Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.7.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16812	0.602
27DAP/17DAP	0.95067	0.873
39DAP/27DAP	1.89059	0.064
41DAP/39DAP	0.49459	0.041
42DAP/41DAP	1.15081	0.868
43DAP/42DAP	0.90376	0.813
47DAP/43DAP	0.69341	0.175
52DAP/47DAP	0.86203	0.619
57DAP/52DAP	1.38357	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04854	0.638
17DAP/reference	0.75128	0.079
27DAP/reference	0.77759	0.073
39DAP/reference	0.7654	0.124
41DAP/reference	0.60396	0.013
42DAP/reference	0.74703	0.002
43DAP/reference	0.7824	0.061
47DAP/reference	0.81041	0.03
52DAP/reference	0.65581	0.035
57DAP/reference	0.95567	0.176

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28906	0.036
27DAP/17DAP	0.91533	0.164
39DAP/27DAP	0.89034	0.283
41DAP/39DAP	1.19597	0.763
42DAP/41DAP	1.01903	1
43DAP/42DAP	0.86642	0.097
47DAP/43DAP	1.04616	0.827
52DAP/47DAP	0.74466	0.183
57DAP/52DAP	0.89702	0.441
57DAP/7DAP	0.79702	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08641	0.298
17DAP/reference	0.99541	0.693
27DAP/reference	0.65667	0.01
39DAP/reference	0.63623	0.016
41DAP/reference	0.56988	0.009
42DAP/reference	0.59128	0.01
43DAP/reference	0.49225	0.011
47DAP/reference	0.71054	0.168
52DAP/reference	0.59873	0.011
57DAP/reference	0.51625	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69865	0.032
17DAP/reference	0.97842	0.51
27DAP/reference	1.15703	0.692
39DAP/reference	0.92533	0.298
41DAP/reference	0.83086	0.061
42DAP/reference	0.89524	0.189
43DAP/reference	0.48342	0.006
47DAP/reference	0.83105	0.071
52DAP/reference	0.7519	0.007
57DAP/reference	0.49191	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.73091	0.022
17DAP/reference	1.48643	0.112
27DAP/reference	1.21119	0.12
39DAP/reference	1.04607	0.578
41DAP/reference	0.77667	0.022
42DAP/reference	0.66836	0.019
43DAP/reference	0.84937	0.246
47DAP/reference	0.53907	0.006
52DAP/reference	0.59748	0.051
57DAP/reference	1.22537	0.233

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88741	1
26DAP/20DAP	1.87258	0.21
34DAP/26DAP	1.21019	1
51DAP/34DAP	0.83188	0.117
52DAP/51DAP	0.71822	0.079
53DAP/52DAP	0.89509	0.465
55DAP/53DAP	0.7435	0.022
57DAP/55DAP	1.0343	0.935
62DAP/57DAP	0.8743	0.466
68DAP/62DAP	1.08871	0.899
68DAP/14DAP	0.94464	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.47002	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.88011	0.384
Mature Green Tomato/Ripe Tomato	1.71931	0.017
Immature Eggplant/Mature Eggplant	1.23897	0.05
Ripe Pepper/Ripe Tomato	2.09674	0.258
Mature Eggplant/Ripe Tomato	3.59774	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.77612
1-1-2/M82	0.90148	0.804
12-2/M82	0.66652	0.74
12-4/M82	N/A	N/A
1-3/M82	0.8879
2-1-1/M82	0.99399	1
2-1/M82	N/A	N/A
2-6/M82	1.3105	0.452
3-2/M82	1.20509	0.549
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	2.0478
4-3/M82	1.15521	0.268
5-3/M82	1.34967	0.455
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.84608	0.803
7-2/M82	0.94608	1
9-3-2/M82	1.39374	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82084	0.247
IL2-6/WTpooled	1.20296	0.531
IL7-5/WTpooled	2.55183	1
IL7-3/WTpooled	0.98643	1
IL12-4/WTpooled	1.03956	0.891
IL1-4/WTpooled	0.95693	0.834
WT/WTpooled	1.13373	0.874

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	1.23716	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99191	1
DC3000/delta hrp 6h	0.87374	0.95
DC3000/delta hrp 12h	1.10419	1
DC3000/delta hrp 24h	1.01617	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.46304
DC3000 delta B/DC3000 delta AB	1.02979	0.714

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	0.99383	1
Var 0h	0.99671	1
Var 12h I row2-row1	0.98425	1
Var 12h NI row2-row1	0.98734	1
Var 36h I row2-row1	1.23776	0.601
Var 36h NI row2-row1	0.86405	0.478
Var 60h I row2-row1	1.05258	1
Var 60h NI row2-row1	0.7916	0.292
Time course 0hI-0hNI	0.85495	0.071
Time course 12hI-12hNI	1.08927	0.213
Time course 36hI-36hNI	1.24168	0.07
Time course 60hI-60hNI	1.38117	0.029

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)	1.01615	0.798
transgenic ySAMdc/azygous control (breaker)	0.96808	1
transgenic ySAMdc/azygous control (red)	0.93084	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.75587	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.46908	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.12635	0.09
Manapal/WT (break)	1.58856	0.123
Manapal/WT (red)	1.48587	0.413