Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.19.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.64345	0.281
27DAP/17DAP	2.00076	0.332
39DAP/27DAP	1.06863	0.927
41DAP/39DAP	1.01361	0.854
42DAP/41DAP	1.18575	0.941
43DAP/42DAP	1.04575	0.932
47DAP/43DAP	1.18657	0.647
52DAP/47DAP	0.78606	0.545
57DAP/52DAP	1.61486	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95646	0.455
17DAP/reference	0.90259	0.342
27DAP/reference	0.91158	0.208
39DAP/reference	1.0024	0.941
41DAP/reference	0.80112	0.049
42DAP/reference	0.96341	0.295
43DAP/reference	1.02923	1
47DAP/reference	1.00844	0.72
52DAP/reference	1.33646	0.121
57DAP/reference	1.03355	0.952

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88943	0.245
27DAP/17DAP	1.37993	0.068
39DAP/27DAP	1.13624	0.285
41DAP/39DAP	0.68004	0.064
42DAP/41DAP	1.43976	0.003
43DAP/42DAP	1.29736	0.013
47DAP/43DAP	0.8391	0.15
52DAP/47DAP	0.98867	0.93
57DAP/52DAP	0.75122	0.144
57DAP/7DAP	1.35564	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13475	0.705
17DAP/reference	1.00141	0.599
27DAP/reference	0.85307	0.035
39DAP/reference	1.32807	0.008
41DAP/reference	1.06354	0.918
42DAP/reference	1.02834	0.791
43DAP/reference	1.31543	0.093
47DAP/reference	0.84855	0.168
52DAP/reference	1.04476	1
57DAP/reference	1.15885	0.214

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94243	0.518
17DAP/reference	0.97051	0.576
27DAP/reference	0.93696	0.269
39DAP/reference	1.04447	0.868
41DAP/reference	1.10866	0.587
42DAP/reference	0.897	0.189
43DAP/reference	0.96906	0.516
47DAP/reference	0.82467	0.026
52DAP/reference	0.9299	0.302
57DAP/reference	1.12184	0.771

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13188	0.153
17DAP/reference	0.96084	0.592
27DAP/reference	1.04297	1
39DAP/reference	0.9855	0.693
41DAP/reference	1.10845	0.486
42DAP/reference	1.21934	0.265
43DAP/reference	1.19763	0.403
47DAP/reference	0.85157	0.093
52DAP/reference	1.30008	0.289
57DAP/reference	1.40032	0.058

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89945	1
26DAP/20DAP	1.345	1
34DAP/26DAP	1.45148	0.819
51DAP/34DAP	3.69722
52DAP/51DAP	1.26845	0.708
53DAP/52DAP	1.03315	1
55DAP/53DAP	1.18037	0.876
57DAP/55DAP	0.92747	0.703
62DAP/57DAP	1.01176	1
68DAP/62DAP	0.74626	0.464
68DAP/14DAP	1.04442	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	6.66675	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.08557	0.898
Immature Eggplant/Mature Eggplant	1.43413
Ripe Pepper/Ripe Tomato	0.16804	0.293
Mature Eggplant/Ripe Tomato	0.24772	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	1.09145	1
12-4/M82	1.46181	0.655
1-3/M82	1.78948
2-1-1/M82	1.43191	0.457
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.82323
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.0983	1
4-3/M82	2.39568
5-3/M82	1.09213
6-2/M82	1.46136
6-3/M82	1.31662	1
7-1/M82	1.12739
7-2/M82	1.34281
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.84533
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.91029
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.0214	1
WT/WTpooled	0.8557	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	0.80142	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04303	1
DC3000/delta hrp 6h	0.89383	0.95
DC3000/delta hrp 12h	1.18937	1
DC3000/delta hrp 24h	1.00302	1

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	1.08299	0.655

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03199	1
Exp 36h	1.58868	1
Exp 60h	1.25435	0.215

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01665	1
Var 0h	0.84767	0.936
Var 12h I row2-row1	1.06892	0.58
Var 12h NI row2-row1	1.1085	1
Var 36h I row2-row1	1.32308	0.601
Var 36h NI row2-row1	1.33267	0.253
Var 60h I row2-row1	0.89274	0.293
Var 60h NI row2-row1	1.0153	1
Time course 0hI-0hNI	1.37792	0.085
Time course 12hI-12hNI	0.97678	0.882
Time course 36hI-36hNI	0.89879	0.29
Time course 60hI-60hNI	1.01354	1

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)	1.05254	0.612
transgenic ySAMdc/azygous control (breaker)	0.92488	1
transgenic ySAMdc/azygous control (red)	0.97666	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98105	0.343

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.822	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95048	1
Manapal/WT (break)	0.7266	1
Manapal/WT (red)	1.00163	0.863