Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.10.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.31379	0.414
27DAP/17DAP	0.49534	0.027
39DAP/27DAP	0.48959	0.232
41DAP/39DAP	0.61712	0.047
42DAP/41DAP	0.77272	1
43DAP/42DAP	1.11791	1
47DAP/43DAP	0.55777	0.067
52DAP/47DAP	1.07414	0.891
57DAP/52DAP	0.87614	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75326	0.073
17DAP/reference	0.63557	0.015
27DAP/reference	0.61254	0.012
39DAP/reference	0.69972	0.042
41DAP/reference	0.48089	0.008
42DAP/reference	0.43826	0.001
43DAP/reference	0.42514	0.013
47DAP/reference	0.35975	0.001
52DAP/reference	0.4124	0.012
57DAP/reference	0.41931	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.16562	0.036
27DAP/17DAP	0.67953	0.164
39DAP/27DAP	0.31268	0.028
41DAP/39DAP	1.33449	0.058
42DAP/41DAP	0.74323	0.011
43DAP/42DAP	0.44074	0.022
47DAP/43DAP	0.72588	0.012
52DAP/47DAP	0.92016	0.671
57DAP/52DAP	0.85846	0.528
57DAP/7DAP	0.36572	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27477	0.06
17DAP/reference	0.96113	0.389
27DAP/reference	0.97632	0.43
39DAP/reference	0.45219	0.012
41DAP/reference	0.36331	0.01
42DAP/reference	0.3475	0.01
43DAP/reference	0.28731	0.008
47DAP/reference	0.27769	0.03
52DAP/reference	0.29763	0.01
57DAP/reference	0.37341	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.43894	0.008
17DAP/reference	0.48891	0.013
27DAP/reference	0.64509	0.069
39DAP/reference	0.31983	0.008
41DAP/reference	0.43764	0.005
42DAP/reference	0.49778	0.012
43DAP/reference	0.38627	0.002
47DAP/reference	0.53095	0.015
52DAP/reference	0.28224	0.003
57DAP/reference	0.16087	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.66373	0.019
17DAP/reference	2.0162	0.215
27DAP/reference	1.66902	0.02
39DAP/reference	1.28186	0.169
41DAP/reference	0.85294	0.185
42DAP/reference	0.6398	0.016
43DAP/reference	0.48527	0.023
47DAP/reference	0.334	0.004
52DAP/reference	0.58795	0.134
57DAP/reference	0.98872	0.623

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03801	1
26DAP/20DAP	1.19154	0.598
34DAP/26DAP	0.84857	0.387
51DAP/34DAP	0.43622	0.049
52DAP/51DAP	0.93372	1
53DAP/52DAP	0.88152	0.259
55DAP/53DAP	0.81857	0.049
57DAP/55DAP	1.23966	0.51
62DAP/57DAP	1.06889	0.994
68DAP/62DAP	0.87561	0.668
68DAP/14DAP	0.41492	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.33664	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.31406	0.058
Mature Green Tomato/Ripe Tomato	271.168	1
Immature Eggplant/Mature Eggplant	0.33888	0.061
Ripe Pepper/Ripe Tomato	44.3278	0.258
Mature Eggplant/Ripe Tomato	19.523	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	1.37485
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	1.13863	0.277
IL2-6/WTpooled	1.1951	0.584
IL7-5/WTpooled	1.32067	0.792
IL7-3/WTpooled	1.01889	1
IL12-4/WTpooled	1.04309	0.785
IL1-4/WTpooled	0.986	1
WT/WTpooled	0.91167	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	0.86101	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96912	1
DC3000/delta hrp 6h	0.98024	0.95
DC3000/delta hrp 12h	0.92101	1
DC3000/delta hrp 24h	0.90884	0.313

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.7345	0.043
DC3000 delta B/DC3000 delta AB	0.57468	0.029

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00318	1
Exp 36h	0.85498	0.589
Exp 60h	0.6217	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05673	1
Var 0h	0.97851	0.339
Var 12h I row2-row1	1.11723	0.654
Var 12h NI row2-row1	0.93456	0.627
Var 36h I row2-row1	0.75497	0.805
Var 36h NI row2-row1	1.62022	1
Var 60h I row2-row1	1.49381	0.562
Var 60h NI row2-row1	1.1259	0.904
Time course 0hI-0hNI	1.04742	0.852
Time course 12hI-12hNI	1.03691	0.836
Time course 36hI-36hNI	1.08498	0.401
Time course 60hI-60hNI	0.17151	0.008

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)	1.03237	1
transgenic ySAMdc/azygous control (breaker)	3.84544	0.162
transgenic ySAMdc/azygous control (red)	1.39455	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.61958	0.095

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.05689	0.227

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	17.6693	0.088
Manapal/WT (break)	15.2567	0.123
Manapal/WT (red)	3.71504	0.413