Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.20.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81365	0.285
27DAP/17DAP	1.18719	0.832
39DAP/27DAP	1.27045	0.765
41DAP/39DAP	1.05774	0.921
42DAP/41DAP	0.83489	0.774
43DAP/42DAP	0.98926	0.937
47DAP/43DAP	0.87867	0.599
52DAP/47DAP	0.88553	0.67
57DAP/52DAP	1.75175	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19982	0.018
17DAP/reference	1.0894	0.813
27DAP/reference	1.16083	0.637
39DAP/reference	1.15132	0.286
41DAP/reference	1.26197	0.043
42DAP/reference	1.06114	0.523
43DAP/reference	0.88088
47DAP/reference	1.03823	1
52DAP/reference	0.95044	0.504
57DAP/reference	0.7406	0.04

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12396	0.881
27DAP/17DAP	0.98832	0.919
39DAP/27DAP	1.38244	0.071
41DAP/39DAP	0.87119	0.567
42DAP/41DAP	1.26623	0.07
43DAP/42DAP	1.09628	0.382
47DAP/43DAP	0.91745	0.439
52DAP/47DAP	0.8899	0.612
57DAP/52DAP	1.25003	0.513
57DAP/7DAP	1.26396	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77845	0.042
17DAP/reference	0.85741	0.144
27DAP/reference	0.92704	0.231
39DAP/reference	0.78884	0.083
41DAP/reference	0.80378	0.139
42DAP/reference	0.87124	0.211
43DAP/reference	0.9558	0.385
47DAP/reference	1.04804	0.915
52DAP/reference	1.02713	1
57DAP/reference	0.89578	0.109

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29651	0.224
17DAP/reference	0.8161	0.153
27DAP/reference	0.83552	0.071
39DAP/reference	0.85242	0.119
41DAP/reference	0.88435	0.108
42DAP/reference	1.07241	1
43DAP/reference	0.95383	0.478
47DAP/reference	1.15514	0.775
52DAP/reference	0.87269	0.131
57DAP/reference	0.99142	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90928	0.098
17DAP/reference	0.88705	0.262
27DAP/reference	0.94234	0.27
39DAP/reference	0.82765	0.025
41DAP/reference	0.82303	0.086
42DAP/reference	0.7455	0.036
43DAP/reference	0.87403	0.216
47DAP/reference	0.81285	0.066
52DAP/reference	0.94127	0.551
57DAP/reference	0.76449	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13504	0.966
26DAP/20DAP	0.89475	1
34DAP/26DAP	0.72645	0.076
51DAP/34DAP	1.60573	0.055
52DAP/51DAP	0.88505	1
53DAP/52DAP	1.56615	0.054
55DAP/53DAP	1.12362	0.629
57DAP/55DAP	0.78179	0.127
62DAP/57DAP	0.843	0.28
68DAP/62DAP	1.11776	0.919
68DAP/14DAP	1.00918	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92657	0.239

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.87261	0.364
Mature Green Tomato/Ripe Tomato	1.34611	0.04
Immature Eggplant/Mature Eggplant	2.64212	0.05
Ripe Pepper/Ripe Tomato	3.08315	0.256
Mature Eggplant/Ripe Tomato	1.66852

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93916	0.961
1-1-2/M82	1.03364	1
12-2/M82	1.09045	1
12-4/M82	0.97354	1
1-3/M82	1.62959	0.255
2-1-1/M82	0.77562	0.565
2-1/M82	0.98631
2-6/M82	0.91201	1
3-2/M82	0.91293	0.428
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.01576	1
4-3/M82	0.69437	0.72
5-3/M82	0.97113	1
6-2/M82	1.62661
6-3/M82	1.02094	1
7-1/M82	N/A	N/A
7-2/M82	1.02638	0.385
9-3-2/M82	1.17377	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15176	0.277
IL2-6/WTpooled	0.95739	1
IL7-5/WTpooled	1.57409
IL7-3/WTpooled	1.21032	0.362
IL12-4/WTpooled	1.02538	0.891
IL1-4/WTpooled	1.13295	0.426
WT/WTpooled	0.99385	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	1.28784	0.177

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88726
DC3000/delta hrp 6h	0.81467	0.95
DC3000/delta hrp 12h	0.97509	1
DC3000/delta hrp 24h	2.78846	0.022

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.67562	0.042
DC3000 delta B/DC3000 delta AB	1.48583	0.088

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.22879	1
Exp 36h	1.30504	0.489
Exp 60h	1.23044	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01531	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.98037	0.948
Var 12h NI row2-row1	1.34898	0.649
Var 36h I row2-row1	1.09045	1
Var 36h NI row2-row1	0.85483	0.645
Var 60h I row2-row1	0.74865	0.293
Var 60h NI row2-row1	0.84683	0.483
Time course 0hI-0hNI	1.01159	0.867
Time course 12hI-12hNI	0.97929	0.874
Time course 36hI-36hNI	1.61179	0.006
Time course 60hI-60hNI	4.96677	0.008

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)	0.91233	0.315
transgenic ySAMdc/azygous control (breaker)	0.99919	1
transgenic ySAMdc/azygous control (red)	0.9503	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09485	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.156	0.096
Manapal/WT (break)	1.26057	0.183
Manapal/WT (red)	0.77406	0.229