Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.3.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08282	0.681
27DAP/17DAP	0.99463	1
39DAP/27DAP	1.03502	1
41DAP/39DAP	1.09436	0.728
42DAP/41DAP	0.98423	1
43DAP/42DAP	1.09829	1
47DAP/43DAP	1.00589	0.902
52DAP/47DAP	1.05472	0.906
57DAP/52DAP	1.16153	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90762	0.2
17DAP/reference	1.05411	0.27
27DAP/reference	0.96293	0.444
39DAP/reference	0.92098	0.261
41DAP/reference	1.03544	0.587
42DAP/reference	0.86709	0.005
43DAP/reference	1.01432	0.957
47DAP/reference	0.9408	0.09
52DAP/reference	0.87296	0.065
57DAP/reference	0.82347	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02594	1
27DAP/17DAP	1.01895	0.951
39DAP/27DAP	1.00058	1
41DAP/39DAP	1.01443	0.909
42DAP/41DAP	0.86781	0.247
43DAP/42DAP	1.1065	0.382
47DAP/43DAP	1.03646	0.848
52DAP/47DAP	1.06249	0.779
57DAP/52DAP	0.99299	0.875
57DAP/7DAP	1.18801	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84222	0.095
17DAP/reference	0.82536	0.064
27DAP/reference	0.84695	0.303
39DAP/reference	0.7527	0.027
41DAP/reference	0.98795	0.677
42DAP/reference	1.02355	0.828
43DAP/reference	0.94644	0.321
47DAP/reference	0.83658	0.101
52DAP/reference	1.03277	0.636
57DAP/reference	0.96968	0.426

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88168	0.14
17DAP/reference	0.90488	0.129
27DAP/reference	0.79778	0.048
39DAP/reference	0.82426	0.015
41DAP/reference	0.87057	0.073
42DAP/reference	0.85942	0.037
43DAP/reference	0.72999	0.033
47DAP/reference	0.87567	0.012
52DAP/reference	0.84358	0.005
57DAP/reference	0.83436	0.026

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96636	0.566
17DAP/reference	1.1465	0.289
27DAP/reference	1.0737	0.805
39DAP/reference	1.05941	0.836
41DAP/reference	1.07218	0.867
42DAP/reference	1.06712	0.943
43DAP/reference	1.06205	0.858
47DAP/reference	0.83806	0.007
52DAP/reference	0.99943	0.718
57DAP/reference	0.67536	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04243	0.966
26DAP/20DAP	1.01771	1
34DAP/26DAP	1.01057	1
51DAP/34DAP	1.20599	0.121
52DAP/51DAP	1.01944	0.925
53DAP/52DAP	1.02048	0.935
55DAP/53DAP	1.12019	0.764
57DAP/55DAP	1.05685	0.906
62DAP/57DAP	0.95123	0.994
68DAP/62DAP	1.07079	0.914
68DAP/14DAP	1.12181	0.636

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.08307	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.22668	0.059
Mature Green Tomato/Ripe Tomato	1.10441	0.881
Immature Eggplant/Mature Eggplant	0.74046	0.084
Ripe Pepper/Ripe Tomato	1.23163	1
Mature Eggplant/Ripe Tomato	1.05522

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99004	1
1-1-2/M82	0.97491	1
12-2/M82	1.0583	1
12-4/M82	1.23876
1-3/M82	0.72762	0.378
2-1-1/M82	0.80092
2-1/M82	N/A	N/A
2-6/M82	1.32162	0.505
3-2/M82	0.76942
4-1-1/M82	N/A	N/A
4-1/M82	0.74901
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.93522	1
6-2/M82	1.13407
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.03047
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86515	0.321
IL2-6/WTpooled	1.06689	0.584
IL7-5/WTpooled	0.83029	1
IL7-3/WTpooled	1.14213	1
IL12-4/WTpooled	1.12981	0.839
IL1-4/WTpooled	1.0023	1
WT/WTpooled	0.99122	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	1.11684	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.8925	1
DC3000/delta hrp 6h	0.91324	0.95
DC3000/delta hrp 12h	1.08319	1
DC3000/delta hrp 24h	0.87372	0.202

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.8341	0.059
DC3000 delta B/DC3000 delta AB	1.16117	0.311

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10136	1
Exp 36h	1.00704	1
Exp 60h	0.85387	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00906	1
Var 0h	0.43417	0.933
Var 12h I row2-row1	0.94509	0.77
Var 12h NI row2-row1	1.56065	0.34
Var 36h I row2-row1	1.29607	0.601
Var 36h NI row2-row1	0.44764	0.432
Var 60h I row2-row1	1.86257	0.562
Var 60h NI row2-row1	0.7084	0.458
Time course 0hI-0hNI	1.09894	0.833
Time course 12hI-12hNI	1.02738	1
Time course 36hI-36hNI	2.17765	0.005
Time course 60hI-60hNI	4.77268	0.01

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)	1.03683	0.798
transgenic ySAMdc/azygous control (breaker)	1.5463	0.161
transgenic ySAMdc/azygous control (red)	0.90297	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90673	0.214

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.453	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.82558	0.083
Manapal/WT (break)	2.47084	0.123
Manapal/WT (red)	1.1747	1