Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.13.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.61816	0.098
27DAP/17DAP	1.09614	0.902
39DAP/27DAP	1.86362	0.127
41DAP/39DAP	1.75689	0.437
42DAP/41DAP	0.80411	1
43DAP/42DAP	0.98029	0.925
47DAP/43DAP	0.80746	0.424
52DAP/47DAP	2.60556	0.055
57DAP/52DAP	0.79806	0.779

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25947	0.081
17DAP/reference	1.0857	0.306
27DAP/reference	0.9253	0.395
39DAP/reference	0.90828	0.159
41DAP/reference	0.87179	0.026
42DAP/reference	1.08063	0.523
43DAP/reference	0.96821	0.631
47DAP/reference	0.89297	0.019
52DAP/reference	0.87686	0.099
57DAP/reference	0.91296	0.054

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.58655	0.032
27DAP/17DAP	1.09819	0.706
39DAP/27DAP	1.20692	0.236
41DAP/39DAP	1.8826	0.012
42DAP/41DAP	0.68908	0.012
43DAP/42DAP	1.16174	0.351
47DAP/43DAP	1.17447	0.448
52DAP/47DAP	1.68139	0.069
57DAP/52DAP	1.6435	0.111
57DAP/7DAP	1.03406	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00811	1
17DAP/reference	0.95149	0.144
27DAP/reference	0.91407	0.035
39DAP/reference	1.07477	0.059
41DAP/reference	0.99249	0.646
42DAP/reference	0.98701	0.371
43DAP/reference	1.11973	0.066
47DAP/reference	1.42374	0.037
52DAP/reference	1.0462	0.308
57DAP/reference	1.02761	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10725	0.463
17DAP/reference	1.05074	1
27DAP/reference	0.90746	0.195
39DAP/reference	1.05288	0.67
41DAP/reference	0.93671	0.277
42DAP/reference	0.97989	0.534
43DAP/reference	1.13231	0.205
47DAP/reference	1.05037	0.658
52DAP/reference	0.99425	0.666
57DAP/reference	0.90984	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99187	0.653
17DAP/reference	0.9801	0.668
27DAP/reference	1.07802	0.049
39DAP/reference	0.988	0.643
41DAP/reference	0.96492	0.371
42DAP/reference	0.85622	0.22
43DAP/reference	0.89933	0.226
47DAP/reference	0.86103	0.097
52DAP/reference	1.07939	0.592
57DAP/reference	0.84419	0.04

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12465	0.966
26DAP/20DAP	0.81245	0.512
34DAP/26DAP	1.13334	1
51DAP/34DAP	0.90695	0.563
52DAP/51DAP	1.08471	0.704
53DAP/52DAP	0.98427	0.897
55DAP/53DAP	1.1293	0.452
57DAP/55DAP	1.05627	0.881
62DAP/57DAP	1.04897	0.935
68DAP/62DAP	0.90609	0.7
68DAP/14DAP	0.91501	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.59091	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	0.058	0.019
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.11736	0.224
Mature Eggplant/Ripe Tomato	0.02666	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09084	0.877
1-1-2/M82	0.93298
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	1.20026
3-2/M82	0.8972
4-1-1/M82	N/A	N/A
4-1/M82	1.04156
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.72445
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	1.61777
IL2-6/WTpooled	1.00882	1
IL7-5/WTpooled	0.55597
IL7-3/WTpooled	1.04558	1
IL12-4/WTpooled	0.9906	1
IL1-4/WTpooled	1.08211	1
WT/WTpooled	0.97693	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	1.5055	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00482	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.01273	1
DC3000/delta hrp 24h	1.8774	0.027

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.78532	0.043
DC3000 delta B/DC3000 delta AB	0.96605	0.961

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	2.49426	0.409
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	N/A	N/A
Var 0h	0.79807	1
Var 12h I row2-row1	0.92719	0.77
Var 12h NI row2-row1	0.99411	1
Var 36h I row2-row1	1.28619	0.368
Var 36h NI row2-row1	0.28351	0.225
Var 60h I row2-row1	0.80749
Var 60h NI row2-row1	0.85678	0.572
Time course 0hI-0hNI	1.11727	0.344
Time course 12hI-12hNI	1.52283	0.082
Time course 36hI-36hNI	5.11578	0.005
Time course 60hI-60hNI	3.54244	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)	2.66231	0.238
transgenic ySAMdc/azygous control (breaker)	0.20245	0.119
transgenic ySAMdc/azygous control (red)	1.72126	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94346	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84733	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.7846	1
Manapal/WT (break)	0.78741	1
Manapal/WT (red)	0.30251	0.242