Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.13.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00976	1
27DAP/17DAP	1.02545	0.91
39DAP/27DAP	0.92153	0.631
41DAP/39DAP	0.95065	0.772
42DAP/41DAP	0.97237	1
43DAP/42DAP	1.04574	1
47DAP/43DAP	1.15932	0.463
52DAP/47DAP	0.92364	0.769
57DAP/52DAP	1.02735	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97654	0.455
17DAP/reference	1.04491	0.096
27DAP/reference	0.99811	0.885
39DAP/reference	1.11775	0.214
41DAP/reference	1.01864	0.624
42DAP/reference	0.96765	0.157
43DAP/reference	1.01689	0.812
47DAP/reference	1.03634	0.306
52DAP/reference	0.93419	0.23
57DAP/reference	1.03634	0.548

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93695	0.238
27DAP/17DAP	0.99788	0.969
39DAP/27DAP	1.05097	0.663
41DAP/39DAP	1.06027	0.801
42DAP/41DAP	1.02126	1
43DAP/42DAP	1.01246	0.746
47DAP/43DAP	1.00963	0.957
52DAP/47DAP	0.99096	0.935
57DAP/52DAP	1.0297	0.864
57DAP/7DAP	0.91216	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85412	0.074
17DAP/reference	0.8816	0.012
27DAP/reference	0.87479	0.028
39DAP/reference	0.87484	0.02
41DAP/reference	0.84383	0.032
42DAP/reference	0.92244	0.117
43DAP/reference	0.80487	0.013
47DAP/reference	0.8808	0.03
52DAP/reference	0.83575	0.012
57DAP/reference	0.86129	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99858	0.951
17DAP/reference	0.99663	0.786
27DAP/reference	0.95249	0.34
39DAP/reference	0.96188	0.265
41DAP/reference	1.00991	1
42DAP/reference	1.04849	0.583
43DAP/reference	1.05084	0.466
47DAP/reference	1.06853	0.247
52DAP/reference	0.9958	0.666
57DAP/reference	1.07035	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95688	0.422
17DAP/reference	0.97856	0.592
27DAP/reference	0.87243	0.065
39DAP/reference	0.85729	0.033
41DAP/reference	0.85696	0.019
42DAP/reference	0.84433	0.025
43DAP/reference	0.85558	0.023
47DAP/reference	1.0044	0.731
52DAP/reference	0.79993	0.164
57DAP/reference	0.87082	0.127

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93149	0.708
26DAP/20DAP	0.94051	0.512
34DAP/26DAP	1.08253	1
51DAP/34DAP	0.88911	0.217
52DAP/51DAP	0.96489	1
53DAP/52DAP	1.00964	1
55DAP/53DAP	1.04557	0.748
57DAP/55DAP	1.12906	0.461
62DAP/57DAP	0.91387	0.871
68DAP/62DAP	1.10927	0.754
68DAP/14DAP	0.97116	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88325	0.065

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.08385
Mature Green Tomato/Ripe Tomato	1.03909	0.881
Immature Eggplant/Mature Eggplant	1.31195	0.181
Ripe Pepper/Ripe Tomato	1.28009
Mature Eggplant/Ripe Tomato	2.8214	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04914	0.742
1-1-2/M82	0.96035	0.958
12-2/M82	1.01425	1
12-4/M82	0.95646	1
1-3/M82	0.94818	0.501
2-1-1/M82	1.12949	0.689
2-1/M82	N/A	N/A
2-6/M82	0.94455	1
3-2/M82	0.92275	0.752
4-1-1/M82	0.95117	1
4-1/M82	0.93215	1
4-3-2/M82	0.77356	0.487
4-3/M82	1.04641	1
5-3/M82	1.06933	0.496
6-2/M82	1.04216	1
6-3/M82	1.0187	1
7-1/M82	1.06514	0.925
7-2/M82	0.97903	1
9-3-2/M82	0.95919	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.06085	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07966	1
IL12-4/WTpooled	3.17037	0.516
IL1-4/WTpooled	0.60233
WT/WTpooled	0.97178	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	1.24947	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06055	0.921
DC3000/delta hrp 6h	1.2814	1
DC3000/delta hrp 12h	0.99725	1
DC3000/delta hrp 24h	1.02253	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16654	0.145
DC3000 delta B/DC3000 delta AB	1.07003	0.423

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97347	1
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	0.97971	1
Var 0h	0.55963	0.311
Var 12h I row2-row1	1.07139	0.406
Var 12h NI row2-row1	0.97972	0.906
Var 36h I row2-row1	0.90891	0.805
Var 36h NI row2-row1	0.99799	1
Var 60h I row2-row1	1.23613	1
Var 60h NI row2-row1	1.09735	1
Time course 0hI-0hNI	1.11125	0.764
Time course 12hI-12hNI	1.02491	0.842
Time course 36hI-36hNI	1.04112	0.651
Time course 60hI-60hNI	1.10777	0.096

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)	0.83355	0.454
transgenic ySAMdc/azygous control (breaker)	1.49996	0.248
transgenic ySAMdc/azygous control (red)	1.41053	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97838	0.163

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.13884	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.17341	0.083
Manapal/WT (break)	0.84569	0.333
Manapal/WT (red)	0.69681	0.181