTpooled	0.95247	0.834
WT/WTpooled	1.01327	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	1.02278

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95585	1
DC3000/delta hrp 6h	2.62511
DC3000/delta hrp 12h	0.98424	1
DC3000/delta hrp 24h	1.00293	1

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	1.13826	1
Exp 36h	N/A	N/A
Exp 60h	1.23451	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.29447
Var 0h	1.01313	1
Var 12h I row2-row1	1.09637	1
Var 12h NI row2-row1	1.40655	1
Var 36h I row2-row1	0.45106	1
Var 36h NI row2-row1	1.21294
Var 60h I row2-row1	1.21164	1
Var 60h NI row2-row1	0.7239	0.818
Time course 0hI-0hNI	1.28427	0.833
Time course 12hI-12hNI	0.90017	0.761
Time course 36hI-36hNI	1.1444	0.58
Time course 60hI-60hNI	1.31021	0.359

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)	1.16743	0.455
transgenic ySAMdc/azygous control (breaker)	1.27437	0.248
transgenic ySAMdc/azygous control (red)	0.99582	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95111	0.122

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88407	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07131	1
Manapal/WT (break)	1.06041	1
Manapal/WT (red)	1.07121	1