Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.3.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76619	0.278
27DAP/17DAP	0.84793	0.577
39DAP/27DAP	2.39474	0.07
41DAP/39DAP	0.84722	0.419
42DAP/41DAP	1.0781	1
43DAP/42DAP	1.00466	0.937
47DAP/43DAP	0.65862	0.17
52DAP/47DAP	1.21644	0.867
57DAP/52DAP	1.39717	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11659	0.116
17DAP/reference	0.8611	0.393
27DAP/reference	1.13633	0.038
39DAP/reference	0.76779	0.017
41DAP/reference	0.68138	0.008
42DAP/reference	0.80161
43DAP/reference	N/A	N/A
47DAP/reference	1.47437
52DAP/reference	1.0007	0.768
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36073	0.052
27DAP/17DAP	1.1581	0.639
39DAP/27DAP	0.96047	0.747
41DAP/39DAP	1.32041	1
42DAP/41DAP	1.36331	0.327
43DAP/42DAP	0.85838	0.165
47DAP/43DAP	1.06835	0.857
52DAP/47DAP	1.11492	0.734
57DAP/52DAP	1.19443	0.197
57DAP/7DAP	1.39469	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39846	0.047
17DAP/reference	1.07281	0.477
27DAP/reference	1.28827	0.007
39DAP/reference	1.18012	0.048
41DAP/reference	1.34151	0.032
42DAP/reference	1.49703	0.024
43DAP/reference	1.3908	0.013
47DAP/reference	2.47632	0.014
52DAP/reference	1.65511	0.015
57DAP/reference	1.19276	0.125

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06018	0.943
17DAP/reference	0.7919	0.214
27DAP/reference	1.36649	0.254
39DAP/reference	1.0742	0.868
41DAP/reference	0.97357	0.451
42DAP/reference	1.35344	0.025
43DAP/reference	0.9179	0.285
47DAP/reference	1.08352	0.388
52DAP/reference	0.64776	0.004
57DAP/reference	0.58447	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16394	0.106
17DAP/reference	1.01323	0.825
27DAP/reference	1.04998	0.392
39DAP/reference	1.56998	0.004
41DAP/reference	1.09039	0.174
42DAP/reference	1.28287	0.053
43DAP/reference	1.35945	0.038
47DAP/reference	0.95613	0.465
52DAP/reference	1.34868	0.228
57DAP/reference	2.44893	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.71962	0.229
26DAP/20DAP	1.81003	0.109
34DAP/26DAP	0.74808	0.343
51DAP/34DAP	3.24027	0.029
52DAP/51DAP	0.87603	1
53DAP/52DAP	1.45789	0.049
55DAP/53DAP	0.67487	0.037
57DAP/55DAP	0.66535	0.087
62DAP/57DAP	0.69015	0.05
68DAP/62DAP	1.66196	0.026
68DAP/14DAP	2.76477	0.023

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.46133	0.077

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.78951	0.241
Mature Green Tomato/Ripe Tomato	1.2007	0.632
Immature Eggplant/Mature Eggplant	1.86038	0.05
Ripe Pepper/Ripe Tomato	1.17082	0.256
Mature Eggplant/Ripe Tomato	0.84306	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88486
1-1-2/M82	1.4671
12-2/M82	1.48861
12-4/M82	0.659	0.33
1-3/M82	2.66123
2-1-1/M82	N/A	N/A
2-1/M82	0.85825
2-6/M82	0.74758
3-2/M82	N/A	N/A
4-1-1/M82	0.67428	1
4-1/M82	0.63722
4-3-2/M82	0.94049	1
4-3/M82	0.9494	1
5-3/M82	1.17124	0.572
6-2/M82	1.0137
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.0029
9-3-2/M82	1.35992

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95617	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.99598	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.92173	0.834
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	1.09167	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1596	0.692
DC3000/delta hrp 6h	0.9361	0.95
DC3000/delta hrp 12h	1.07084	1
DC3000/delta hrp 24h	0.93109	0.67

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1308
DC3000 delta B/DC3000 delta AB	1.42342	0.114

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.21053	1
Exp 36h	1.46351	0.693
Exp 60h	1.52765	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01357	1
Var 0h	0.95294	1
Var 12h I row2-row1	1.12388	0.692
Var 12h NI row2-row1	1.19706	0.34
Var 36h I row2-row1	1.24041	0.339
Var 36h NI row2-row1	0.90872	0.522
Var 60h I row2-row1	0.76061	0.306
Var 60h NI row2-row1	1.08244	1
Time course 0hI-0hNI	0.99494	1
Time course 12hI-12hNI	1.17144	0.115
Time course 36hI-36hNI	1.38664	0.006
Time course 60hI-60hNI	2.73661	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)	0.80374	0.32
transgenic ySAMdc/azygous control (breaker)	0.64878	0.15
transgenic ySAMdc/azygous control (red)	0.95172	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91293	0.353

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72703	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07673	1
Manapal/WT (break)	1.37635	0.14
Manapal/WT (red)	0.94684	0.315