Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.11.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98781	0.867
27DAP/17DAP	1.12627	0.845
39DAP/27DAP	0.84643	0.443
41DAP/39DAP	1.02269	0.78
42DAP/41DAP	0.9322	1
43DAP/42DAP	1.00352	0.94
47DAP/43DAP	1.05731	0.702
52DAP/47DAP	1.15351	0.769
57DAP/52DAP	0.9807	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97014	0.379
17DAP/reference	0.9585	0.321
27DAP/reference	0.98579	0.538
39DAP/reference	1.00661	0.816
41DAP/reference	1.02769	0.714
42DAP/reference	0.96893	0.099
43DAP/reference	0.98281	0.691
47DAP/reference	0.97178	0.207
52DAP/reference	1.01833	1
57DAP/reference	1.01932	0.783

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01267	0.934
27DAP/17DAP	1.04358	0.932
39DAP/27DAP	1.01863	0.779
41DAP/39DAP	0.9651	0.764
42DAP/41DAP	1.02245	0.991
43DAP/42DAP	1.04133	0.086
47DAP/43DAP	0.9866	0.93
52DAP/47DAP	0.98514	0.925
57DAP/52DAP	0.95041	0.572
57DAP/7DAP	0.91827	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92057	0.071
17DAP/reference	0.92872	0.019
27DAP/reference	0.95573	0.017
39DAP/reference	0.91376	0.011
41DAP/reference	0.8126	0.024
42DAP/reference	0.76924	0.01
43DAP/reference	0.90092	0.091
47DAP/reference	0.89337	0.079
52DAP/reference	0.87033	0.072
57DAP/reference	0.8691	0.015

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97445	0.639
17DAP/reference	0.95724	0.326
27DAP/reference	0.90206	0.081
39DAP/reference	0.89815	0.122
41DAP/reference	0.94153	0.262
42DAP/reference	0.93812	0.015
43DAP/reference	1.04191	0.598
47DAP/reference	1.00702	1
52DAP/reference	0.95686	0.203
57DAP/reference	1.0164	0.887

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90676	0.077
17DAP/reference	0.92525	0.165
27DAP/reference	0.96238	0.053
39DAP/reference	0.96488	0.199
41DAP/reference	0.93492	0.185
42DAP/reference	0.91028	0.108
43DAP/reference	0.94049	0.226
47DAP/reference	0.92397	0.24
52DAP/reference	0.96023	0.573
57DAP/reference	0.87156	0.04

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02239	0.966
26DAP/20DAP	1.02039	1
34DAP/26DAP	0.99995	1
51DAP/34DAP	1.22767	0.154
52DAP/51DAP	0.96349	1
53DAP/52DAP	1.06989	0.868
55DAP/53DAP	0.93176
57DAP/55DAP	0.98978	0.867
62DAP/57DAP	0.84559	0.466
68DAP/62DAP	1.40294	0.129
68DAP/14DAP	1.08447	0.541

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92386	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.62088	0.172
Mature Green Tomato/Ripe Tomato	1.0152	1
Immature Eggplant/Mature Eggplant	1.06018	0.439
Ripe Pepper/Ripe Tomato	1.17794	1
Mature Eggplant/Ripe Tomato	0.66183	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97036	0.944
1-1-2/M82	1.02184	1
12-2/M82	0.96776	0.955
12-4/M82	0.9743	1
1-3/M82	0.95217	0.441
2-1-1/M82	1.00428	1
2-1/M82	1.17336	1
2-6/M82	0.90525	1
3-2/M82	0.96031	1
4-1-1/M82	0.92804	1
4-1/M82	0.97188	1
4-3-2/M82	0.88873	0.698
4-3/M82	0.95979	1
5-3/M82	1.04164	0.572
6-2/M82	0.98179	1
6-3/M82	1.06585	1
7-1/M82	0.98173	1
7-2/M82	1.10329	0.385
9-3-2/M82	0.90285	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09898
IL2-6/WTpooled	1.00855	1
IL7-5/WTpooled	0.74177
IL7-3/WTpooled	1.17955	1
IL12-4/WTpooled	1.07021	0.673
IL1-4/WTpooled	0.91911	0.476
WT/WTpooled	0.89923	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	1.03994	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00093	1
DC3000/delta hrp 6h	1.21105	1
DC3000/delta hrp 12h	1.10392	1
DC3000/delta hrp 24h	1.04468	0.655

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9422	0.46
DC3000 delta B/DC3000 delta AB	0.95694	0.589

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.05596	1
Exp 60h	1.06985	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03779	1
Var 0h	0.71074	0.933
Var 12h I row2-row1	1.18209	0.187
Var 12h NI row2-row1	0.98889	0.906
Var 36h I row2-row1	1.0164	1
Var 36h NI row2-row1	0.91887	0.478
Var 60h I row2-row1	1.34791	0.562
Var 60h NI row2-row1	0.98518	1
Time course 0hI-0hNI	1.03422	0.867
Time course 12hI-12hNI	0.98483	0.909
Time course 36hI-36hNI	0.96917	0.29
Time course 60hI-60hNI	0.93111	0.081

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)	0.93354	0.428
transgenic ySAMdc/azygous control (breaker)	1.23989	1
transgenic ySAMdc/azygous control (red)	1.21978	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97282	0.12

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04733	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00385	1
Manapal/WT (break)	0.75837	0.285
Manapal/WT (red)	1.31181	0.222