Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.2.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29859	0.428
27DAP/17DAP	1.09405	0.922
39DAP/27DAP	0.78998	0.361
41DAP/39DAP	1.15275	0.612
42DAP/41DAP	0.98918	1
43DAP/42DAP	1.01682	0.937
47DAP/43DAP	1.17464	0.49
52DAP/47DAP	1.14196	0.869
57DAP/52DAP	0.91993	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77308	0.045
17DAP/reference	0.75963	0.009
27DAP/reference	0.76024	0.011
39DAP/reference	0.78736	0.018
41DAP/reference	0.76156	0.014
42DAP/reference	0.89582	0.069
43DAP/reference	0.9767	0.675
47DAP/reference	0.89385	0.083
52DAP/reference	1.07701	0.84
57DAP/reference	1.09004	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.33676	0.132
27DAP/17DAP	0.89006	0.748
39DAP/27DAP	0.81782	0.156
41DAP/39DAP	1.07252	0.896
42DAP/41DAP	0.94322	0.612
43DAP/42DAP	1.10801	0.103
47DAP/43DAP	1.1659	0.352
52DAP/47DAP	0.95605	0.884
57DAP/52DAP	0.76892	0.081
57DAP/7DAP	1.26307	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13633	0.894
17DAP/reference	1.16332	0.754
27DAP/reference	0.98622	0.698
39DAP/reference	1.19472	0.237
41DAP/reference	1.11511	0.637
42DAP/reference	1.40237	0.233
43DAP/reference	1.0144	0.637
47DAP/reference	1.02629	0.868
52DAP/reference	1.0364	0.802
57DAP/reference	1.44385	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78321	0.015
17DAP/reference	0.64018	0.004
27DAP/reference	1.02557	1
39DAP/reference	0.99254	0.569
41DAP/reference	1.15291	0.215
42DAP/reference	0.9399	0.355
43DAP/reference	0.67726	0.026
47DAP/reference	0.82878	0.029
52DAP/reference	0.87602	0.051
57DAP/reference	0.57999	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05649	0.75
17DAP/reference	0.75933	0.189
27DAP/reference	1.50078	0.111
39DAP/reference	1.16207	0.578
41DAP/reference	1.11872	0.306
42DAP/reference	1.33801	0.251
43DAP/reference	1.61407	0.109
47DAP/reference	0.89081	0.191
52DAP/reference	1.11393	0.89
57DAP/reference	2.35318	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05136	0.966
26DAP/20DAP	0.9037	1
34DAP/26DAP	1.23196	1
51DAP/34DAP	1.14587	0.445
52DAP/51DAP	1.14277	0.439
53DAP/52DAP	1.21516	0.643
55DAP/53DAP	1.24979	0.049
57DAP/55DAP	0.93093	0.754
62DAP/57DAP	1.17373	0.8
68DAP/62DAP	2.07285	0.056
68DAP/14DAP	2.33825	0.029

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85151	0.065

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.05899	1
Immature Eggplant/Mature Eggplant	0.44167	0.062
Ripe Pepper/Ripe Tomato	1.34946	1
Mature Eggplant/Ripe Tomato	2.3015

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95135	0.944
1-1-2/M82	0.97034	1
12-2/M82	1.1036	1
12-4/M82	1.05417	1
1-3/M82	0.94198	1
2-1-1/M82	1.24133	0.457
2-1/M82	N/A	N/A
2-6/M82	1.02143	1
3-2/M82	0.95325
4-1-1/M82	1.14622	1
4-1/M82	1.28925
4-3-2/M82	1.11325
4-3/M82	0.99053	1
5-3/M82	0.87647	0.642
6-2/M82	0.88566	1
6-3/M82	1.06124	1
7-1/M82	0.95122
7-2/M82	0.99856	1
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	0.9402	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10232	1
IL12-4/WTpooled	0.92386	0.581
IL1-4/WTpooled	0.99151
WT/WTpooled	0.96057	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	1.92664	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97162	1
DC3000/delta hrp 6h	1.23316	0.672
DC3000/delta hrp 12h	1.0977	1
DC3000/delta hrp 24h	1.05176	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95624	1
DC3000 delta B/DC3000 delta AB	1.003	0.787

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07185	1
Exp 36h	1.06835	1
Exp 60h	1.08984	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03688	1
Var 0h	0.74347	0.933
Var 12h I row2-row1	1.13415	0.506
Var 12h NI row2-row1	0.86469	0.443
Var 36h I row2-row1	1.04543	1
Var 36h NI row2-row1	1.91849	0.482
Var 60h I row2-row1	0.92956	0.306
Var 60h NI row2-row1	1.23252	0.904
Time course 0hI-0hNI	1.23158	0.63
Time course 12hI-12hNI	1.16833	0.55
Time course 36hI-36hNI	1.28049	0.401
Time course 60hI-60hNI	0.34514	0.006

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)	1.01388	0.748
transgenic ySAMdc/azygous control (breaker)	1.18499	0.248
transgenic ySAMdc/azygous control (red)	1.05545	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08431	0.034

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92209	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04931	1
Manapal/WT (break)	1.24617	0.13
Manapal/WT (red)	1.10737	1