Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.20.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99165	0.801
27DAP/17DAP	1.09574	0.92
39DAP/27DAP	0.81226	0.549
41DAP/39DAP	0.62352	0.17
42DAP/41DAP	0.83561	0.774
43DAP/42DAP	1.04439	0.937
47DAP/43DAP	1.1444	0.926
52DAP/47DAP	1.03244	0.712
57DAP/52DAP	1.06374	0.995

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29969	0.788
17DAP/reference	0.7169	0.012
27DAP/reference	1.326	0.115
39DAP/reference	0.74535	0.012
41DAP/reference	0.68814	0.016
42DAP/reference	1.30562	0.523
43DAP/reference	0.98597	0.763
47DAP/reference	1.322	0.646
52DAP/reference	2.42338	0.014
57DAP/reference	1.92711	0.019

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.77771	0.075
27DAP/17DAP	1.26476	0.262
39DAP/27DAP	0.92203	0.579
41DAP/39DAP	1.28939	0.04
42DAP/41DAP	0.96569	0.612
43DAP/42DAP	1.3414	0.513
47DAP/43DAP	1.05716	0.973
52DAP/47DAP	0.89368	0.591
57DAP/52DAP	1.10402	0.627
57DAP/7DAP	1.73687	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33393	0.033
17DAP/reference	1.51089	0.006
27DAP/reference	1.31939	0.008
39DAP/reference	1.3433	0.006
41DAP/reference	1.34555	0.02
42DAP/reference	1.21301	0.021
43DAP/reference	1.25058	0.07
47DAP/reference	1.39561	0.018
52DAP/reference	1.16696	0.139
57DAP/reference	1.08024	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87482	0.277
17DAP/reference	0.82065	0.083
27DAP/reference	1.14115	0.607
39DAP/reference	1.4722	0.071
41DAP/reference	1.46322	0.008
42DAP/reference	1.58847	0.007
43DAP/reference	0.72844	0.068
47DAP/reference	1.07761	0.4
52DAP/reference	1.40851	0.038
57DAP/reference	1.00355	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24804	0.149
17DAP/reference	1.20081	0.657
27DAP/reference	1.45959	0.02
39DAP/reference	1.41519	0.022
41DAP/reference	1.56192	0.012
42DAP/reference	1.82471	0.02
43DAP/reference	2.03132	0.028
47DAP/reference	1.10125	0.994
52DAP/reference	1.39763	0.086
57DAP/reference	3.90084	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86758	1
26DAP/20DAP	1.42916	0.518
34DAP/26DAP	1.48719	0.819
51DAP/34DAP	1.33616	0.759
52DAP/51DAP	0.81881	1
53DAP/52DAP	1.22275	0.552
55DAP/53DAP	0.93871	0.807
57DAP/55DAP	0.98382	0.709
62DAP/57DAP	1.3525	0.515
68DAP/62DAP	3.47808	0.097
68DAP/14DAP	6.64584	0.02

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.67041	0.027

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	6.11875	1
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.22173
1-1-2/M82	0.9736
12-2/M82	N/A	N/A
12-4/M82	1.0119
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	1.2701
6-2/M82	N/A	N/A
6-3/M82	1.57021
7-1/M82	0.74947
7-2/M82	0.60423
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.44621
IL2-6/WTpooled	1.33651	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.81967	1
IL12-4/WTpooled	1.10444	0.737
IL1-4/WTpooled	0.94558
WT/WTpooled	1.14849	0.911

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	0.74791	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05521
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.13404	1
DC3000/delta hrp 24h	0.99971	1

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94333	1
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	1.00796	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.84059	0.58
Var 12h NI row2-row1	2.86693	1
Var 36h I row2-row1	0.93691	1
Var 36h NI row2-row1	0.95467	0.791
Var 60h I row2-row1	1.30164	1
Var 60h NI row2-row1	1.15058	0.904
Time course 0hI-0hNI	0.87643	0.254
Time course 12hI-12hNI	0.90855	0.341
Time course 36hI-36hNI	0.6687	0.025
Time course 60hI-60hNI	0.60033	0.047

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	0.9454	1
transgenic ySAMdc/azygous control (red)	1.06063	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02546	0.909

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8501	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.15706	1
Manapal/WT (break)	1.24899	1
Manapal/WT (red)	2.78725	0.137