Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.3.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.47168	0.111
27DAP/17DAP	0.42198	0.036
39DAP/27DAP	0.54862	0.335
41DAP/39DAP	0.63542	0.143
42DAP/41DAP	0.75095	0.774
43DAP/42DAP	1.03156	1
47DAP/43DAP	0.93135	0.705
52DAP/47DAP	0.82853	0.627
57DAP/52DAP	1.53646	0.839

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90902	0.194
17DAP/reference	0.8129	0.057
27DAP/reference	0.88306	0.232
39DAP/reference	0.75317	0.027
41DAP/reference	0.62966	0.009
42DAP/reference	0.79175	0.006
43DAP/reference	0.8763	0.08
47DAP/reference	0.90269	0.161
52DAP/reference	1.28299	0.059
57DAP/reference	1.47308	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22357	0.379
27DAP/17DAP	0.87262	0.58
39DAP/27DAP	0.38109	0.028
41DAP/39DAP	1.48494	0.169
42DAP/41DAP	0.64284	0.016
43DAP/42DAP	0.77389	0.116
47DAP/43DAP	1.05655	0.772
52DAP/47DAP	1.10973	0.624
57DAP/52DAP	1.49315	0.048
57DAP/7DAP	0.21329	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	4.95723	0.024
17DAP/reference	2.60984	0.006
27DAP/reference	1.34281	0.041
39DAP/reference	1.58186	0.018
41DAP/reference	1.47243	0.013
42DAP/reference	1.46169	0.013
43DAP/reference	1.32825	0.118
47DAP/reference	1.25625	0.059
52DAP/reference	1.2574	0.014
57DAP/reference	1.2459	0.037

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93398	0.441
17DAP/reference	1.20442	0.216
27DAP/reference	1.00814	0.711
39DAP/reference	0.99663	0.586
41DAP/reference	1.21413	0.072
42DAP/reference	1.02212	1
43DAP/reference	0.68149	0.04
47DAP/reference	0.83888	0.02
52DAP/reference	0.88185	0.051
57DAP/reference	0.64603	0.015

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.74385	0.019
17DAP/reference	1.96017	0.39
27DAP/reference	1.58731	0.029
39DAP/reference	1.42495	0.043
41DAP/reference	1.42774	0.031
42DAP/reference	1.37264	0.052
43DAP/reference	1.28577	0.202
47DAP/reference	1.02016	0.61
52DAP/reference	1.25698	0.301
57DAP/reference	2.37202	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16422	0.966
26DAP/20DAP	3.44825	0.097
34DAP/26DAP	0.22039	0.044
51DAP/34DAP	0.34052	0.059
52DAP/51DAP	1.04327	0.904
53DAP/52DAP	1.03725	0.895
55DAP/53DAP	0.93075	0.675
57DAP/55DAP	0.83495	0.42
62DAP/57DAP	1.02056	1
68DAP/62DAP	2.32811	0.037
68DAP/14DAP	2.30741	0.029

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.70052	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.03562	0.058
Mature Green Tomato/Ripe Tomato	16.3535	0.015
Immature Eggplant/Mature Eggplant	1.24669	0.363
Ripe Pepper/Ripe Tomato	1.77333	1
Mature Eggplant/Ripe Tomato	1.41095

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	0.84674	0.321
IL2-6/WTpooled	2.01159	0.788
IL7-5/WTpooled	0.9767	1
IL7-3/WTpooled	0.94074	1
IL12-4/WTpooled	0.77587	0.566
IL1-4/WTpooled	0.96353	0.834
WT/WTpooled	1.13591	0.855

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	0.55277	0.216

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02472	1
DC3000/delta hrp 6h	1.04649	1
DC3000/delta hrp 12h	0.76371	1
DC3000/delta hrp 24h	0.38435	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.67293	0.027
DC3000 delta B/DC3000 delta AB	0.62369	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04979	1
Exp 36h	0.86451	0.749
Exp 60h	1.11678	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01922	1
Var 0h	0.93387	1
Var 12h I row2-row1	0.91488	0.77
Var 12h NI row2-row1	1.21202	0.34
Var 36h I row2-row1	1.28851	1
Var 36h NI row2-row1	0.94127	0.791
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.24785	0.904
Time course 0hI-0hNI	0.88961	0.292
Time course 12hI-12hNI	0.803	0.101
Time course 36hI-36hNI	0.85432	0.194
Time course 60hI-60hNI	0.21576	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)	1.15222	0.347
transgenic ySAMdc/azygous control (breaker)	0.86947	0.251
transgenic ySAMdc/azygous control (red)	1.08011	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05101	0.194

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.4293	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.51905	0.307
Manapal/WT (break)	1.33374	0.123
Manapal/WT (red)	1.01509	0.863