Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.3.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99973	0.919
27DAP/17DAP	0.7972	0.491
39DAP/27DAP	1.05688	0.995
41DAP/39DAP	1.44012	0.413
42DAP/41DAP	1.00383	1
43DAP/42DAP	0.86015	0.783
47DAP/43DAP	1.17266	0.733
52DAP/47DAP	1.29907	0.556
57DAP/52DAP	0.93443	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96936	0.513
17DAP/reference	0.93766	0.138
27DAP/reference	1.03243	0.684
39DAP/reference	0.81601	0.02
41DAP/reference	0.84845	0.031
42DAP/reference	0.89094	0.012
43DAP/reference	0.94704	0.211
47DAP/reference	0.98989	0.535
52DAP/reference	1.03658	1
57DAP/reference	1.16341	0.016

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00587	0.899
27DAP/17DAP	1.12311	0.867
39DAP/27DAP	0.9645	0.768
41DAP/39DAP	1.12049	0.641
42DAP/41DAP	0.88925	0.259
43DAP/42DAP	0.99706	1
47DAP/43DAP	0.95658	0.787
52DAP/47DAP	1.06543	0.779
57DAP/52DAP	1.21371	0.284
57DAP/7DAP	1.31482	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00129	0.613
17DAP/reference	1.00294	0.693
27DAP/reference	0.97681	0.571
39DAP/reference	0.99313	0.64
41DAP/reference	1.02816	0.709
42DAP/reference	1.1595	0.686
43DAP/reference	0.96066	0.44
47DAP/reference	1.22295	0.885
52DAP/reference	0.97967	0.621
57DAP/reference	0.83865	0.114

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85926	0.016
17DAP/reference	0.81824	0.01
27DAP/reference	0.93038	0.155
39DAP/reference	0.86068	0.018
41DAP/reference	0.90105	0.083
42DAP/reference	0.92785	0.135
43DAP/reference	0.85254	0.062
47DAP/reference	0.84813	0.015
52DAP/reference	0.90495	0.025
57DAP/reference	0.81246	0.028

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05322	1
17DAP/reference	0.82981	0.452
27DAP/reference	1.4279	0.26
39DAP/reference	0.86983	0.43
41DAP/reference	0.91354	0.618
42DAP/reference	1.0828	0.759
43DAP/reference	0.97651	0.614
47DAP/reference	0.96292	0.421
52DAP/reference	1.34609	0.623
57DAP/reference	1.244	0.045

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94945	1
26DAP/20DAP	0.93125	1
34DAP/26DAP	0.78475	0.237
51DAP/34DAP	1.07273	0.581
52DAP/51DAP	0.95041	1
53DAP/52DAP	1.40078	0.1
55DAP/53DAP	0.92465	0.325
57DAP/55DAP	0.80444	0.132
62DAP/57DAP	1.12649	0.569
68DAP/62DAP	1.34219	0.198
68DAP/14DAP	1.20896	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81228	0.155

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.7493	0.058
Mature Green Tomato/Ripe Tomato	0.71487	0.014
Immature Eggplant/Mature Eggplant	0.62667	0.117
Ripe Pepper/Ripe Tomato	1.47867	1
Mature Eggplant/Ripe Tomato	0.4003

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88411	0.944
1-1-2/M82	0.84736	1
12-2/M82	0.89561	0.955
12-4/M82	1.00861
1-3/M82	0.62967
2-1-1/M82	1.33593
2-1/M82	N/A	N/A
2-6/M82	0.98359	1
3-2/M82	0.93376
4-1-1/M82	0.98858	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.64978	0.466
5-3/M82	1.13573
6-2/M82	0.9132
6-3/M82	1.40381
7-1/M82	1.50219
7-2/M82	1.00031
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.28704	0.493
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.8239
IL7-3/WTpooled	3.95248	1
IL12-4/WTpooled	1.12161	1
IL1-4/WTpooled	1.68968	0.426
WT/WTpooled	1.11049	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	0.74492	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.87077	0.839
DC3000/delta hrp 6h	0.9722	0.95
DC3000/delta hrp 12h	0.94199	1
DC3000/delta hrp 24h	0.89178	0.148

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.75402	0.059
DC3000 delta B/DC3000 delta AB	0.62294	0.024

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.76814	0.245
Exp 36h	0.61831	0.426
Exp 60h	0.64586	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97012	1
Var 0h	0.92055	0.457
Var 12h I row2-row1	1.01685	0.795
Var 12h NI row2-row1	0.97872	0.906
Var 36h I row2-row1	0.99703	1
Var 36h NI row2-row1	1.08116	0.482
Var 60h I row2-row1	1.08747	0.543
Var 60h NI row2-row1	1.20583	0.904
Time course 0hI-0hNI	0.87788	0.334
Time course 12hI-12hNI	0.9795	0.889
Time course 36hI-36hNI	0.80602	0.024
Time course 60hI-60hNI	0.4485	0.006

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)	0.92192	0.213
transgenic ySAMdc/azygous control (breaker)	0.99094	1
transgenic ySAMdc/azygous control (red)	1.25556	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99368	0.712

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.00563	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.36022	0.105
Manapal/WT (break)	1.5025	0.14
Manapal/WT (red)	1.15196	0.222