Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.31377	0.365
27DAP/17DAP	1.07656	0.877
39DAP/27DAP	0.92415	0.573
41DAP/39DAP	1.01759	0.964
42DAP/41DAP	0.78146	0.774
43DAP/42DAP	0.94397	0.867
47DAP/43DAP	1.04988	0.825
52DAP/47DAP	0.98833	0.816
57DAP/52DAP	0.90232	0.844

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02038	0.71
17DAP/reference	1.08041	0.029
27DAP/reference	1.0225	0.672
39DAP/reference	1.00174	1
41DAP/reference	1.01127	1
42DAP/reference	0.92743	0.007
43DAP/reference	1.03075	0.34
47DAP/reference	0.96879	0.345
52DAP/reference	0.86933	0.125
57DAP/reference	1.09831	0.037

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18401	0.372
27DAP/17DAP	1.45549	0.32
39DAP/27DAP	0.45338	0.029
41DAP/39DAP	1.42371	0.023
42DAP/41DAP	0.78819	0.014
43DAP/42DAP	0.45574	0.022
47DAP/43DAP	0.82505	0.1
52DAP/47DAP	1.06796	0.816
57DAP/52DAP	1.27422	0.352
57DAP/7DAP	0.42682	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24362	0.108
17DAP/reference	1.18358	0.477
27DAP/reference	1.22312	0.012
39DAP/reference	0.91482	0.17
41DAP/reference	1.19397	0.057
42DAP/reference	1.08144	0.534
43DAP/reference	0.91978	0.292
47DAP/reference	1.1583	0.458
52DAP/reference	0.98408	0.621
57DAP/reference	0.87585	0.057

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07817	0.538
17DAP/reference	1.11388	0.139
27DAP/reference	1.01031	1
39DAP/reference	1.37503	0.043
41DAP/reference	0.90621	0.242
42DAP/reference	0.97444	0.261
43DAP/reference	1.23984	0.152
47DAP/reference	1.02946	0.775
52DAP/reference	1.34401	0.006
57DAP/reference	1.23828	0.123

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04541	0.422
17DAP/reference	1.3857	0.043
27DAP/reference	1.43894	0.028
39DAP/reference	1.2454	0.022
41DAP/reference	1.03813	0.84
42DAP/reference	0.94269	0.445
43DAP/reference	0.84613	0.081
47DAP/reference	0.93335	0.139
52DAP/reference	0.78888	0.073
57DAP/reference	0.90033	0.141

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0041	1
26DAP/20DAP	1.35647	0.334
34DAP/26DAP	0.83055	0.374
51DAP/34DAP	0.37747	0.058
52DAP/51DAP	1.17086	0.565
53DAP/52DAP	0.8202	0.544
55DAP/53DAP	1.02861	0.925
57DAP/55DAP	1.18765	0.754
62DAP/57DAP	0.84217
68DAP/62DAP	0.82498
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.37905	0.026

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.48427	0.058
Mature Green Tomato/Ripe Tomato	1.96146	0.237
Immature Eggplant/Mature Eggplant	0.46092	0.062
Ripe Pepper/Ripe Tomato	1.13133	1
Mature Eggplant/Ripe Tomato	6.55951	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13763	1
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.08427
1-3/M82	0.45769
2-1-1/M82	0.85993
2-1/M82	N/A	N/A
2-6/M82	0.89332	1
3-2/M82	0.82382
4-1-1/M82	N/A	N/A
4-1/M82	0.60458
4-3-2/M82	0.99617	1
4-3/M82	N/A	N/A
5-3/M82	0.84725	0.49
6-2/M82	N/A	N/A
6-3/M82	1.41849
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
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	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
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	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	0.97327	1
DC3000/delta hrp 6h	1.12965	1
DC3000/delta hrp 12h	0.95648	1
DC3000/delta hrp 24h	0.87291	0.257

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05558	0.476
DC3000 delta B/DC3000 delta AB	0.7181	0.195

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.77744	0.265
Exp 36h	0.75772	0.419
Exp 60h	0.46018	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07455	1
Var 0h	1.06167	1
Var 12h I row2-row1	1.12453	0.654
Var 12h NI row2-row1	1.35512	0.649
Var 36h I row2-row1	1.23145	1
Var 36h NI row2-row1	1.19413	0.253
Var 60h I row2-row1	1.0279	1
Var 60h NI row2-row1	1.24304	0.904
Time course 0hI-0hNI	1.10134	0.486
Time course 12hI-12hNI	0.85161	0.054
Time course 36hI-36hNI	0.64234	0.023
Time course 60hI-60hNI	0.37909	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)	1.06024	0.571
transgenic ySAMdc/azygous control (breaker)	0.57181	0.142
transgenic ySAMdc/azygous control (red)	1.43721	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96229	0.077

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.43778	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00095	1
Manapal/WT (break)	0.64062	0.333
Manapal/WT (red)	1.33965	1