Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.4.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00713	0.997
27DAP/17DAP	1.13087	0.902
39DAP/27DAP	0.96264	0.67
41DAP/39DAP	1.00648	1
42DAP/41DAP	0.97653	1
43DAP/42DAP	0.76368	0.514
47DAP/43DAP	1.179	0.809
52DAP/47DAP	0.84579	0.618
57DAP/52DAP	0.79777	0.833

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7536	0.036
17DAP/reference	0.97396	0.597
27DAP/reference	1.01798	1
39DAP/reference	1.04201	0.57
41DAP/reference	0.98708	0.814
42DAP/reference	0.96322	0.233
43DAP/reference	1.01429	1
47DAP/reference	0.98047	0.258
52DAP/reference	0.9424	0.275
57DAP/reference	1.08524	0.419

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85297	0.388
27DAP/17DAP	1.00092	0.969
39DAP/27DAP	0.97798	0.844
41DAP/39DAP	0.81775	0.169
42DAP/41DAP	1.09223	0.879
43DAP/42DAP	1.16825	0.034
47DAP/43DAP	1.06603	0.779
52DAP/47DAP	0.86964	0.512
57DAP/52DAP	1.20099	0.507
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18297	0.181
17DAP/reference	1.13241	0.112
27DAP/reference	1.16452	0.197
39DAP/reference	0.95506	0.411
41DAP/reference	1.057	0.745
42DAP/reference	0.8188	0.077
43DAP/reference	1.05021	1
47DAP/reference	1.00838	1
52DAP/reference	0.98525	0.621
57DAP/reference	0.96889	0.443

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84833	0.145
17DAP/reference	0.87197	0.109
27DAP/reference	0.84286	0.01
39DAP/reference	0.89413	0.183
41DAP/reference	0.88197	0.043
42DAP/reference	0.95403	0.237
43DAP/reference	0.97712	0.561
47DAP/reference	0.87343	0.017
52DAP/reference	0.95766	0.407
57DAP/reference	0.8542	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18238	0.172
17DAP/reference	0.91285	0.47
27DAP/reference	1.30799	0.467
39DAP/reference	1.08983	0.836
41DAP/reference	0.96455	0.512
42DAP/reference	1.11069	0.5
43DAP/reference	1.10048	0.71
47DAP/reference	0.84935	0.031
52DAP/reference	0.92862	0.493
57DAP/reference	0.97579	0.583

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06143	0.966
26DAP/20DAP	1.58575	0.453
34DAP/26DAP	1.27563	1
51DAP/34DAP	0.85392	0.537
52DAP/51DAP	0.9438	1
53DAP/52DAP	1.29827	0.83
55DAP/53DAP	1.28867	0.782
57DAP/55DAP	0.65667	0.333
62DAP/57DAP	1.10758	0.935
68DAP/62DAP	1.20592	0.689
68DAP/14DAP	1.11568	0.131

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.23659	0.391

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.73765	0.377
Immature Eggplant/Mature Eggplant	2.43375	0.051
Ripe Pepper/Ripe Tomato	0.37676
Mature Eggplant/Ripe Tomato	0.76478	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.70567
1-1-2/M82	1.28941	1
12-2/M82	N/A	N/A
12-4/M82	0.83802	0.33
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	0.81255
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	0.99229	1
5-3/M82	0.98593	1
6-2/M82	0.84625
6-3/M82	1.14142
7-1/M82	N/A	N/A
7-2/M82	0.9729
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.8774	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.7004	1
IL12-4/WTpooled	0.84521	0.71
IL1-4/WTpooled	1.16931
WT/WTpooled	0.94136	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	0.94941	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11299
DC3000/delta hrp 6h	0.81679	0.95
DC3000/delta hrp 12h	1.05025	1
DC3000/delta hrp 24h	1.02649	0.821

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	1.23025	1
Exp 60h	1.14283	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98453	1
Var 0h	0.76965	1
Var 12h I row2-row1	0.9956	1
Var 12h NI row2-row1	0.93878	0.627
Var 36h I row2-row1	0.93135	0.575
Var 36h NI row2-row1	0.87622	0.549
Var 60h I row2-row1	0.95291	0.439
Var 60h NI row2-row1	1.13182	0.904
Time course 0hI-0hNI	1.04107	0.833
Time course 12hI-12hNI	1.05472	0.587
Time course 36hI-36hNI	0.92515	0.312
Time course 60hI-60hNI	1.07065	0.037

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)	1.081	0.261
transgenic ySAMdc/azygous control (breaker)	0.50173	0.139
transgenic ySAMdc/azygous control (red)	1.43732	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01834	0.619

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)	0.99433	1
Manapal/WT (break)	0.84509	0.333
Manapal/WT (red)	0.62347	0.181