Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.5.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78712	0.221
27DAP/17DAP	0.89525	0.736
39DAP/27DAP	1.22683	0.539
41DAP/39DAP	1.11222	0.426
42DAP/41DAP	1.15146	0.712
43DAP/42DAP	1.02738	1
47DAP/43DAP	0.79041	0.386
52DAP/47DAP	1.00739	0.982
57DAP/52DAP	1.07748	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.55345	0.007
17DAP/reference	1.14716	0.193
27DAP/reference	1.10067	0.468
39DAP/reference	1.12292	0.377
41DAP/reference	0.98451	0.814
42DAP/reference	1.2661	0.003
43DAP/reference	1.2239	0.019
47DAP/reference	1.23893	0.002
52DAP/reference	1.39615	0.027
57DAP/reference	1.21537	0.045

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92881	0.484
27DAP/17DAP	1.02317	0.96
39DAP/27DAP	0.96314	0.754
41DAP/39DAP	1.10167	0.849
42DAP/41DAP	1.00142	0.91
43DAP/42DAP	0.84558	0.056
47DAP/43DAP	1.05535	0.464
52DAP/47DAP	0.84702	0.1
57DAP/52DAP	0.90498	0.384
57DAP/7DAP	0.80561	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.24907	0.024
17DAP/reference	1.21268	0.023
27DAP/reference	1.29023	0.06
39DAP/reference	1.47963	0.006
41DAP/reference	1.49253	0.015
42DAP/reference	1.47223	0.007
43DAP/reference	1.69846	0.008
47DAP/reference	1.79791	0.014
52DAP/reference	1.4643	0.013
57DAP/reference	1.35544	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31086	0.038
17DAP/reference	1.19068	0.063
27DAP/reference	1.38297	0.021
39DAP/reference	1.05659	0.956
41DAP/reference	1.04923	0.846
42DAP/reference	1.2991	0.016
43DAP/reference	0.83332	0.14
47DAP/reference	1.26236	0.089
52DAP/reference	0.88112	0.121
57DAP/reference	0.89603	0.144

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.651	0.015
17DAP/reference	1.0973	0.474
27DAP/reference	1.18405	0.125
39DAP/reference	1.28172	0.026
41DAP/reference	1.08106	0.357
42DAP/reference	1.09071	0.521
43DAP/reference	1.29947	0.048
47DAP/reference	0.88138	0.103
52DAP/reference	1.28732	0.155
57DAP/reference	1.15479	0.058

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15653	0.966
26DAP/20DAP	1.31281	0.353
34DAP/26DAP	0.94839	0.803
51DAP/34DAP	1.10739	0.535
52DAP/51DAP	0.83245	1
53DAP/52DAP	1.43316	0.057
55DAP/53DAP	0.79926	0.05
57DAP/55DAP	0.98189	0.863
62DAP/57DAP	0.83745	0.681
68DAP/62DAP	0.94262	0.769
68DAP/14DAP	0.70031	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.39506	0.057

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.23958	0.058
Mature Green Tomato/Ripe Tomato	0.86026	0.226
Immature Eggplant/Mature Eggplant	1.4329	0.05
Ripe Pepper/Ripe Tomato	0.88857	0.293
Mature Eggplant/Ripe Tomato	1.2843	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89041	0.944
1-1-2/M82	1.18003	1
12-2/M82	1.16485	0.519
12-4/M82	1.1577	1
1-3/M82	1.91779	0.248
2-1-1/M82	1.48685	0.439
2-1/M82	0.99123	1
2-6/M82	1.12753	0.505
3-2/M82	1.03907	1
4-1-1/M82	0.97347	1
4-1/M82	1.42176	1
4-3-2/M82	1.25761	0.253
4-3/M82	1.1897	1
5-3/M82	0.95036	1
6-2/M82	1.26658
6-3/M82	0.91301	1
7-1/M82	0.98799	1
7-2/M82	1.07467	0.385
9-3-2/M82	1.31318	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98212	1
IL2-6/WTpooled	1.10196	0.441
IL7-5/WTpooled	1.05054	1
IL7-3/WTpooled	0.87733	0.418
IL12-4/WTpooled	0.97665	0.71
IL1-4/WTpooled	0.8599	0.457
WT/WTpooled	1.00063	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	0.83318	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11254	0.774
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.54697	0.043

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.57342	0.024
DC3000 delta B/DC3000 delta AB	0.42224	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9401	1
Var 0h	1.24585	0.594
Var 12h I row2-row1	0.79217	0.565
Var 12h NI row2-row1	0.96887	0.906
Var 36h I row2-row1	0.72151	0.805
Var 36h NI row2-row1	1.15072	1
Var 60h I row2-row1	1.0269	1
Var 60h NI row2-row1	1.03897	1
Time course 0hI-0hNI	1.08483	0.63
Time course 12hI-12hNI	0.98553	0.935
Time course 36hI-36hNI	0.78647	0.041
Time course 60hI-60hNI	0.17678	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)	1.07128	0.36
transgenic ySAMdc/azygous control (breaker)	0.85673	0.173
transgenic ySAMdc/azygous control (red)	0.90898	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89593	0.065

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.71707	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9028	0.172
Manapal/WT (break)	0.77937	0.299
Manapal/WT (red)	0.71486	0.184