Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.14.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.48131	0.019
27DAP/17DAP	1.05407	1
39DAP/27DAP	2.15008	0.122
41DAP/39DAP	1.38597	0.447
42DAP/41DAP	0.59808	0.774
43DAP/42DAP	0.74471	0.456
47DAP/43DAP	0.79026	0.308
52DAP/47DAP	1.90514	0.327
57DAP/52DAP	0.79562	0.737

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.84662	0.043
17DAP/reference	1.3065	0.021
27DAP/reference	1.15414	0.365
39DAP/reference	1.50819	0.061
41DAP/reference	1.20545	0.133
42DAP/reference	1.89362	0.002
43DAP/reference	1.12868	0.495
47DAP/reference	1.03851	0.764
52DAP/reference	1.09695	0.476
57DAP/reference	1.07769	0.984

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.49402	0.032
27DAP/17DAP	0.95094	0.878
39DAP/27DAP	0.91494	0.437
41DAP/39DAP	2.38871	0.009
42DAP/41DAP	0.68953	0.024
43DAP/42DAP	1.33195	0.351
47DAP/43DAP	1.33505	0.406
52DAP/47DAP	2.44727	0.06
57DAP/52DAP	1.62603	0.069
57DAP/7DAP	1.35724	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00648	1
17DAP/reference	0.77081	0.011
27DAP/reference	0.7782	0.01
39DAP/reference	0.99409	0.64
41DAP/reference	0.9076	0.076
42DAP/reference	1.01352	0.791
43DAP/reference	0.91239	0.175
47DAP/reference	0.96598	0.671
52DAP/reference	0.87602	0.137
57DAP/reference	0.99928	0.513

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12704	0.979
17DAP/reference	1.39797	0.11
27DAP/reference	1.35468	0.303
39DAP/reference	1.16799	1
41DAP/reference	1.00698	0.718
42DAP/reference	1.42108	0.027
43DAP/reference	1.0569	1
47DAP/reference	1.3289	0.028
52DAP/reference	0.62586
57DAP/reference	1.08468	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01148	1
17DAP/reference	0.87057	0.292
27DAP/reference	0.76403	0.031
39DAP/reference	0.77692	0.028
41DAP/reference	0.75559	0.046
42DAP/reference	0.78079	0.134
43DAP/reference	0.85183	0.171
47DAP/reference	0.74553	0.296
52DAP/reference	0.90425	0.424
57DAP/reference	0.88513	0.238

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.70827	1
26DAP/20DAP	1.03239	1
34DAP/26DAP	1.06875	1
51DAP/34DAP	1.11039	0.869
52DAP/51DAP	0.85744	1
53DAP/52DAP	0.82592	0.631
55DAP/53DAP	1.06075	0.813
57DAP/55DAP	1.27156	0.626
62DAP/57DAP	1.03765	1
68DAP/62DAP	0.62011	0.025
68DAP/14DAP	1.40043

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.46689	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.07184	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.15495	0.293
Mature Eggplant/Ripe Tomato	0.01998	0.234

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	1.15711
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	0.8041
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	0.76853	0.247
IL2-6/WTpooled	0.77821	0.358
IL7-5/WTpooled	0.87257	1
IL7-3/WTpooled	0.94765	1
IL12-4/WTpooled	0.88964	0.71
IL1-4/WTpooled	0.98421	1
WT/WTpooled	1.10618	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	1.39422	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99887	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	2.1171	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.72317
DC3000 delta B/DC3000 delta AB	0.86423

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.49445	0.254
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	0.94771	1
Var 0h	1.16408	0.252
Var 12h I row2-row1	1.36175	0.379
Var 12h NI row2-row1	2.08605	1
Var 36h I row2-row1	1.14732	0.298
Var 36h NI row2-row1	0.70438	0.61
Var 60h I row2-row1	1.2655	0.523
Var 60h NI row2-row1	0.99946	1
Time course 0hI-0hNI	0.97414	0.603
Time course 12hI-12hNI	1.60133	0.014
Time course 36hI-36hNI	3.70735	0.004
Time course 60hI-60hNI	2.43298	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)	1.43166	0.268
transgenic ySAMdc/azygous control (breaker)	0.32472	0.129
transgenic ySAMdc/azygous control (red)	1.20603	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90691	0.051

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.79843	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.6795	0.333
Manapal/WT (red)	0.37637	0.187