Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.5.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2875	0.588
27DAP/17DAP	1.13789	0.849
39DAP/27DAP	0.84575	0.458
41DAP/39DAP	1.1081	0.498
42DAP/41DAP	0.97126	1
43DAP/42DAP	1.04491	1
47DAP/43DAP	1.0349	0.943
52DAP/47DAP	0.78555	0.455
57DAP/52DAP	1.0639	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.56713	0.065
17DAP/reference	1.3974	0.037
27DAP/reference	1.4111	0.239
39DAP/reference	1.27717	0.224
41DAP/reference	0.96748	0.667
42DAP/reference	1.06696	0.901
43DAP/reference	1.05438	0.982
47DAP/reference	0.85117	0.023
52DAP/reference	0.90491	0.275
57DAP/reference	0.87199	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	N/A	N/A
27DAP/17DAP	1.44053
39DAP/27DAP	1.69943
41DAP/39DAP	1.17741	0.853
42DAP/41DAP	9.47118	0.365
43DAP/42DAP	N/A	N/A
47DAP/43DAP	1.09068	0.884
52DAP/47DAP	2.21385
57DAP/52DAP	1.21811	1
57DAP/7DAP	1.55211

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41171	0.048
17DAP/reference	1.08319	0.822
27DAP/reference	1.21461	0.014
39DAP/reference	1.02321	0.865
41DAP/reference	1.022	1
42DAP/reference	0.95389	0.436
43DAP/reference	0.99823	0.665
47DAP/reference	0.9293	0.383
52DAP/reference	1.08251	0.684
57DAP/reference	1.00493	0.694

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4403	0.042
17DAP/reference	1.30555	0.171
27DAP/reference	1.13086	0.704
39DAP/reference	1.114	1
41DAP/reference	1.1094	1
42DAP/reference	1.01589	0.594
43DAP/reference	1.19113	0.633
47DAP/reference	1.00472	0.695
52DAP/reference	0.98915	0.576
57DAP/reference	1.01275	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40218	0.02
17DAP/reference	1.13068	0.206
27DAP/reference	1.07776	0.425
39DAP/reference	1.00523	0.819
41DAP/reference	0.97831	0.618
42DAP/reference	0.88014	0.287
43DAP/reference	0.83733	0.024
47DAP/reference	0.79806	0.109
52DAP/reference	0.76346	0.103
57DAP/reference	0.85034	0.229

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.83768	0.566
26DAP/20DAP	0.48514	0.512
34DAP/26DAP	N/A	N/A
51DAP/34DAP	0.77862	0.606
52DAP/51DAP	1.18198	0.792
53DAP/52DAP	1.39328	0.688
55DAP/53DAP	1.25907	0.589
57DAP/55DAP	1.02616
62DAP/57DAP	1.05284	1
68DAP/62DAP	0.8749	0.722
68DAP/14DAP	0.89387	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89023	0.443

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.02697	0.058
Mature Green Tomato/Ripe Tomato	1.37921	0.025
Immature Eggplant/Mature Eggplant	0.93017	0.292
Ripe Pepper/Ripe Tomato	2.54765	0.258
Mature Eggplant/Ripe Tomato	4.74275

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.89252
12-2/M82	N/A	N/A
12-4/M82	0.728
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	0.85184
4-1-1/M82	N/A	N/A
4-1/M82	0.72858
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.78666
7-2/M82	N/A	N/A
9-3-2/M82	0.73783	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.71934	1
IL2-6/WTpooled	0.70905	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.77047	0.418
IL12-4/WTpooled	0.95672	1
IL1-4/WTpooled	0.97862	0.834
WT/WTpooled	1.03014	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.97366	1
DC3000/delta hrp 12h	1.03712	1
DC3000/delta hrp 24h	N/A	N/A

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	0.86969	1
Exp 36h	0.86072	0.471
Exp 60h	0.85759	0.664

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	1.00154	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.15675	0.36
transgenic ySAMdc/azygous control (breaker)	1.02826	1
transgenic ySAMdc/azygous control (red)	0.90264	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09623	0.057

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82491	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.22353	0.307
Manapal/WT (break)	0.87523	1
Manapal/WT (red)	N/A	N/A