Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.4.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.48169	0.893
27DAP/17DAP	1.23962	0.845
39DAP/27DAP	1.16251	0.663
41DAP/39DAP	1.03098	1
42DAP/41DAP	1.1358	0.967
43DAP/42DAP	1.03549	1
47DAP/43DAP	1.11046	0.497
52DAP/47DAP	0.9625	0.87
57DAP/52DAP	1.19793	0.878

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09188	0.162
17DAP/reference	1.15341	0.201
27DAP/reference	1.42506	0.044
39DAP/reference	1.36706	0.079
41DAP/reference	1.42312	0.032
42DAP/reference	1.08187	0.231
43DAP/reference	1.13786	0.014
47DAP/reference	1.15944	0.004
52DAP/reference	1.33288	0.009
57DAP/reference	1.24219	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29657	0.305
27DAP/17DAP	1.90314
39DAP/27DAP	1.59347	0.081
41DAP/39DAP	0.62618	0.033
42DAP/41DAP	1.22108	0.46
43DAP/42DAP	1.51091	0.134
47DAP/43DAP	1.01739	0.973
52DAP/47DAP	1.08892	0.831
57DAP/52DAP	1.24756	0.845
57DAP/7DAP	1.26442	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0786	0.418
17DAP/reference	1.06912	0.437
27DAP/reference	1.09493	0.197
39DAP/reference	1.31991	0.009
41DAP/reference	1.20863	0.042
42DAP/reference	1.22638	0.046
43DAP/reference	1.16066	0.087
47DAP/reference	1.08836	0.386
52DAP/reference	1.18458	0.139
57DAP/reference	1.12768	0.1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14479	0.284
17DAP/reference	1.15595	0.229
27DAP/reference	1.04898	0.933
39DAP/reference	1.02807	1
41DAP/reference	0.81468	0.063
42DAP/reference	1.22781	0.072
43DAP/reference	1.14964	0.226
47DAP/reference	0.99645	0.695
52DAP/reference	0.95378	0.433
57DAP/reference	0.97193	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36827	0.019
17DAP/reference	1.02695	0.839
27DAP/reference	1.13699	0.298
39DAP/reference	1.08997	0.125
41DAP/reference	1.20483	0.1
42DAP/reference	1.27533	0.044
43DAP/reference	1.20513	0.331
47DAP/reference	1.14641	0.218
52DAP/reference	1.21679	0.19
57DAP/reference	1.3036	0.118

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01914	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	0.52085
51DAP/34DAP	1.07814	0.706
52DAP/51DAP	0.66457	1
53DAP/52DAP	0.9554	0.797
55DAP/53DAP	1.64028	0.681
57DAP/55DAP	2.48867	0.682
62DAP/57DAP	0.92936	0.871
68DAP/62DAP	1.12791	0.582
68DAP/14DAP	0.92789	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.58823

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.90123	0.481
Mature Green Tomato/Ripe Tomato	0.682	0.119
Immature Eggplant/Mature Eggplant	1.08887	0.439
Ripe Pepper/Ripe Tomato	1.93265	0.256
Mature Eggplant/Ripe Tomato	1.13025	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.96552	1
12-2/M82	0.80219	0.692
12-4/M82	1.00561	1
1-3/M82	1.31858	0.248
2-1-1/M82	0.81497	0.683
2-1/M82	1.0248	1
2-6/M82	1.40577	0.329
3-2/M82	N/A	N/A
4-1-1/M82	1.08377	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.35682
5-3/M82	1.08306	1
6-2/M82	0.96973	1
6-3/M82	1.07653	1
7-1/M82	1.00193
7-2/M82	1.06276	1
9-3-2/M82	1.24417	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.72667	0.243
IL2-6/WTpooled	2.43585	0.395
IL7-5/WTpooled	1.08087	0.792
IL7-3/WTpooled	0.41598	0.294
IL12-4/WTpooled	0.8893	1
IL1-4/WTpooled	0.91752	0.834
WT/WTpooled	0.99601	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91663	1
DC3000/delta hrp 6h	1.03225	1
DC3000/delta hrp 12h	1.03252	1
DC3000/delta hrp 24h	0.94814	0.67

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9855	1
Exp 36h	0.73354	0.589
Exp 60h	0.6981	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
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	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.99895	0.931
transgenic ySAMdc/azygous control (breaker)	0.90694	0.49
transgenic ySAMdc/azygous control (red)	0.89467	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03677	0.045

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.20225	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.14398	1
Manapal/WT (break)	1.03099	1
Manapal/WT (red)	1.0901	0.413