Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.17.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98966	0.867
27DAP/17DAP	1.19588	0.8
39DAP/27DAP	1.55901	0.046
41DAP/39DAP	0.87109	0.503
42DAP/41DAP	1.12181	0.903
43DAP/42DAP	1.1201	1
47DAP/43DAP	1.01663	0.902
52DAP/47DAP	0.84673	0.602
57DAP/52DAP	1.16383	0.944

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97943	0.562
17DAP/reference	1.55599	0.014
27DAP/reference	1.7596	0.008
39DAP/reference	1.48282	0.042
41DAP/reference	1.80606	0.012
42DAP/reference	1.98722	0.001
43DAP/reference	1.42652	0.013
47DAP/reference	2.2732	0.001
52DAP/reference	2.3175	0.008
57DAP/reference	2.01051	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07114	0.797
27DAP/17DAP	1.45103	0.043
39DAP/27DAP	1.12634	0.441
41DAP/39DAP	0.86153	0.31
42DAP/41DAP	1.02696	1
43DAP/42DAP	1.19214	0.025
47DAP/43DAP	1.04937	0.744
52DAP/47DAP	1.13902	0.524
57DAP/52DAP	1.15981	0.335
57DAP/7DAP	1.55028	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92024	0.246
17DAP/reference	0.85478	0.021
27DAP/reference	1.05866	0.804
39DAP/reference	0.97406	0.354
41DAP/reference	1.08759	0.56
42DAP/reference	1.19732	0.046
43DAP/reference	1.17349	0.083
47DAP/reference	1.22803	0.158
52DAP/reference	1.03707	0.886
57DAP/reference	1.01083	0.831

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91678	0.441
17DAP/reference	2.01765	0.044
27DAP/reference	1.62394	0.083
39DAP/reference	1.6927	0.023
41DAP/reference	1.58585	0.011
42DAP/reference	1.74769	0.051
43DAP/reference	1.47749	0.024
47DAP/reference	1.54519	0.008
52DAP/reference	1.25726	0.223
57DAP/reference	1.11161	0.705

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91851	0.214
17DAP/reference	0.9251	0.47
27DAP/reference	0.98662	0.657
39DAP/reference	1.07617	0.203
41DAP/reference	1.05166	0.796
42DAP/reference	1.62447	0.029
43DAP/reference	1.84502	0.114
47DAP/reference	1.42399	0.02
52DAP/reference	1.25657	0.097
57DAP/reference	1.84787	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98579	1
26DAP/20DAP	1.31833	0.212
34DAP/26DAP	0.85963	0.488
51DAP/34DAP	1.30193	0.053
52DAP/51DAP	0.71991	0.151
53DAP/52DAP	1.31263	0.166
55DAP/53DAP	0.95707	0.686
57DAP/55DAP	1.04347	0.955
62DAP/57DAP	0.53935	0.003
68DAP/62DAP	0.90116	0.7
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.83679	0.097

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03211	0.063
Mature Green Tomato/Ripe Tomato	0.64553	0.025
Immature Eggplant/Mature Eggplant	1.00342	1
Ripe Pepper/Ripe Tomato	1.03373	1
Mature Eggplant/Ripe Tomato	0.7943	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92338	0.944
1-1-2/M82	1.20511	1
12-2/M82	1.08222	1
12-4/M82	1.24648	1
1-3/M82	2.25814	0.248
2-1-1/M82	1.07364	0.689
2-1/M82	0.86132	1
2-6/M82	0.95662	1
3-2/M82	1.18281	0.967
4-1-1/M82	1.12974	1
4-1/M82	1.47379
4-3-2/M82	1.41179	0.284
4-3/M82	0.95304
5-3/M82	1.00552	1
6-2/M82	1.34254	0.235
6-3/M82	1.05453	1
7-1/M82	N/A	N/A
7-2/M82	1.40925	0.385
9-3-2/M82	1.11357	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.47342	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.90244	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.35596	0.426
WT/WTpooled	N/A	N/A

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	0.97011	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14232	0.921
DC3000/delta hrp 6h	1.15949	0.392
DC3000/delta hrp 12h	1.10064	1
DC3000/delta hrp 24h	0.94052	0.598

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16071	0.27
DC3000 delta B/DC3000 delta AB	1.27827	0.154

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.29206	1
Exp 36h	0.62821	0.266
Exp 60h	1.08044	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98082	1
Var 0h	1.42977	0.98
Var 12h I row2-row1	0.96578	0.856
Var 12h NI row2-row1	1.16998	0.34
Var 36h I row2-row1	1.22248	0.309
Var 36h NI row2-row1	1.00426	1
Var 60h I row2-row1	0.79809	0.582
Var 60h NI row2-row1	0.81026	0.516
Time course 0hI-0hNI	1.09825	0.799
Time course 12hI-12hNI	1.01693	0.842
Time course 36hI-36hNI	1.08158	0.128
Time course 60hI-60hNI	1.20302	0.053

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)	0.93968	0.409
transgenic ySAMdc/azygous control (breaker)	0.75983	0.15
transgenic ySAMdc/azygous control (red)	0.93688	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01489	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.03339	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90957	1
Manapal/WT (break)	0.85071	1
Manapal/WT (red)	0.77366	0.216