Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.14.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.40502	0.281
27DAP/17DAP	1.37556	0.693
39DAP/27DAP	1.426	0.305
41DAP/39DAP	0.60871	0.059
42DAP/41DAP	0.62032	0.774
43DAP/42DAP	0.78824	0.639
47DAP/43DAP	1.13635	0.481
52DAP/47DAP	0.84431	0.595
57DAP/52DAP	1.1828	0.883

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41059	0.049
17DAP/reference	1.47048	0.059
27DAP/reference	1.72041	0.035
39DAP/reference	1.56761	0.035
41DAP/reference	2.01513	0.012
42DAP/reference	0.90775	0.019
43DAP/reference	0.97546	0.653
47DAP/reference	1.13663	0.182
52DAP/reference	1.06945	0.695
57DAP/reference	1.20269	0.029

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.81724	0.038
27DAP/17DAP	1.67562	0.045
39DAP/27DAP	0.93366	0.737
41DAP/39DAP	1.6634	0.868
42DAP/41DAP	0.92217	0.486
43DAP/42DAP	0.6837	0.041
47DAP/43DAP	0.76571	0.016
52DAP/47DAP	1.35986	0.34
57DAP/52DAP	1.23661	0.308
57DAP/7DAP	1.50146	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29242	0.093
17DAP/reference	1.01508	1
27DAP/reference	1.18566	0.197
39DAP/reference	1.17478	0.12
41DAP/reference	1.18894	0.097
42DAP/reference	1.28083	0.174
43DAP/reference	0.94692	0.368
47DAP/reference	1.80646	0.045
52DAP/reference	1.07235	0.599
57DAP/reference	0.85316	0.077

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18074	0.206
17DAP/reference	1.13715	0.139
27DAP/reference	2.53738	0.012
39DAP/reference	2.26372	0.011
41DAP/reference	1.33702	0.005
42DAP/reference	2.57447	0.007
43DAP/reference	1.39398	0.099
47DAP/reference	1.75531	0.012
52DAP/reference	2.39369	0.006
57DAP/reference	0.98747	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96722	0.455
17DAP/reference	0.93229	0.281
27DAP/reference	1.04104	0.903
39DAP/reference	1.08153	0.296
41DAP/reference	1.03609	0.916
42DAP/reference	1.05509	0.635
43DAP/reference	0.80281	0.054
47DAP/reference	0.75544	0.049
52DAP/reference	0.91847	0.464
57DAP/reference	1.7494	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20591	0.786
26DAP/20DAP	2.24185	0.099
34DAP/26DAP	0.6473	0.141
51DAP/34DAP	0.51209	0.058
52DAP/51DAP	1.29481	0.154
53DAP/52DAP	1.14369	0.688
55DAP/53DAP	0.82114	0.14
57DAP/55DAP	1.34522	0.249
62DAP/57DAP	1.20762	0.8
68DAP/62DAP	1.19369	1
68DAP/14DAP	1.95572	0.024

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.96905	0.034

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.1237	0.068
Mature Green Tomato/Ripe Tomato	4.45857	0.086
Immature Eggplant/Mature Eggplant	0.82627	0.1
Ripe Pepper/Ripe Tomato	1.08322	1
Mature Eggplant/Ripe Tomato	2.88894	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.84022	0.616
1-1-2/M82	0.97779	1
12-2/M82	0.87617	0.721
12-4/M82	0.83944	0.268
1-3/M82	1.27244	0.479
2-1-1/M82	1.10084	1
2-1/M82	0.79418	0.74
2-6/M82	0.64841	0.501
3-2/M82	1.06088
4-1-1/M82	0.92219	1
4-1/M82	0.96883
4-3-2/M82	0.56872	0.698
4-3/M82	0.86204	0.72
5-3/M82	0.98459	1
6-2/M82	0.86893	1
6-3/M82	1.00989	1
7-1/M82	1.34704	0.539
7-2/M82	0.77045	0.57
9-3-2/M82	0.80053	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.88868	1
IL1-4/WTpooled	1.04695
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	0.84997	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10438	0.75
DC3000/delta hrp 6h	1.33058	1
DC3000/delta hrp 12h	1.1126	1
DC3000/delta hrp 24h	2.42534	0.023

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95086	0.568
DC3000 delta B/DC3000 delta AB	0.91863	0.418

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0984	1
Exp 36h	1.08693	1
Exp 60h	0.94606	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04505	1
Var 0h	1.56011	0.936
Var 12h I row2-row1	1.54056	0.544
Var 12h NI row2-row1	1.07295	0.34
Var 36h I row2-row1	0.90825	1
Var 36h NI row2-row1	1.47699	1
Var 60h I row2-row1	0.76428	0.292
Var 60h NI row2-row1	1.04952	0.904
Time course 0hI-0hNI	1.03869	0.852
Time course 12hI-12hNI	1.04421	0.867
Time course 36hI-36hNI	0.86374	0.042
Time course 60hI-60hNI	0.92781	0.319

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)	1.08692	0.798
transgenic ySAMdc/azygous control (breaker)	0.59469	0.132
transgenic ySAMdc/azygous control (red)	0.83757	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.35412	0.223

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74098	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98222	1
Manapal/WT (break)	0.71949	0.297
Manapal/WT (red)	1.22589	0.222