Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.4.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.57737	0.033
27DAP/17DAP	1.21891	0.808
39DAP/27DAP	1.49224	0.242
41DAP/39DAP	1.05335	1
42DAP/41DAP	1.56602	0.054
43DAP/42DAP	0.97486	0.898
47DAP/43DAP	1.1015	0.733
52DAP/47DAP	0.68136	0.339
57DAP/52DAP	1.05708	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75822	0.046
17DAP/reference	0.78282	0.017
27DAP/reference	0.81869	0.095
39DAP/reference	0.79148	0.049
41DAP/reference	0.64276	0.012
42DAP/reference	0.77993	0.001
43DAP/reference	0.88883	0.129
47DAP/reference	0.94083	0.279
52DAP/reference	0.91928	0.21
57DAP/reference	0.88515	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.9301	0.071
27DAP/17DAP	0.5553	0.144
39DAP/27DAP	1.38224	0.102
41DAP/39DAP	1.11541	0.656
42DAP/41DAP	1.51527	0.006
43DAP/42DAP	0.63968	0.025
47DAP/43DAP	1.13731	0.601
52DAP/47DAP	0.69656	0.131
57DAP/52DAP	1.03143	0.73
57DAP/7DAP	1.91433

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03033	1
17DAP/reference	1.05527	1
27DAP/reference	0.9927	0.571
39DAP/reference	1.04265	1
41DAP/reference	1.1347	0.614
42DAP/reference	1.00498	0.828
43DAP/reference	0.87412	0.151
47DAP/reference	0.84574	0.079
52DAP/reference	1.15268	0.171
57DAP/reference	1.03815	0.746

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86803	0.374
17DAP/reference	0.67538	0.011
27DAP/reference	0.81479	0.115
39DAP/reference	0.68524	0.089
41DAP/reference	1.05703	0.749
42DAP/reference	0.8185	0.017
43DAP/reference	0.72683	0.046
47DAP/reference	0.8704	0.073
52DAP/reference	0.64831	0.008
57DAP/reference	0.67718	0.05

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0115	0.804
17DAP/reference	0.86819	0.342
27DAP/reference	0.99308	0.624
39DAP/reference	0.92205	0.147
41DAP/reference	0.96299	0.459
42DAP/reference	0.9604	0.552
43DAP/reference	0.90792	0.256
47DAP/reference	0.76266	0.019
52DAP/reference	1.01839	0.888
57DAP/reference	0.82773	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04675	1
26DAP/20DAP	0.93159	1
34DAP/26DAP	1.49991	0.819
51DAP/34DAP	7.61975	0.016
52DAP/51DAP	0.64889	0.151
53DAP/52DAP	1.44523	0.043
55DAP/53DAP	0.51467	0.023
57DAP/55DAP	0.93224	0.612
62DAP/57DAP	0.80146	0.28
68DAP/62DAP	1.08749	0.8
68DAP/14DAP	3.94864	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.06078	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.175	0.056
Mature Green Tomato/Ripe Tomato	2.24834	0.048
Immature Eggplant/Mature Eggplant	5.52758	0.05
Ripe Pepper/Ripe Tomato	24.6257	0.256
Mature Eggplant/Ripe Tomato	7.5551	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.83604
12-2/M82	N/A	N/A
12-4/M82	1.09168
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	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	N/A	N/A
5-3/M82	2.18781
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	0.96156	0.321
IL2-6/WTpooled	0.96872	1
IL7-5/WTpooled	1.10816	1
IL7-3/WTpooled	0.81916	0.31
IL12-4/WTpooled	0.99245	1
IL1-4/WTpooled	1.11184	1
WT/WTpooled	0.98442	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	1.09221	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12581	0.846
DC3000/delta hrp 6h	1.23989	1
DC3000/delta hrp 12h	1.35453	1
DC3000/delta hrp 24h	0.72737	0.036

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.39509	0.042
DC3000 delta B/DC3000 delta AB	1.63648	0.085

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.71792	0.254
Exp 36h	1.11646	0.693
Exp 60h	1.5261	0.399

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	1.16254	0.594
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)	1.31482	0.612
transgenic ySAMdc/azygous control (breaker)	1.0011	1
transgenic ySAMdc/azygous control (red)	0.90897	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.92942	0.028

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93898	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.63941	0.093
Manapal/WT (break)	1.17296	1
Manapal/WT (red)	0.78718	0.184