Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.4.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81683	0.331
27DAP/17DAP	1.10433	1
39DAP/27DAP	1.28104	0.524
41DAP/39DAP	1.26634	0.437
42DAP/41DAP	0.99913	1
43DAP/42DAP	0.95759	0.906
47DAP/43DAP	0.98612	0.895
52DAP/47DAP	1.66124	0.525
57DAP/52DAP	0.95324	0.932

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12684	0.154
17DAP/reference	0.96455	0.536
27DAP/reference	1.02436	0.966
39DAP/reference	1.03282	0.706
41DAP/reference	0.87911	0.049
42DAP/reference	0.88119	0.009
43DAP/reference	1.10768	0.287
47DAP/reference	1.01993	1
52DAP/reference	1.03505	0.991
57DAP/reference	1.08116	0.463

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03658	0.881
27DAP/17DAP	1.13543	0.541
39DAP/27DAP	1.05958	0.654
41DAP/39DAP	1.00083	1
42DAP/41DAP	1.14049	0.539
43DAP/42DAP	0.91546	0.269
47DAP/43DAP	1.15139	0.281
52DAP/47DAP	0.942	0.807
57DAP/52DAP	1.02751	1
57DAP/7DAP	1.02694	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03169	0.625
17DAP/reference	1.09655	0.627
27DAP/reference	1.2372	0.073
39DAP/reference	1.33908	0.012
41DAP/reference	1.40527	0.077
42DAP/reference	1.39347	0.024
43DAP/reference	1.258	0.105
47DAP/reference	1.29718	0.112
52DAP/reference	1.31215	0.023
57DAP/reference	1.17851	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89723	0.518
17DAP/reference	0.68679	0.011
27DAP/reference	0.95382	0.366
39DAP/reference	1.08367	0.571
41DAP/reference	1.01869	1
42DAP/reference	0.86517	0.021
43DAP/reference	0.98375	0.67
47DAP/reference	0.88756	0.105
52DAP/reference	0.82794	0.004
57DAP/reference	0.87057	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15044	0.32
17DAP/reference	1.12171	0.376
27DAP/reference	1.29437	0.056
39DAP/reference	1.22902	0.01
41DAP/reference	1.10094	0.455
42DAP/reference	1.04449	0.743
43DAP/reference	1.03057	0.767
47DAP/reference	0.92831	0.296
52DAP/reference	1.15006	0.257
57DAP/reference	1.10542	0.233

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.945	1
26DAP/20DAP	1.13434	0.707
34DAP/26DAP	0.85907	0.584
51DAP/34DAP	1.01487	1
52DAP/51DAP	1.08206	0.704
53DAP/52DAP	1.31302	0.458
55DAP/53DAP	0.88426	0.404
57DAP/55DAP	1.00164	0.93
62DAP/57DAP	2.65761
68DAP/62DAP	0.313
68DAP/14DAP	0.37616

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.3064	0.068

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.1453	0.287
Mature Green Tomato/Ripe Tomato	1.57728	0.019
Immature Eggplant/Mature Eggplant	0.83789	0.448
Ripe Pepper/Ripe Tomato	1.88054	1
Mature Eggplant/Ripe Tomato	1.70402	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89325	0.934
1-1-2/M82	1.18225	1
12-2/M82	0.96045	0.955
12-4/M82	0.91642	1
1-3/M82	1.35585	0.277
2-1-1/M82	1.10242	1
2-1/M82	0.87242	1
2-6/M82	0.93205	1
3-2/M82	0.72149
4-1-1/M82	0.97692	1
4-1/M82	0.64172
4-3-2/M82	1.10374	1
4-3/M82	1.02764	1
5-3/M82	1.20837	0.496
6-2/M82	1.07913	1
6-3/M82	1.04433	1
7-1/M82	0.83003	0.803
7-2/M82	0.82023	0.414
9-3-2/M82	1.28339	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95655	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.03623	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.05745	1
WT/WTpooled	N/A	N/A

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	0.9582	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95989	1
DC3000/delta hrp 6h	1.05196	1
DC3000/delta hrp 12h	1.00443	1
DC3000/delta hrp 24h	0.88219	0.145

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07933	0.333
DC3000 delta B/DC3000 delta AB	1.17028	0.265

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.2817	1
Exp 36h	0.96705	0.749
Exp 60h	0.99745	1

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	N/A	N/A
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)	0.83639	0.295
transgenic ySAMdc/azygous control (breaker)	0.59971	0.124
transgenic ySAMdc/azygous control (red)	1.04829	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.038	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77842	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85905	1
Manapal/WT (break)	0.86469	0.299
Manapal/WT (red)	0.77634	0.188