Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.19.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05845	0.851
27DAP/17DAP	1.47709	0.849
39DAP/27DAP	1.21828	0.985
41DAP/39DAP	0.90282	0.597
42DAP/41DAP	1.43129	0.086
43DAP/42DAP	1.33608	0.671
47DAP/43DAP	1.67533	0.226
52DAP/47DAP	1.17383	0.601
57DAP/52DAP	1.15144	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80028	0.048
17DAP/reference	0.70777	0.009
27DAP/reference	0.98929	0.711
39DAP/reference	1.22606	0.162
41DAP/reference	0.97408	0.667
42DAP/reference	1.49342	0.002
43DAP/reference	1.5578	0.008
47DAP/reference	1.41309	0.007
52DAP/reference	1.15102	0.176
57DAP/reference	1.39976	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96815	0.679
27DAP/17DAP	0.97316	0.887
39DAP/27DAP	0.97351	0.833
41DAP/39DAP	1.06763	0.827
42DAP/41DAP	1.02189	1
43DAP/42DAP	1.1569	0.021
47DAP/43DAP	0.96689	0.833
52DAP/47DAP	1.08234	0.766
57DAP/52DAP	0.99181	0.838
57DAP/7DAP	1.31544	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82746	0.104
17DAP/reference	0.88736	0.167
27DAP/reference	0.90699	0.159
39DAP/reference	0.93805	0.264
41DAP/reference	0.93031	0.271
42DAP/reference	0.77262	0.016
43DAP/reference	0.91312	0.028
47DAP/reference	0.93158	0.222
52DAP/reference	0.86666	0.057
57DAP/reference	0.96367	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86863	0.231
17DAP/reference	1.15142	0.644
27DAP/reference	1.0716	1
39DAP/reference	0.82923	0.038
41DAP/reference	0.9436	0.291
42DAP/reference	0.92044	0.261
43DAP/reference	1.16554	0.751
47DAP/reference	0.90384	0.246
52DAP/reference	0.84717	0.018
57DAP/reference	1.00223	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73962	0.036
17DAP/reference	0.95193	0.528
27DAP/reference	0.87627	0.133
39DAP/reference	0.85047	0.018
41DAP/reference	0.88587	0.148
42DAP/reference	1.16516	0.6
43DAP/reference	1.23943	0.803
47DAP/reference	1.45726	0.008
52DAP/reference	2.64752	0.448
57DAP/reference	1.23077	0.113

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0714	1
26DAP/20DAP	0.88358	0.512
34DAP/26DAP	0.99836	1
51DAP/34DAP	0.86169	0.402
52DAP/51DAP	1.05066	0.651
53DAP/52DAP	1.02387	1
55DAP/53DAP	1.19619	0.087
57DAP/55DAP	0.90978	0.575
62DAP/57DAP	1.08998	0.678
68DAP/62DAP	1.19182	0.336
68DAP/14DAP	1.34038	0.328

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95774	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.43725	0.089
Mature Green Tomato/Ripe Tomato	0.33333	0.018
Immature Eggplant/Mature Eggplant	1.22394
Ripe Pepper/Ripe Tomato	0.35188	0.224
Mature Eggplant/Ripe Tomato	0.39165

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	0.97513
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	1.02721	1
IL2-6/WTpooled	0.88074
IL7-5/WTpooled	1.08439	0.587
IL7-3/WTpooled	1.26761
IL12-4/WTpooled	1.17444
IL1-4/WTpooled	0.76336	0.457
WT/WTpooled	1.05542	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	1.13356	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01106	1
DC3000/delta hrp 6h	1.17556	1
DC3000/delta hrp 12h	1.02153	1
DC3000/delta hrp 24h	0.97984	0.934

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.80589	0.365
DC3000 delta B/DC3000 delta AB	0.789	0.085

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88711	1
Exp 36h	0.60688	0.419
Exp 60h	0.75192	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02149	1
Var 0h	1.01665	1
Var 12h I row2-row1	0.96942	0.856
Var 12h NI row2-row1	0.96767	0.82
Var 36h I row2-row1	1.05048	0.908
Var 36h NI row2-row1	0.69208	0.61
Var 60h I row2-row1	1.01149	1
Var 60h NI row2-row1	1.10126	0.904
Time course 0hI-0hNI	1.04827	0.662
Time course 12hI-12hNI	1.00113	1
Time course 36hI-36hNI	1.10487	0.08
Time course 60hI-60hNI	1.34218	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)	0.82449	0.485
transgenic ySAMdc/azygous control (breaker)	0.95157	1
transgenic ySAMdc/azygous control (red)	1.01004	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99368	0.313

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.57794	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92383	1
Manapal/WT (break)	1.21145	0.381
Manapal/WT (red)	N/A	N/A