Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.2.16.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10186	0.561
27DAP/17DAP	0.9379	0.892
39DAP/27DAP	1.04684	1
41DAP/39DAP	1.2546	0.437
42DAP/41DAP	1.16383	0.873
43DAP/42DAP	0.99154	0.937
47DAP/43DAP	0.88397	0.603
52DAP/47DAP	1.48171	0.401
57DAP/52DAP	0.8027	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94319	0.326
17DAP/reference	1.06262	0.239
27DAP/reference	0.94236	0.304
39DAP/reference	0.94704	0.254
41DAP/reference	1.07929	0.158
42DAP/reference	0.86077	0.011
43DAP/reference	1.03243	0.812
47DAP/reference	0.8996	0.004
52DAP/reference	0.89376	0.06
57DAP/reference	0.84127	0.049

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99394	0.847
27DAP/17DAP	1.14463	0.65
39DAP/27DAP	1.11394	0.505
41DAP/39DAP	0.9558	0.893
42DAP/41DAP	1.1	0.425
43DAP/42DAP	1.11807	0.23
47DAP/43DAP	1.0814	0.61
52DAP/47DAP	1.02573	0.915
57DAP/52DAP	1.10464	0.574
57DAP/7DAP	1.08847	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86721	0.115
17DAP/reference	0.86671	0.02
27DAP/reference	0.84283	0.016
39DAP/reference	0.93728	0.064
41DAP/reference	0.84188	0.032
42DAP/reference	0.87749	0.01
43DAP/reference	0.84391	0.016
47DAP/reference	0.99432	1
52DAP/reference	0.8792	0.115
57DAP/reference	0.86957	0.041

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14138	0.258
17DAP/reference	0.95685	0.378
27DAP/reference	0.85835	0.035
39DAP/reference	0.95089	0.235
41DAP/reference	0.8558	0.042
42DAP/reference	0.79267	0.042
43DAP/reference	1.07678	0.457
47DAP/reference	0.83665	0.012
52DAP/reference	0.96441	0.22
57DAP/reference	1.04778	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87521	0.087
17DAP/reference	0.97485	0.624
27DAP/reference	0.83993	0.025
39DAP/reference	0.87568	0.033
41DAP/reference	0.8948	0.086
42DAP/reference	0.87576	0.071
43DAP/reference	0.83897	0.043
47DAP/reference	0.976	0.494
52DAP/reference	0.89645	0.334
57DAP/reference	0.80399	0.035

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00014	1
26DAP/20DAP	1.00105	1
34DAP/26DAP	0.91187	0.783
51DAP/34DAP	0.888	0.482
52DAP/51DAP	0.98399	1
53DAP/52DAP	0.92991	0.684
55DAP/53DAP	1.25021	0.387
57DAP/55DAP	0.92812	0.698
62DAP/57DAP	1.29141	0.01
68DAP/62DAP	0.79589	0.087
68DAP/14DAP	0.94616	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97572	0.607

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.94962	0.618
Mature Green Tomato/Ripe Tomato	1.2031	0.237
Immature Eggplant/Mature Eggplant	1.30944	0.056
Ripe Pepper/Ripe Tomato	0.50147	0.293
Mature Eggplant/Ripe Tomato	1.67028	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09858	0.877
1-1-2/M82	0.93463	1
12-2/M82	0.9521	0.955
12-4/M82	1.06422	N/A
1-3/M82	0.77918	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.98561	0.223
3-2/M82	0.73839	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.95481	1
4-3/M82	1.02264	1
5-3/M82	0.90103	0.642
6-2/M82	N/A	N/A
6-3/M82	1.20206	N/A
7-1/M82	0.85619	N/A
7-2/M82	1.01186	1
9-3-2/M82	0.82243	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.14654	N/A
IL2-6/WTpooled	0.88463	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.01813	1
IL12-4/WTpooled	1.05728	0.891
IL1-4/WTpooled	1.06598	1
WT/WTpooled	0.90776	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	1.04116	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99983	1
DC3000/delta hrp 6h	0.99983	0.95
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.92491	0.285

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.69783	0.063
DC3000 delta B/DC3000 delta AB	1.07916	0.472

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88431	1
Exp 36h	1.31359	1
Exp 60h	1.37533	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01322	1
Var 0h	0.76941	1
Var 12h I row2-row1	1.05053	0.58
Var 12h NI row2-row1	0.87996	0.488
Var 36h I row2-row1	0.76637	1
Var 36h NI row2-row1	1.05648	1
Var 60h I row2-row1	1.16056	0.562
Var 60h NI row2-row1	1.19185	0.904
Time course 0hI-0hNI	1.06556	0.719
Time course 12hI-12hNI	1.02344	0.803
Time course 36hI-36hNI	1.05267	0.248
Time course 60hI-60hNI	1.09928	0.216

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)	1.05294	0.318
transgenic ySAMdc/azygous control (breaker)	0.92002	0.251
transgenic ySAMdc/azygous control (red)	1.0151	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03229	0.194

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.80969	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.81036	0.172
Manapal/WT (break)	0.7793	0.333
Manapal/WT (red)	0.85965	0.36