Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.4.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92003	0.558
27DAP/17DAP	1.54035	0.62
39DAP/27DAP	1.1351	0.622
41DAP/39DAP	0.91994	0.785
42DAP/41DAP	0.95959	1
43DAP/42DAP	1.01639	0.937
47DAP/43DAP	1.06892	0.934
52DAP/47DAP	0.95544	0.816
57DAP/52DAP	0.992	0.978

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8125	0.05
17DAP/reference	0.78014	0.009
27DAP/reference	0.96147	0.595
39DAP/reference	0.84962	0.029
41DAP/reference	0.71779	0.009
42DAP/reference	0.94908	0.091
43DAP/reference	0.94937	0.48
47DAP/reference	0.94826	0.137
52DAP/reference	1.15133	0.134
57DAP/reference	1.19643	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08649	0.662
27DAP/17DAP	1.09997	0.942
39DAP/27DAP	0.95881	0.754
41DAP/39DAP	1.11046	0.656
42DAP/41DAP	0.94076	0.654
43DAP/42DAP	0.77495	0.097
47DAP/43DAP	1.03783	0.973
52DAP/47DAP	1.20145	0.639
57DAP/52DAP	1.37095	0.143
57DAP/7DAP	1.26215	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17483	0.318
17DAP/reference	1.10647	0.437
27DAP/reference	1.21788	0.246
39DAP/reference	1.17087	0.333
41DAP/reference	1.00525	0.646
42DAP/reference	1.05857	0.889
43DAP/reference	1.0838	0.537
47DAP/reference	1.01372	0.98
52DAP/reference	0.92568	0.278
57DAP/reference	1.00428	0.694

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.899	0.386
17DAP/reference	0.80805	0.016
27DAP/reference	0.86555	0.079
39DAP/reference	0.82109	0.06
41DAP/reference	1.0369	0.799
42DAP/reference	0.99004	0.594
43DAP/reference	0.70797	0.02
47DAP/reference	0.86077	0.02
52DAP/reference	0.95661	0.38
57DAP/reference	0.76292	0.107

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09772	0.545
17DAP/reference	1.08058	0.488
27DAP/reference	0.95094	0.416
39DAP/reference	0.96704	0.643
41DAP/reference	1.21351	0.239
42DAP/reference	1.0501	0.994
43DAP/reference	1.09139	0.634
47DAP/reference	0.97363	0.465
52DAP/reference	0.88746	0.395
57DAP/reference	1.02017	0.892

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02907	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.21579	1
51DAP/34DAP	1.32563	0.666
52DAP/51DAP	0.77591	0.151
53DAP/52DAP	1.23774	0.398
55DAP/53DAP	1.14037	0.733
57DAP/55DAP	1.16724	0.242
62DAP/57DAP	0.84045	0.466
68DAP/62DAP	1.43373	0.729
68DAP/14DAP	1.51851	0.113

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.24119	0.439

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.53536	0.139
Mature Green Tomato/Ripe Tomato	0.43673	0.021
Immature Eggplant/Mature Eggplant	1.17923	0.417
Ripe Pepper/Ripe Tomato	1.98295	0.256
Mature Eggplant/Ripe Tomato	0.69255	1

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	N/A	N/A
12-4/M82	0.7866
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	0.89322
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	1.10023	1
5-3/M82	0.83317
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	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	0.83392	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.24024	1
IL12-4/WTpooled	0.90937	0.581
IL1-4/WTpooled	0.98734
WT/WTpooled	0.98523	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	1.10231	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.46874	0.921
DC3000/delta hrp 6h	1.05978	1
DC3000/delta hrp 12h	0.99039	1
DC3000/delta hrp 24h	1.44076	0.103

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.95679
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	0.92763	1
Exp 36h	1.22995	0.693
Exp 60h	1.05967	0.563

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	0.85372	0.457
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)	1.11585	0.212
transgenic ySAMdc/azygous control (breaker)	0.91438	0.49
transgenic ySAMdc/azygous control (red)	0.93127	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04924	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.49621	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84506	0.172
Manapal/WT (break)	0.88888	0.333
Manapal/WT (red)	1.20753	0.164