Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.3.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28755	0.303
27DAP/17DAP	0.67149	0.08
39DAP/27DAP	0.69162	0.241
41DAP/39DAP	1.2846	0.293
42DAP/41DAP	0.86348	1
43DAP/42DAP	1.07029	1
47DAP/43DAP	1.05006	0.727
52DAP/47DAP	0.82398	0.551
57DAP/52DAP	0.96412	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86441	0.033
17DAP/reference	0.9348	0.194
27DAP/reference	0.8993	0.083
39DAP/reference	0.91902	0.206
41DAP/reference	0.91502	0.085
42DAP/reference	0.86841	0.001
43DAP/reference	1.02078	0.866
47DAP/reference	0.91128	0.005
52DAP/reference	0.82697	0.082
57DAP/reference	0.98765	0.61

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07529	0.536
27DAP/17DAP	0.93647	0.58
39DAP/27DAP	0.96901	0.859
41DAP/39DAP	1.14385	0.849
42DAP/41DAP	0.95444	0.662
43DAP/42DAP	1.00939	1
47DAP/43DAP	0.98037	0.909
52DAP/47DAP	0.98902	0.93
57DAP/52DAP	0.87166	0.129
57DAP/7DAP	0.95982	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4498	0.09
17DAP/reference	1.35463	0.084
27DAP/reference	0.88677	0.125
39DAP/reference	1.36916	0.042
41DAP/reference	1.17341	0.191
42DAP/reference	1.97206	0.308
43DAP/reference	1.25231	0.056
47DAP/reference	1.0316	1
52DAP/reference	1.37198	0.016
57DAP/reference	1.21503	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8198	0.023
17DAP/reference	0.88984	0.089
27DAP/reference	0.91579	0.15
39DAP/reference	0.78964	0.021
41DAP/reference	0.92408	0.152
42DAP/reference	0.95452	0.261
43DAP/reference	0.87445	0.08
47DAP/reference	0.94146	0.099
52DAP/reference	0.83259	0.025
57DAP/reference	0.80669	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19815	0.303
17DAP/reference	1.13956	0.641
27DAP/reference	1.31127	0.038
39DAP/reference	1.32103	0.203
41DAP/reference	1.22881	0.156
42DAP/reference	1.17943	0.5
43DAP/reference	1.08864	0.625
47DAP/reference	0.86958	0.109
52DAP/reference	1.02695	0.917
57DAP/reference	1.03255	0.991

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0068	1
26DAP/20DAP	0.96949	1
34DAP/26DAP	1.06957	1
51DAP/34DAP	0.74994	0.209
52DAP/51DAP	0.97051	1
53DAP/52DAP	0.93828	0.703
55DAP/53DAP	1.07518	0.782
57DAP/55DAP	0.94096	0.744
62DAP/57DAP	1.46061
68DAP/62DAP	0.95085
68DAP/14DAP	0.94028	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.8011	0.054

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.69213	0.058
Mature Green Tomato/Ripe Tomato	3.06834	0.025
Immature Eggplant/Mature Eggplant	0.5861	0.064
Ripe Pepper/Ripe Tomato	8.94684	1
Mature Eggplant/Ripe Tomato	9.57906	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05884	1
1-1-2/M82	1.01341	1
12-2/M82	0.94867	0.955
12-4/M82	0.8662	1
1-3/M82	1.01748	1
2-1-1/M82	1.0761	0.764
2-1/M82	1.49847	0.345
2-6/M82	0.97451	1
3-2/M82	1.02371
4-1-1/M82	0.83503	1
4-1/M82	1.01881
4-3-2/M82	0.8033	0.487
4-3/M82	1.08587	1
5-3/M82	1.00008	1
6-2/M82	0.96303	1
6-3/M82	0.87988	1
7-1/M82	0.9541	1
7-2/M82	1.04013	1
9-3-2/M82	0.76449	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.77972	0.243
IL2-6/WTpooled	0.98368	1
IL7-5/WTpooled	1.14618
IL7-3/WTpooled	1.0671	1
IL12-4/WTpooled	0.99033	1
IL1-4/WTpooled	0.96925	1
WT/WTpooled	0.94031	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	1.0317	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94543	1
DC3000/delta hrp 6h	1.01885	1
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.02539	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.56895	0.03
DC3000 delta B/DC3000 delta AB	0.48468	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00547	1
Exp 36h	0.81959	0.589
Exp 60h	0.72489	0.258

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93084	1
Var 0h	1.13447	0.782
Var 12h I row2-row1	0.81231	0.514
Var 12h NI row2-row1	0.98072	0.906
Var 36h I row2-row1	0.87666	1
Var 36h NI row2-row1	1.15631	1
Var 60h I row2-row1	3.58001
Var 60h NI row2-row1	1.00568	1
Time course 0hI-0hNI	0.9618	0.808
Time course 12hI-12hNI	0.95077	0.628
Time course 36hI-36hNI	0.91881	0.28
Time course 60hI-60hNI	0.11418	0.005

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)	0.99164	0.862
transgenic ySAMdc/azygous control (breaker)	2.6361	0.178
transgenic ySAMdc/azygous control (red)	1.14649	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.77756	0.126

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.29259	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	7.9638	0.09
Manapal/WT (break)	5.25879	0.126
Manapal/WT (red)	1.53193	1