Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.13.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95726	0.689
27DAP/17DAP	1.10187	0.947
39DAP/27DAP	0.76608	0.462
41DAP/39DAP	1.68752	0.38
42DAP/41DAP	1.77551	0.73
43DAP/42DAP	1.01459	0.912
47DAP/43DAP	1.15087	1
52DAP/47DAP	1.35166	0.538
57DAP/52DAP	0.9224	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98036	0.55
17DAP/reference	0.87836	0.013
27DAP/reference	0.96374	0.444
39DAP/reference	0.9035	0.085
41DAP/reference	0.85201	0.114
42DAP/reference	0.9132	0.03
43DAP/reference	0.966	0.36
47DAP/reference	0.89762	0.001
52DAP/reference	0.81675	0.02
57DAP/reference	0.9189	0.059

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85788	0.415
27DAP/17DAP	1.04776	0.938
39DAP/27DAP	1.07222	0.672
41DAP/39DAP	0.97868	0.997
42DAP/41DAP	1.08281	0.984
43DAP/42DAP	1.22583	0.103
47DAP/43DAP	0.91554	0.525
52DAP/47DAP	0.98183	0.907
57DAP/52DAP	0.89469	0.379
57DAP/7DAP	0.91036	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79236	0.104
17DAP/reference	0.83253	0.017
27DAP/reference	0.83154	0.016
39DAP/reference	0.79994	0.012
41DAP/reference	0.78383	0.017
42DAP/reference	0.7558	0.01
43DAP/reference	0.83369	0.046
47DAP/reference	0.66168	0.033
52DAP/reference	0.72668	0.017
57DAP/reference	0.82614	0.077

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05983	0.456
17DAP/reference	0.92614	0.129
27DAP/reference	0.85551	0.048
39DAP/reference	0.70596	0.014
41DAP/reference	0.85353	0.066
42DAP/reference	0.83271	0.019
43DAP/reference	0.93077	0.352
47DAP/reference	0.94073	0.133
52DAP/reference	0.79283	0.005
57DAP/reference	0.84713	0.028

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0705	0.237
17DAP/reference	1.00048	0.87
27DAP/reference	0.7978	0.029
39DAP/reference	0.907	0.046
41DAP/reference	0.77023	0.096
42DAP/reference	0.82796	0.036
43DAP/reference	0.78635	0.021
47DAP/reference	0.81478	0.006
52DAP/reference	1.07861	0.65
57DAP/reference	0.67747	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98987	1
26DAP/20DAP	0.75931	0.317
34DAP/26DAP	1.50669	0.542
51DAP/34DAP	0.81991	0.213
52DAP/51DAP	1.05617	1
53DAP/52DAP	1.01643	0.882
55DAP/53DAP	1.28856	0.275
57DAP/55DAP	0.9263	0.677
62DAP/57DAP	1.05082	0.767
68DAP/62DAP	0.90746	0.722
68DAP/14DAP	0.98379	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.52255	0.041

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.67463	0.096
Immature Eggplant/Mature Eggplant	3.04378	0.052
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	10.2018	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04124	1
1-1-2/M82	0.93882	1
12-2/M82	1.23011	0.61
12-4/M82	1.19575	0.694
1-3/M82	1.18645	1
2-1-1/M82	1.14219	0.457
2-1/M82	1.04037	1
2-6/M82	1.25795	0.594
3-2/M82	1.33478	0.84
4-1-1/M82	1.23844	0.963
4-1/M82	0.96756	1
4-3-2/M82	1.35503	0.284
4-3/M82	1.98861
5-3/M82	1.039	1
6-2/M82	0.93803	1
6-3/M82	0.99785	1
7-1/M82	0.94964
7-2/M82	1.04708	1
9-3-2/M82	1.90648	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.81743	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.89786	1
IL12-4/WTpooled	0.79198	0.71
IL1-4/WTpooled	0.9357
WT/WTpooled	1.01221	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	0.71876

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98946	1
DC3000/delta hrp 6h	0.89693	0.95
DC3000/delta hrp 12h	1.13361	1
DC3000/delta hrp 24h	1.38354	0.033

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.8331	0.042
DC3000 delta B/DC3000 delta AB	1.20857	0.147

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00776	1
Var 0h	0.90643	0.332
Var 12h I row2-row1	1.02079	0.795
Var 12h NI row2-row1	0.79075	0.394
Var 36h I row2-row1	0.9178	1
Var 36h NI row2-row1	0.82066	0.645
Var 60h I row2-row1	1.04932	1
Var 60h NI row2-row1	1.4089	0.904
Time course 0hI-0hNI	1.05863	0.833
Time course 12hI-12hNI	1.04021	0.777
Time course 36hI-36hNI	0.96784	0.514
Time course 60hI-60hNI	1.55538	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)	0.77881	0.324
transgenic ySAMdc/azygous control (breaker)	1.13235	1
transgenic ySAMdc/azygous control (red)	1.18347	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01668	0.273

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92443	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09896	1
Manapal/WT (break)	0.9253	1
Manapal/WT (red)	0.52517	0.181