Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.3.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72612	0.159
27DAP/17DAP	0.86207	0.724
39DAP/27DAP	0.94866	0.652
41DAP/39DAP	0.88087	0.558
42DAP/41DAP	1.13585	0.92
43DAP/42DAP	1.0222	0.937
47DAP/43DAP	0.64455	0.107
52DAP/47DAP	1.93677	0.436
57DAP/52DAP	0.79957	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91686	0.145
17DAP/reference	0.8687	0.05
27DAP/reference	0.98117	0.694
39DAP/reference	0.63909	0.007
41DAP/reference	0.76435	0.008
42DAP/reference	0.92442	0.05
43DAP/reference	1.05507
47DAP/reference	0.77185	0.002
52DAP/reference	0.97294	0.53
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7073	0.048
27DAP/17DAP	0.77602	0.475
39DAP/27DAP	0.92789	0.482
41DAP/39DAP	1.17904	0.07
42DAP/41DAP	0.90032	0.495
43DAP/42DAP	1.37239	0.122
47DAP/43DAP	1.29006	0.61
52DAP/47DAP	1.50327	0.194
57DAP/52DAP	2.25255	0.029
57DAP/7DAP	1.69808	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23737	0.085
17DAP/reference	1.2974	0.038
27DAP/reference	1.06697	0.804
39DAP/reference	0.97995	0.552
41DAP/reference	1.14267	0.314
42DAP/reference	1.18	0.046
43DAP/reference	1.27158	0.099
47DAP/reference	1.01496	1
52DAP/reference	1.21763	0.086
57DAP/reference	1.34965	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87004	0.124
17DAP/reference	0.8227	0.159
27DAP/reference	0.99592	0.663
39DAP/reference	1.11956	0.346
41DAP/reference	1.09439	0.327
42DAP/reference	0.85953	0.03
43DAP/reference	0.79372	0.162
47DAP/reference	0.84792	0.016
52DAP/reference	1.21899	1
57DAP/reference	0.93865	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29029	0.06
17DAP/reference	1.17572	0.792
27DAP/reference	1.32307	0.036
39DAP/reference	1.398	0.033
41DAP/reference	1.0661	1
42DAP/reference	1.09661	0.589
43DAP/reference	1.40039	0.037
47DAP/reference	1.01505	1
52DAP/reference	1.2313	0.252
57DAP/reference	1.42139	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.33071	0.966
26DAP/20DAP	0.81214	1
34DAP/26DAP	1.07519	1
51DAP/34DAP	0.76312	0.143
52DAP/51DAP	0.89091	1
53DAP/52DAP	1.15238	0.845
55DAP/53DAP	1.05775	0.964
57DAP/55DAP	0.80914	0.337
62DAP/57DAP	1.19407	0.393
68DAP/62DAP	1.11264	0.899
68DAP/14DAP	1.9183	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92609	0.399

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.98642	0.058
Mature Green Tomato/Ripe Tomato	0.3992	0.03
Immature Eggplant/Mature Eggplant	0.42946	0.062
Ripe Pepper/Ripe Tomato	0.24844	0.224
Mature Eggplant/Ripe Tomato	0.4047	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11741	0.877
1-1-2/M82	1.0621	1
12-2/M82	N/A	N/A
12-4/M82	0.83476
1-3/M82	1.77136
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.96164	1
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	0.91264	0.578
5-3/M82	0.94918	1
6-2/M82	1.69717	1
6-3/M82	1.01628	1
7-1/M82	1.31991
7-2/M82	1.1594	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15416	0.277
IL2-6/WTpooled	0.56103	0.348
IL7-5/WTpooled	0.80023	1
IL7-3/WTpooled	0.88971	0.298
IL12-4/WTpooled	1.1127	0.891
IL1-4/WTpooled	0.76547	0.402
WT/WTpooled	1.01121	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	1.17881	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96271	1
DC3000/delta hrp 6h	1.163	1
DC3000/delta hrp 12h	0.97438	1
DC3000/delta hrp 24h	0.54846	0.037

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.44711	0.023
DC3000 delta B/DC3000 delta AB	0.52893	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.71265	1
Exp 36h	0.72514	0.661
Exp 60h	0.76301	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04643	1
Var 0h	1.10839	0.98
Var 12h I row2-row1	0.86835	0.627
Var 12h NI row2-row1	0.90868	0.627
Var 36h I row2-row1	0.78305	0.805
Var 36h NI row2-row1	0.81494	1
Var 60h I row2-row1	1.09922	0.562
Var 60h NI row2-row1	1.13241	0.904
Time course 0hI-0hNI	1.05693	0.833
Time course 12hI-12hNI	0.86036	0.284
Time course 36hI-36hNI	0.68376	0.023
Time course 60hI-60hNI	0.13544	0.005

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)	1.23089	0.654
transgenic ySAMdc/azygous control (breaker)	0.53897	0.125
transgenic ySAMdc/azygous control (red)	1.11743	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92672	0.053

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.71961	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.45435	0.105
Manapal/WT (break)	1.09664	1
Manapal/WT (red)	1.58756	0.164