Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.12.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.60595	0.016
27DAP/17DAP	0.84735	0.572
39DAP/27DAP	1.2981	0.575
41DAP/39DAP	0.62892	0.058
42DAP/41DAP	0.81845	1
43DAP/42DAP	1.11557	0.976
47DAP/43DAP	1.00624	0.904
52DAP/47DAP	1.18992	0.844
57DAP/52DAP	1.04495	0.987

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57461	0.011
17DAP/reference	0.72021	0.009
27DAP/reference	0.96138	0.581
39DAP/reference	0.78549	0.1
41DAP/reference	0.58919	0.011
42DAP/reference	0.80991	0.012
43DAP/reference	0.57053	0.013
47DAP/reference	0.75304	0.007
52DAP/reference	0.57525	0.028
57DAP/reference	0.81227	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74931	0.099
27DAP/17DAP	1.85163	0.023
39DAP/27DAP	0.52167	0.028
41DAP/39DAP	1.05695	0.79
42DAP/41DAP	1.01518	0.913
43DAP/42DAP	0.8643	0.28
47DAP/43DAP	0.98258	0.923
52DAP/47DAP	0.88489	0.617
57DAP/52DAP	0.97397	0.709
57DAP/7DAP	0.57825	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.09335	0.036
17DAP/reference	1.31149	0.016
27DAP/reference	1.03439	0.804
39DAP/reference	0.90701	0.17
41DAP/reference	0.94083	0.271
42DAP/reference	1.00096	0.675
43DAP/reference	0.80277	0.025
47DAP/reference	0.76115	0.079
52DAP/reference	0.90196	0.097
57DAP/reference	0.73235	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27561	0.164
17DAP/reference	0.94824	0.326
27DAP/reference	0.91866	0.317
39DAP/reference	0.5959	0.013
41DAP/reference	0.91445	0.256
42DAP/reference	0.69787	0.016
43DAP/reference	0.52685	0.003
47DAP/reference	0.59535	0.008
52DAP/reference	0.47066	0.003
57DAP/reference	0.43947	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.09206	0.034
17DAP/reference	1.30692	0.333
27DAP/reference	1.23335	0.062
39DAP/reference	0.96763	0.504
41DAP/reference	0.89093	0.264
42DAP/reference	0.93034	0.22
43DAP/reference	0.99179	0.738
47DAP/reference	0.96735	0.478
52DAP/reference	1.0166	1
57DAP/reference	1.21479	0.311

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10491	1
26DAP/20DAP	1.30704	0.374
34DAP/26DAP	1.24314	1
51DAP/34DAP	1.85052	0.033
52DAP/51DAP	0.61183	1
53DAP/52DAP	1.2588	0.565
55DAP/53DAP	0.69323	0.181
57DAP/55DAP	0.96905	0.819
62DAP/57DAP	0.82272	0.162
68DAP/62DAP	1.00421	1
68DAP/14DAP	1.03741	0.915

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.19595	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.92426	0.527
Mature Green Tomato/Ripe Tomato	6.44606	0.015
Immature Eggplant/Mature Eggplant	0.33263	0.059
Ripe Pepper/Ripe Tomato	3.05961	1
Mature Eggplant/Ripe Tomato	2.92309	0.373

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	N/A	N/A
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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.66914	0.243
IL2-6/WTpooled	0.94006	1
IL7-5/WTpooled	1.01696	1
IL7-3/WTpooled	0.78033	0.31
IL12-4/WTpooled	0.97276	1
IL1-4/WTpooled	0.93525	0.834
WT/WTpooled	0.98542	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	0.69282	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93258	1
DC3000/delta hrp 6h	1.10232	1
DC3000/delta hrp 12h	0.48883	1
DC3000/delta hrp 24h	1.22364	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.20076	0.073
DC3000 delta B/DC3000 delta AB	0.96492	0.693

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13142	1
Exp 36h	0.81061	0.504
Exp 60h	0.76875	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99455	1
Var 0h	1.00716	1
Var 12h I row2-row1	0.78156	0.344
Var 12h NI row2-row1	0.88545	0.384
Var 36h I row2-row1	1.23036	0.742
Var 36h NI row2-row1	1.07301	1
Var 60h I row2-row1	0.90219	0.832
Var 60h NI row2-row1	0.93697	1
Time course 0hI-0hNI	0.99249	0.991
Time course 12hI-12hNI	0.91159	0.231
Time course 36hI-36hNI	0.83184	0.026
Time course 60hI-60hNI	0.27136	0.005

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)	0.9467	0.324
transgenic ySAMdc/azygous control (breaker)	1.34408	0.248
transgenic ySAMdc/azygous control (red)	1.25508	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.81671	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.79426	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.80828	0.083
Manapal/WT (break)	3.36883	0.13
Manapal/WT (red)	2.67348	0.15