Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.4.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.6012	0.019
27DAP/17DAP	0.6176	0.092
39DAP/27DAP	0.71328	0.41
41DAP/39DAP	0.8213	0.381
42DAP/41DAP	0.56453	0.262
43DAP/42DAP	1.42664	0.478
47DAP/43DAP	0.47855	0.054
52DAP/47DAP	1.14531	0.927
57DAP/52DAP	0.89327	0.889

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59491	0.018
17DAP/reference	1.23655	0.015
27DAP/reference	1.61443	0.089
39DAP/reference	0.9057	0.455
41DAP/reference	1.84295	0.48
42DAP/reference	1.01516	1
43DAP/reference	0.56724
47DAP/reference	1.03574	0.503
52DAP/reference	0.61009	0.018
57DAP/reference	1.85543

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.64577	0.034
27DAP/17DAP	1.18974	0.262
39DAP/27DAP	0.49979	0.028
41DAP/39DAP	0.64999	0.036
42DAP/41DAP	0.93188	0.535
43DAP/42DAP	0.95705	0.597
47DAP/43DAP	0.93009	0.647
52DAP/47DAP	1.02195	0.987
57DAP/52DAP	0.70893	0.102
57DAP/7DAP	0.39986	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.88682	0.024
17DAP/reference	1.37913	0.006
27DAP/reference	1.11075	0.371
39DAP/reference	1.00816	1
41DAP/reference	0.98425	0.565
42DAP/reference	1.00976	0.751
43DAP/reference	0.92068	0.23
47DAP/reference	0.86344	0.066
52DAP/reference	0.93171	0.163
57DAP/reference	1.03616	0.698

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41892	0.325
17DAP/reference	1.42757	0.008
27DAP/reference	1.206	0.182
39DAP/reference	0.8815	0.173
41DAP/reference	0.82285	0.016
42DAP/reference	0.89957	0.261
43DAP/reference	0.91301	0.314
47DAP/reference	0.82618	0.055
52DAP/reference	0.7612	0.006
57DAP/reference	0.94247	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.13906	0.015
17DAP/reference	1.44056	0.148
27DAP/reference	1.40735	0.039
39DAP/reference	0.9969	0.755
41DAP/reference	0.93824	0.237
42DAP/reference	0.85435	0.036
43DAP/reference	0.80185	0.051
47DAP/reference	0.68689	0.005
52DAP/reference	0.97221	0.65
57DAP/reference	0.70408	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.903	1
26DAP/20DAP	1.71125	0.102
34DAP/26DAP	0.75555	0.078
51DAP/34DAP	0.60064	0.049
52DAP/51DAP	0.98376	1
53DAP/52DAP	0.60651	0.049
55DAP/53DAP	0.50754	0.022
57DAP/55DAP	0.75403	0.427
62DAP/57DAP	1.22266	0.35
68DAP/62DAP	0.65685	0.641
68DAP/14DAP	0.50532	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.27192	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.66619	0.058
Mature Green Tomato/Ripe Tomato	16.9905	0.015
Immature Eggplant/Mature Eggplant	0.26341	0.057
Ripe Pepper/Ripe Tomato	15.9135	0.258
Mature Eggplant/Ripe Tomato	63.5084	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
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	1.07191	0.493
IL2-6/WTpooled	1.10107	0.419
IL7-5/WTpooled	0.9526	1
IL7-3/WTpooled	1.06906	1
IL12-4/WTpooled	1.04021	0.538
IL1-4/WTpooled	1.17498	0.426
WT/WTpooled	0.9213	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	0.79991	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97494	1
DC3000/delta hrp 6h	1.05456	1
DC3000/delta hrp 12h	1.13247	1
DC3000/delta hrp 24h	0.32677	0.034

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	0.39149	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89858	1
Exp 36h	0.69024	0.434
Exp 60h	0.64225	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02282	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.99426
Var 12h NI row2-row1	0.96723
Var 36h I row2-row1	1.00865	1
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	1.01035	1
Time course 12hI-12hNI	0.99456	1
Time course 36hI-36hNI	1.06697	0.025
Time course 60hI-60hNI	1.03127	0.254

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)	0.86778	0.338
transgenic ySAMdc/azygous control (breaker)	4.36158	0.248
transgenic ySAMdc/azygous control (red)	1.03401	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.84185	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.06603	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.65564	0.083
Manapal/WT (break)	2.52083	1
Manapal/WT (red)	1.86556	0.413