Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.3.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3429	0.403
27DAP/17DAP	1.04259	1
39DAP/27DAP	0.91953	0.449
41DAP/39DAP	0.96558	0.845
42DAP/41DAP	1.31137	0.412
43DAP/42DAP	0.79286	0.467
47DAP/43DAP	1.13029	0.842
52DAP/47DAP	1.13879	0.772
57DAP/52DAP	1.32905	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75882	0.035
17DAP/reference	0.86508	0.031
27DAP/reference	1.00415	0.885
39DAP/reference	0.96045	0.541
41DAP/reference	0.84298	0.049
42DAP/reference	0.92162	0.023
43DAP/reference	0.97311	0.576
47DAP/reference	1.06806	0.391
52DAP/reference	1.13002	0.158
57DAP/reference	1.04306	0.548

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15104	0.208
27DAP/17DAP	0.94761	0.878
39DAP/27DAP	1.11611	0.623
41DAP/39DAP	1.12534	0.455
42DAP/41DAP	0.84888	0.296
43DAP/42DAP	0.89614	0.336
47DAP/43DAP	1.10794	0.674
52DAP/47DAP	0.97719	0.905
57DAP/52DAP	1.00452	1
57DAP/7DAP	0.95221

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36005	0.05
17DAP/reference	1.3101	0.147
27DAP/reference	1.27558	0.246
39DAP/reference	1.27332	0.114
41DAP/reference	1.42071	0.191
42DAP/reference	1.55906	0.03
43DAP/reference	1.18809	0.569
47DAP/reference	1.35981	0.173
52DAP/reference	1.34435	0.113
57DAP/reference	1.24622	0.061

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85376	0.164
17DAP/reference	0.8374	0.089
27DAP/reference	0.89596	0.139
39DAP/reference	1.03699	0.848
41DAP/reference	1.04995	0.657
42DAP/reference	0.88142	0.15
43DAP/reference	0.68804	0.017
47DAP/reference	0.85394	0.049
52DAP/reference	0.97166	0.351
57DAP/reference	0.88491	0.028

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44373	0.084
17DAP/reference	1.09931	0.814
27DAP/reference	1.69248	0.034
39DAP/reference	1.07327	0.912
41DAP/reference	1.57729	0.1
42DAP/reference	1.26349	0.321
43DAP/reference	1.16135	0.459
47DAP/reference	0.92857	0.357
52DAP/reference	1.11606	0.79
57DAP/reference	1.27375	0.037

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09105	0.966
26DAP/20DAP	1.05471	0.875
34DAP/26DAP	0.95424	0.927
51DAP/34DAP	0.91475	0.698
52DAP/51DAP	1.00754	1
53DAP/52DAP	0.9086	0.417
55DAP/53DAP	1.21964	0.387
57DAP/55DAP	0.93174	0.691
62DAP/57DAP	1.07235	1
68DAP/62DAP	1.88781	0.059
68DAP/14DAP	1.97933	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.49758	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.95631	0.692
Mature Green Tomato/Ripe Tomato	1.24807	0.237
Immature Eggplant/Mature Eggplant	0.69081	0.096
Ripe Pepper/Ripe Tomato	1.05745	1
Mature Eggplant/Ripe Tomato	1.20343	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12023	0.742
1-1-2/M82	0.98722
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	1.01925
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.14474	0.496
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.23073
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.75425
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.83187	0.31
IL12-4/WTpooled	0.85768	0.71
IL1-4/WTpooled	1.20553
WT/WTpooled	1.12866	0.999

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	0.97085	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94162	1
DC3000/delta hrp 6h	0.84538	0.942
DC3000/delta hrp 12h	0.96853	1
DC3000/delta hrp 24h	0.81973	0.087

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.17674

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13208	1
Exp 36h	0.79512	0.434
Exp 60h	0.87823	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.91385	1
Var 12h I row2-row1	0.99963	1
Var 12h NI row2-row1	1.09407	0.34
Var 36h I row2-row1	1.33285	0.601
Var 36h NI row2-row1	0.895	0.61
Var 60h I row2-row1	1.5265
Var 60h NI row2-row1	0.95496	0.977
Time course 0hI-0hNI	0.94989	0.522
Time course 12hI-12hNI	0.92128	0.255
Time course 36hI-36hNI	1.06937	0.248
Time course 60hI-60hNI	1.02393	0.673

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)	1.06	0.347
transgenic ySAMdc/azygous control (breaker)	1.04169	1
transgenic ySAMdc/azygous control (red)	0.90834	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06449	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.12167	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.74325	0.172
Manapal/WT (break)	0.99792	1
Manapal/WT (red)	1.16618	0.413