Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.15.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27724	0.477
27DAP/17DAP	1.61409	0.767
39DAP/27DAP	0.94797	0.663
41DAP/39DAP	1.38654	0.37
42DAP/41DAP	0.9357	1
43DAP/42DAP	1.20332	0.867
47DAP/43DAP	1.14392	0.909
52DAP/47DAP	1.04147	0.913
57DAP/52DAP	1.05297	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13802	0.29
17DAP/reference	1.05382	0.294
27DAP/reference	1.03118	0.435
39DAP/reference	1.05156	0.197
41DAP/reference	1.06308	0.421
42DAP/reference	1.13518	0.039
43DAP/reference	1.01487	0.73
47DAP/reference	1.06618	0.254
52DAP/reference	1.01298	0.991
57DAP/reference	1.01613	0.876

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88069	0.201
27DAP/17DAP	0.9999	0.969
39DAP/27DAP	1.09465	0.615
41DAP/39DAP	1.11803	0.895
42DAP/41DAP	0.88995	0.347
43DAP/42DAP	1.14417	0.25
47DAP/43DAP	1.01095	0.973
52DAP/47DAP	1.0059	0.982
57DAP/52DAP	0.95816	0.612
57DAP/7DAP	1.26948	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87542	0.062
17DAP/reference	0.85062	0.014
27DAP/reference	0.87885	0.013
39DAP/reference	0.87926	0.013
41DAP/reference	0.78147	0.017
42DAP/reference	0.84679	0.095
43DAP/reference	0.72616	0.016
47DAP/reference	0.86432	0.293
52DAP/reference	0.73799	0.023
57DAP/reference	0.7164	0.015

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1772	0.09
17DAP/reference	1.35346	0.086
27DAP/reference	1.12568	0.352
39DAP/reference	1.10382	0.489
41DAP/reference	1.22264	0.277
42DAP/reference	1.12177	0.247
43DAP/reference	1.35685	0.111
47DAP/reference	1.10801	0.225
52DAP/reference	1.19462	0.106
57DAP/reference	1.24898	0.045

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92658	0.23
17DAP/reference	1.0123	0.988
27DAP/reference	0.8787	0.048
39DAP/reference	0.87551	0.058
41DAP/reference	0.89158	0.025
42DAP/reference	0.98332	0.671
43DAP/reference	0.89454	0.038
47DAP/reference	0.97185	0.494
52DAP/reference	0.82569	0.158
57DAP/reference	0.82454	0.102

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02674	1
26DAP/20DAP	0.88822	0.512
34DAP/26DAP	1.09227	1
51DAP/34DAP	0.94396	0.563
52DAP/51DAP	1.03414	0.808
53DAP/52DAP	1.07829	0.738
55DAP/53DAP	1.03253	1
57DAP/55DAP	1.18974	0.376
62DAP/57DAP	0.93782	0.681
68DAP/62DAP	0.80407	0.406
68DAP/14DAP	0.84211	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.76056	0.052

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.72018	0.132
Immature Eggplant/Mature Eggplant	1.32829	0.398
Ripe Pepper/Ripe Tomato	0.47527	0.293
Mature Eggplant/Ripe Tomato	0.93526	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05018	1
1-1-2/M82	0.91351	0.958
12-2/M82	1.15884	0.421
12-4/M82	1.0619	0.694
1-3/M82	1.02583	1
2-1-1/M82	1.1229
2-1/M82	N/A	N/A
2-6/M82	1.0086	1
3-2/M82	0.57549	0.752
4-1-1/M82	1.00428	1
4-1/M82	1.39912	0.853
4-3-2/M82	0.79834
4-3/M82	1.03611
5-3/M82	0.96284	1
6-2/M82	0.8298
6-3/M82	0.98683	1
7-1/M82	1.04558	1
7-2/M82	1.08212	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92255	0.321
IL2-6/WTpooled	0.75057	1
IL7-5/WTpooled	1.07834	0.792
IL7-3/WTpooled	0.82412	0.294
IL12-4/WTpooled	1.15602	0.595
IL1-4/WTpooled	0.89639	0.562
WT/WTpooled	1.14412	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	1.26124	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99347	1
DC3000/delta hrp 6h	1.46561	0.857
DC3000/delta hrp 12h	0.96566	1
DC3000/delta hrp 24h	1.01426	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09289	0.556
DC3000 delta B/DC3000 delta AB	1.11691	0.363

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81168	0.265
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98157	1
Var 0h	1.16905	0.98
Var 12h I row2-row1	1.28192	0.443
Var 12h NI row2-row1	0.869	0.713
Var 36h I row2-row1	0.99824	1
Var 36h NI row2-row1	1.02651	1
Var 60h I row2-row1	1.03106	1
Var 60h NI row2-row1	1.00911	1
Time course 0hI-0hNI	1.14116	0.603
Time course 12hI-12hNI	1.12321	0.347
Time course 36hI-36hNI	1.62072	0.005
Time course 60hI-60hNI	3.40494	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)	0.90966	0.362
transgenic ySAMdc/azygous control (breaker)	1.24832	0.248
transgenic ySAMdc/azygous control (red)	1.13825	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9365	0.097

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.3247	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.01689	1
Manapal/WT (red)	0.81493	0.181