Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.10.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37513	0.891
27DAP/17DAP	0.75211	0.295
39DAP/27DAP	6.86415	0.025
41DAP/39DAP	1.04553	0.777
42DAP/41DAP	1.57626	0.856
43DAP/42DAP	1.7391	0.772
47DAP/43DAP	0.35306	0.049
52DAP/47DAP	0.61784	0.134
57DAP/52DAP	0.98701	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.64349	0.197
17DAP/reference	0.49276	0.009
27DAP/reference	0.47477	0.012
39DAP/reference	0.81305	0.188
41DAP/reference	0.49769	0.01
42DAP/reference	2.32525	0.001
43DAP/reference	2.5855	0.006
47DAP/reference	1.28583	0.365
52DAP/reference	0.48306	0.013
57DAP/reference	1.11737	0.767

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.41794	0.03
27DAP/17DAP	1.57431	0.057
39DAP/27DAP	3.28565	0.034
41DAP/39DAP	2.07319	0.129
42DAP/41DAP	0.92741	0.603
43DAP/42DAP	1.29478	0.212
47DAP/43DAP	1.46924	0.071
52DAP/47DAP	0.55186	0.058
57DAP/52DAP	1.00434	0.862
57DAP/7DAP	0.96893

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.77238	0.033
17DAP/reference	1.17037	0.123
27DAP/reference	1.36448	0.018
39DAP/reference	1.21605	0.09
41DAP/reference	1.00339	0.431
42DAP/reference	1.59579	0.012
43DAP/reference	1.49129	0.018
47DAP/reference	3.11326	0.014
52DAP/reference	1.87241	0.009
57DAP/reference	1.1281	0.158

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24481	0.167
17DAP/reference	0.48988	0.004
27DAP/reference	1.37703	0.136
39DAP/reference	0.98251	0.509
41DAP/reference	0.82481	0.027
42DAP/reference	1.20198	0.047
43DAP/reference	1.31309	0.801
47DAP/reference	2.48619	0.042
52DAP/reference	0.48048	0.003
57DAP/reference	1.33237	0.409

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32196	0.218
17DAP/reference	0.76445	0.095
27DAP/reference	0.97568	0.594
39DAP/reference	1.20152	0.019
41DAP/reference	1.16495	0.08
42DAP/reference	1.65379	0.019
43DAP/reference	2.43027	0.034
47DAP/reference	1.18944	0.324
52DAP/reference	1.15942	0.837
57DAP/reference	0.551	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1873	0.966
26DAP/20DAP	1.35537	0.114
34DAP/26DAP	1.11396	1
51DAP/34DAP	0.80976	0.482
52DAP/51DAP	1.20599	0.377
53DAP/52DAP	1.26153	0.935
55DAP/53DAP	1.29354	0.629
57DAP/55DAP	1.06018	0.968
62DAP/57DAP	1.30697	0.185
68DAP/62DAP	1.3567	0.557
68DAP/14DAP	0.95358	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	17.3931	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.33658	0.287
Mature Green Tomato/Ripe Tomato	0.57032	0.045
Immature Eggplant/Mature Eggplant	13.6613	0.05
Ripe Pepper/Ripe Tomato	0.2987	0.224
Mature Eggplant/Ripe Tomato	0.63872	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.42849	0.574
1-1-2/M82	1.16738	1
12-2/M82	1.0857	1
12-4/M82	2.70186	1
1-3/M82	9.28084
2-1-1/M82	1.34975	0.689
2-1/M82	0.7758	0.74
2-6/M82	1.93069	0.505
3-2/M82	1.31791	0.717
4-1-1/M82	1.97928	1
4-1/M82	1.03187
4-3-2/M82	3.98559
4-3/M82	2.72271	0.268
5-3/M82	0.90483	1
6-2/M82	5.47164
6-3/M82	1.92945	1
7-1/M82	0.84357	0.476
7-2/M82	1.28816	0.385
9-3-2/M82	3.71276	0.125

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.56868	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.853	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.49497	1
WT/WTpooled	0.97099	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	1.51065	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98474	1
DC3000/delta hrp 6h	1.12988	0.631
DC3000/delta hrp 12h	1.01187	1
DC3000/delta hrp 24h	2.23608	0.027

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.47343	0.042
DC3000 delta B/DC3000 delta AB	2.88496	0.024

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1977	1
Exp 36h	1.65872	0.409
Exp 60h	1.80019	0.226

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98395	1
Var 0h	1.18989	0.782
Var 12h I row2-row1	1.05223	0.795
Var 12h NI row2-row1	1.3065	0.34
Var 36h I row2-row1	1.43851	0.304
Var 36h NI row2-row1	0.80325	0.61
Var 60h I row2-row1	1.04014	1
Var 60h NI row2-row1	0.66315	0.572
Time course 0hI-0hNI	1.06312	0.603
Time course 12hI-12hNI	2.19407	0.005
Time course 36hI-36hNI	5.11233	0.004
Time course 60hI-60hNI	5.80365	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)	0.69914	0.246
transgenic ySAMdc/azygous control (breaker)	1.00431	1
transgenic ySAMdc/azygous control (red)	1.28836	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98861	0.534

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73912	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89962	1
Manapal/WT (break)	0.9027	1
Manapal/WT (red)	1.86273	0.164