Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.19.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.46088	0.477
27DAP/17DAP	1.85198	0.613
39DAP/27DAP	4.1895	0.262
41DAP/39DAP	1.27164	0.822
42DAP/41DAP	1.48832	0.066
43DAP/42DAP	0.8253	0.7
47DAP/43DAP	0.92907	0.716
52DAP/47DAP	0.89127	0.681
57DAP/52DAP	1.74702	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92318	0.217
17DAP/reference	0.80814	0.012
27DAP/reference	0.86603	0.016
39DAP/reference	0.96664	0.6
41DAP/reference	0.99317	0.814
42DAP/reference	0.98582	0.398
43DAP/reference	0.90661	0.129
47DAP/reference	0.87774	0.148
52DAP/reference	1.13363	0.286
57DAP/reference	1.1428	0.047

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98698	0.763
27DAP/17DAP	1.04773	0.915
39DAP/27DAP	1.62236	0.114
41DAP/39DAP	1.67304	0.018
42DAP/41DAP	0.95493	0.666
43DAP/42DAP	0.83258	0.022
47DAP/43DAP	1.32163	0.276
52DAP/47DAP	0.9375	0.753
57DAP/52DAP	0.93082	0.591
57DAP/7DAP	1.40192	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03956	0.894
17DAP/reference	0.92066	0.144
27DAP/reference	1.00508	0.748
39DAP/reference	0.98585	0.552
41DAP/reference	0.91854	0.298
42DAP/reference	0.99564	0.641
43DAP/reference	1.17259	0.256
47DAP/reference	1.14564	0.458
52DAP/reference	1.49721	0.029
57DAP/reference	1.89053	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92532	0.412
17DAP/reference	0.80525	0.005
27DAP/reference	0.86222	0.051
39DAP/reference	0.94426	0.274
41DAP/reference	0.94244	0.315
42DAP/reference	1.03155	0.759
43DAP/reference	0.98785	0.62
47DAP/reference	0.94971	0.27
52DAP/reference	0.97939	0.469
57DAP/reference	0.864	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97075	0.422
17DAP/reference	0.94106	0.47
27DAP/reference	0.92002	0.302
39DAP/reference	0.91401	0.101
41DAP/reference	1.1034	0.714
42DAP/reference	0.91672	0.361
43DAP/reference	1.04805	1
47DAP/reference	0.99294	0.626
52DAP/reference	0.87526	0.368
57DAP/reference	1.1756	0.041

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1354	1
26DAP/20DAP	0.88309	0.512
34DAP/26DAP	1.04726	1
51DAP/34DAP	0.82813	0.341
52DAP/51DAP	1.02325	0.915
53DAP/52DAP	1.07345	0.565
55DAP/53DAP	1.16001	0.429
57DAP/55DAP	0.87922	0.398
62DAP/57DAP	1.16923	0.445
68DAP/62DAP	1.14766	0.597
68DAP/14DAP	1.68397	0.03

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30359	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.30224
Mature Green Tomato/Ripe Tomato	0.75962	0.096
Immature Eggplant/Mature Eggplant	5.89015
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	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.6422
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	0.23525
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.32012
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.24671
7-2/M82	N/A	N/A
9-3-2/M82	0.42476	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.05527	1
IL2-6/WTpooled	1.29786	0.419
IL7-5/WTpooled	1.34267	1
IL7-3/WTpooled	0.95027	1
IL12-4/WTpooled	1.18803	0.52
IL1-4/WTpooled	1.12071	1
WT/WTpooled	0.95767	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	1.08926	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14791	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.92713	1
DC3000/delta hrp 24h	1.01261	0.662

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.66295	0.024
DC3000 delta B/DC3000 delta AB	0.64278	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00762	1
Exp 36h	N/A	N/A
Exp 60h	1.56027	0.215

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98054	1
Var 0h	1.33656	0.98
Var 12h I row2-row1	0.82716	0.514
Var 12h NI row2-row1	1.03317	1
Var 36h I row2-row1	1.11659	0.908
Var 36h NI row2-row1	1.02152	1
Var 60h I row2-row1	1.11879	1
Var 60h NI row2-row1	0.97327	1
Time course 0hI-0hNI	1.06725	0.833
Time course 12hI-12hNI	0.98035	0.836
Time course 36hI-36hNI	1.33296	0.006
Time course 60hI-60hNI	0.86351	0.161

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)	1.38871	0.862
transgenic ySAMdc/azygous control (breaker)	1.4936	1
transgenic ySAMdc/azygous control (red)	1.58999	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9906	0.712

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.65372	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89988	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.34672	0.222