Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.7.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85686	0.278
27DAP/17DAP	0.87482	0.708
39DAP/27DAP	1.04361	1
41DAP/39DAP	1.09841	0.663
42DAP/41DAP	1.24915	0.644
43DAP/42DAP	1.03239	0.937
47DAP/43DAP	1.00315	0.943
52DAP/47DAP	1.12017	0.96
57DAP/52DAP	0.9575	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90332	0.177
17DAP/reference	0.93216	0.342
27DAP/reference	1.10689	0.339
39DAP/reference	1.03389	0.639
41DAP/reference	0.96525	0.667
42DAP/reference	0.89435	0.075
43DAP/reference	1.01363	0.924
47DAP/reference	0.92438	0.065
52DAP/reference	1.00787	0.768
57DAP/reference	0.82784	0.106

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0786	0.365
27DAP/17DAP	1.00593	1
39DAP/27DAP	1.24802	0.241
41DAP/39DAP	0.95807	0.764
42DAP/41DAP	0.90388	0.292
43DAP/42DAP	1.10342	0.122
47DAP/43DAP	1.16522	0.193
52DAP/47DAP	1.03868	0.844
57DAP/52DAP	1.08482	0.504
57DAP/7DAP	1.23339	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02588	0.91
17DAP/reference	0.778	0.018
27DAP/reference	0.78941	0.01
39DAP/reference	0.8886	0.021
41DAP/reference	0.84841	0.017
42DAP/reference	0.89697	0.117
43DAP/reference	0.9579	0.183
47DAP/reference	1.03489	0.804
52DAP/reference	1.01277	1
57DAP/reference	1.01739	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87325	0.076
17DAP/reference	0.89953	0.102
27DAP/reference	0.9411	0.407
39DAP/reference	0.89042	0.159
41DAP/reference	0.94844	0.412
42DAP/reference	0.97649	0.289
43DAP/reference	1.096	0.835
47DAP/reference	0.94186	0.41
52DAP/reference	0.92403	0.239
57DAP/reference	1.06271	0.887

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92807	0.147
17DAP/reference	0.87287	0.286
27DAP/reference	0.74945	0.032
39DAP/reference	0.82924	0.04
41DAP/reference	0.86275	0.021
42DAP/reference	0.85372	0.108
43DAP/reference	0.83757	0.125
47DAP/reference	1.20343	0.07
52DAP/reference	1.16172	0.542
57DAP/reference	1.25371	0.625

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.79373	0.997
26DAP/20DAP	1.07371	0.798
34DAP/26DAP	0.8589	0.174
51DAP/34DAP	1.00344	1
52DAP/51DAP	0.83736	1
53DAP/52DAP	0.94587	0.715
55DAP/53DAP	1.14482	0.468
57DAP/55DAP	1.07493	0.854
62DAP/57DAP	1.25235	0.678
68DAP/62DAP	1.00291	0.939
68DAP/14DAP	0.93992	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.17302	0.14

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.55506	0.028
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.92735	1
Mature Eggplant/Ripe Tomato	0.65102	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92305	0.605
1-1-2/M82	1.22688	1
12-2/M82	0.98767	1
12-4/M82	0.73573	0.619
1-3/M82	1.1798	0.479
2-1-1/M82	0.84799	0.683
2-1/M82	N/A	N/A
2-6/M82	1.09019	1
3-2/M82	0.84021	0.752
4-1-1/M82	1.04871
4-1/M82	0.54306	1
4-3-2/M82	0.78857	0.698
4-3/M82	0.74549	0.611
5-3/M82	1.15296	0.455
6-2/M82	0.62401	0.497
6-3/M82	1.24026	1
7-1/M82	0.9018	0.803
7-2/M82	1.10393	1
9-3-2/M82	0.80607	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95926	1
IL2-6/WTpooled	1.12451	0.395
IL7-5/WTpooled	1.88416
IL7-3/WTpooled	1.03865	1
IL12-4/WTpooled	0.89354	1
IL1-4/WTpooled	1.07226
WT/WTpooled	0.92741	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	0.77301	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05052	0.846
DC3000/delta hrp 6h	0.31287
DC3000/delta hrp 12h	0.97226	1
DC3000/delta hrp 24h	1.01126	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11033	0.408
DC3000 delta B/DC3000 delta AB	0.98736	0.983

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98327	1
Exp 36h	1.07906	1
Exp 60h	0.8859	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98281	1
Var 0h	0.83586	1
Var 12h I row2-row1	0.96813	0.77
Var 12h NI row2-row1	0.90647	0.627
Var 36h I row2-row1	0.93701	1
Var 36h NI row2-row1	1.084	1
Var 60h I row2-row1	1.02162	1
Var 60h NI row2-row1	1.1334	0.904
Time course 0hI-0hNI	1.07237	0.719
Time course 12hI-12hNI	0.98372	0.889
Time course 36hI-36hNI	1.09848	0.013
Time course 60hI-60hNI	1.46296	0.008

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)	1.05972	0.541
transgenic ySAMdc/azygous control (breaker)	0.94648	0.49
transgenic ySAMdc/azygous control (red)	1.00525	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08827	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84483	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78048	0.172
Manapal/WT (break)	0.99875	1
Manapal/WT (red)	1.38431	0.222