Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.4.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98409	0.617
27DAP/17DAP	1.51565	0.627
39DAP/27DAP	0.90059	0.594
41DAP/39DAP	0.65787	0.112
42DAP/41DAP	1.0936	0.929
43DAP/42DAP	0.95778	0.89
47DAP/43DAP	1.1361	0.569
52DAP/47DAP	1.67296	0.284
57DAP/52DAP	0.89204	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20468	0.097
17DAP/reference	1.13082	0.355
27DAP/reference	1.06354	0.612
39DAP/reference	0.94608	0.5
41DAP/reference	0.69438	0.154
42DAP/reference	1.01187	1
43DAP/reference	N/A	N/A
47DAP/reference	1.36472	0.433
52DAP/reference	0.8797	0.195
57DAP/reference	0.79215	0.34

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95669	0.629
27DAP/17DAP	0.9546	0.748
39DAP/27DAP	1.01096	1
41DAP/39DAP	1.00549	1
42DAP/41DAP	0.97135	0.77
43DAP/42DAP	0.78396	0.157
47DAP/43DAP	1.09643	0.674
52DAP/47DAP	1.11907	0.63
57DAP/52DAP	1.0999	0.722
57DAP/7DAP	0.94812	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94224	0.246
17DAP/reference	0.98443	0.518
27DAP/reference	1.0756	0.246
39DAP/reference	1.15709	0.12
41DAP/reference	1.14024	1
42DAP/reference	1.25157	0.1
43DAP/reference	1.1185	0.118
47DAP/reference	0.83377	0.101
52DAP/reference	1.08751	0.375
57DAP/reference	1.07794	0.571

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01688	0.794
17DAP/reference	1.10789	0.448
27DAP/reference	1.57504	0.025
39DAP/reference	1.17066	0.449
41DAP/reference	1.08697	0.705
42DAP/reference	1.17789	0.136
43DAP/reference	1.09753	0.288
47DAP/reference	1.13515	0.232
52DAP/reference	0.90001	0.351
57DAP/reference	0.85389	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	5.83932	0.031
17DAP/reference	1.1444	0.148
27DAP/reference	1.08773	0.575
39DAP/reference	1.01265	0.935
41DAP/reference	0.9339	0.331
42DAP/reference	6.0459	0.019
43DAP/reference	3.43841	0.032
47DAP/reference	0.84371	0.008
52DAP/reference	10.7965	0.051
57DAP/reference	2.731	0.059

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.26204	0.966
26DAP/20DAP	1.17814	1
34DAP/26DAP	1.16106	1
51DAP/34DAP	1.19697	0.829
52DAP/51DAP	1.09672	0.848
53DAP/52DAP	1.03689	0.91
55DAP/53DAP	0.72611	0.163
57DAP/55DAP	1.17042	0.256
62DAP/57DAP	1.10533	0.445
68DAP/62DAP	0.81389	0.152
68DAP/14DAP	1.54852	0.615

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86001	0.186

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.27715	0.025
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.82865	1
Mature Eggplant/Ripe Tomato	1.55373

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	0.9554
1-3/M82	0.50176
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.82482
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	0.71726	0.642
6-2/M82	0.881
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.91807
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.75011
IL1-4/WTpooled	1.0975	1
WT/WTpooled	N/A	N/A

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	1.3585	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08093	0.921
DC3000/delta hrp 6h	0.90963	0.95
DC3000/delta hrp 12h	0.91878	1
DC3000/delta hrp 24h	0.74683	0.037

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.60984
DC3000 delta B/DC3000 delta AB	0.57082	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.15306	1
Exp 36h	1.1109	1
Exp 60h	1.00797	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98757	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.54199
Var 12h NI row2-row1	0.47729
Var 36h I row2-row1	1.10722	0.368
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	0.98175	0.961
Time course 12hI-12hNI	1.05045	0.65
Time course 36hI-36hNI	1.48127	0.006
Time course 60hI-60hNI	2.21642	0.015

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)	1.33204	0.286
transgenic ySAMdc/azygous control (breaker)	0.54311	0.173
transgenic ySAMdc/azygous control (red)	1.0359	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92314	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.6139	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.26065	0.14
Manapal/WT (break)	1.30316	1
Manapal/WT (red)	1.30647	0.413