Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.2.20.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13972	0.709
27DAP/17DAP	0.953	0.957
39DAP/27DAP	1.03396	0.899
41DAP/39DAP	1.23033	0.772
42DAP/41DAP	1.38681	0.767
43DAP/42DAP	1.21059	0.809
47DAP/43DAP	0.87547	0.584
52DAP/47DAP	1.4672	0.48
57DAP/52DAP	1.01949	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99866	0.787
17DAP/reference	1.02528	0.294
27DAP/reference	0.91822	0.075
39DAP/reference	1.05309	0.119
41DAP/reference	1.00639	1
42DAP/reference	0.92138	0.034
43DAP/reference	1.03849	0.812
47DAP/reference	0.91062	0.161
52DAP/reference	0.90876	0.244
57DAP/reference	0.81522	0.086

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93531	0.454
27DAP/17DAP	0.93516	0.748
39DAP/27DAP	1.08016	0.587
41DAP/39DAP	0.99341	1
42DAP/41DAP	1.07751	0.571
43DAP/42DAP	1.10071	0.446
47DAP/43DAP	1.00717	0.997
52DAP/47DAP	0.97939	0.917
57DAP/52DAP	0.96944	0.697
57DAP/7DAP	1.32468	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86803	0.1
17DAP/reference	0.90106	0.124
27DAP/reference	0.74399	0.01
39DAP/reference	0.88216	0.023
41DAP/reference	0.97019	0.449
42DAP/reference	0.8557	0.022
43DAP/reference	0.86314	0.086
47DAP/reference	0.84976	0.057
52DAP/reference	0.89285	0.077
57DAP/reference	0.79298	0.031

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02766	0.75
17DAP/reference	0.9463	0.23
27DAP/reference	0.88031	0.167
39DAP/reference	0.79101	0.089
41DAP/reference	0.94886	0.291
42DAP/reference	0.93812	0.237
43DAP/reference	1.04495	0.802
47DAP/reference	1.04144	0.413
52DAP/reference	0.99473	0.666
57DAP/reference	1.03279	0.98

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79355	0.071
17DAP/reference	0.95991	0.55
27DAP/reference	0.8934	0.147
39DAP/reference	0.87514	0.046
41DAP/reference	0.92495	0.086
42DAP/reference	0.70957	0.025
43DAP/reference	0.6978	0.037
47DAP/reference	1.00956	0.667
52DAP/reference	0.75316	0.148
57DAP/reference	0.58607	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96928	1
26DAP/20DAP	0.89455	0.512
34DAP/26DAP	1.03242	1
51DAP/34DAP	0.94342	0.563
52DAP/51DAP	1.01921	0.86
53DAP/52DAP	0.94074	0.695
55DAP/53DAP	0.94599	0.376
57DAP/55DAP	0.99208	0.927
62DAP/57DAP	1.08861	0.868
68DAP/62DAP	0.90943	0.543
68DAP/14DAP	0.89091	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81458	0.129

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.83798	0.287
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.64678	N/A
Mature Eggplant/Ripe Tomato	0.50979	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94404	0.944
1-1-2/M82	0.92059	0.958
12-2/M82	0.973	N/A
12-4/M82	1.09998	N/A
1-3/M82	0.64913	0.32
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.23619	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.39548	N/A
4-1/M82	1.03866	N/A
4-3-2/M82	0.93254	N/A
4-3/M82	N/A	N/A
5-3/M82	0.95452	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.03175	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92947	N/A
IL2-6/WTpooled	0.95185	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.10641	0.737
IL1-4/WTpooled	0.77403	N/A
WT/WTpooled	1.09184	0.686

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	0.78351	0.209

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03438	0.921
DC3000/delta hrp 6h	1.15521	0.95
DC3000/delta hrp 12h	1.15845	1
DC3000/delta hrp 24h	1.14429	0.232

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00535	1
DC3000 delta B/DC3000 delta AB	0.94275	0.558

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98594	1
Exp 36h	1.18129	1
Exp 60h	1.08406	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01459	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.06221	0.58
Var 12h NI row2-row1	0.94377	0.82
Var 36h I row2-row1	0.98012	1
Var 36h NI row2-row1	0.90746	0.706
Var 60h I row2-row1	1.48402	0.562
Var 60h NI row2-row1	0.92644	0.932
Time course 0hI-0hNI	0.98547	0.97
Time course 12hI-12hNI	0.96797	0.806
Time course 36hI-36hNI	0.92858	0.15
Time course 60hI-60hNI	1.00833	1

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)	0.94779	0.291
transgenic ySAMdc/azygous control (breaker)	0.73377	0.15
transgenic ySAMdc/azygous control (red)	1.03249	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99953	0.967

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84716	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.60892	0.172
Manapal/WT (break)	0.81346	0.333
Manapal/WT (red)	0.82047	0.181