Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.6.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87976	0.395
27DAP/17DAP	0.85449	0.661
39DAP/27DAP	1.12683	0.782
41DAP/39DAP	1.00657	1
42DAP/41DAP	0.93791	1
43DAP/42DAP	1.06088	1
47DAP/43DAP	0.73184	0.236
52DAP/47DAP	0.91784	0.771
57DAP/52DAP	1.0308	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97104	0.465
17DAP/reference	1.15813	0.048
27DAP/reference	1.10186	0.405
39DAP/reference	1.03189	0.343
41DAP/reference	1.04971	0.587
42DAP/reference	0.89686	0.046
43DAP/reference	0.99678	0.904
47DAP/reference	0.91099	0.025
52DAP/reference	0.79039	0.048
57DAP/reference	0.79047	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02311	0.961
27DAP/17DAP	0.82449	0.684
39DAP/27DAP	0.748	0.45
41DAP/39DAP	0.99813	1
42DAP/41DAP	1.22931	0.354
43DAP/42DAP	1.55346	0.02
47DAP/43DAP	1.02211	1
52DAP/47DAP	0.91937	0.777
57DAP/52DAP	1.2523	0.444
57DAP/7DAP	1.0239	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00645	1
17DAP/reference	0.95266	0.447
27DAP/reference	1.5559	0.551
39DAP/reference	1.14667	0.669
41DAP/reference	1.58694	0.021
42DAP/reference	1.34267	0.132
43DAP/reference	1.21852	0.344
47DAP/reference	0.99672	1
52DAP/reference	1.18125	0.098
57DAP/reference	1.29833	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07074	0.704
17DAP/reference	0.80711	0.17
27DAP/reference	0.87956	0.212
39DAP/reference	0.89117	0.235
41DAP/reference	0.81364	0.02
42DAP/reference	0.83005	0.028
43DAP/reference	0.96075	0.478
47DAP/reference	0.94827	0.253
52DAP/reference	1.06393	0.596
57DAP/reference	1.21356	0.14

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1176	0.258
17DAP/reference	0.96718	0.668
27DAP/reference	0.85895
39DAP/reference	0.99849	0.889
41DAP/reference	1.15087	0.692
42DAP/reference	1.13483	0.994
43DAP/reference	1.14887	0.858
47DAP/reference	0.90222	0.286
52DAP/reference	0.93296	0.573
57DAP/reference	0.60098	0.041

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09785	0.817
26DAP/20DAP	0.78057	0.244
34DAP/26DAP	1.23812	0.19
51DAP/34DAP	0.94236	0.77
52DAP/51DAP	1.19634	0.431
53DAP/52DAP	1.17667	0.104
55DAP/53DAP	1.02418	0.82
57DAP/55DAP	1.01974	0.953
62DAP/57DAP	0.99787	1
68DAP/62DAP	0.64912	0.07
68DAP/14DAP	0.86504	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93747	0.493

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.56834	0.058
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	3.33516	1
Mature Eggplant/Ripe Tomato	2.20901

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	0.92259
12-4/M82	1.06227
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.15895
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	0.82195

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.47578	0.493
IL2-6/WTpooled	1.13202
IL7-5/WTpooled	1.05371
IL7-3/WTpooled	1.12286
IL12-4/WTpooled	0.76275	0.566
IL1-4/WTpooled	1.13115	0.421
WT/WTpooled	0.57571

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	1.36782	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0245	0.921
DC3000/delta hrp 6h	1.07232	1
DC3000/delta hrp 12h	1.06864	1
DC3000/delta hrp 24h	1.2526	0.113

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	N/A	N/A
Exp 36h	0.53877	0.699
Exp 60h	0.93222	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06435	1
Var 0h	0.95181	1
Var 12h I row2-row1	1.18347	0.795
Var 12h NI row2-row1	1.09944	1
Var 36h I row2-row1	1.07242
Var 36h NI row2-row1	0.66852	0.413
Var 60h I row2-row1	0.97288	0.952
Var 60h NI row2-row1	0.63802	0.866
Time course 0hI-0hNI	1.02504	1
Time course 12hI-12hNI	0.88837	0.055
Time course 36hI-36hNI	0.96631	0.504
Time course 60hI-60hNI	0.58787	0.007

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)	0.96368	0.377
transgenic ySAMdc/azygous control (breaker)	1.06121	1
transgenic ySAMdc/azygous control (red)	1.22113	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98605	0.568

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09028	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.53758	0.105
Manapal/WT (break)	1.45075	0.381
Manapal/WT (red)	1.35726	0.15