Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.4.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77352	0.089
27DAP/17DAP	0.85793	0.661
39DAP/27DAP	1.14457	0.755
41DAP/39DAP	0.95903	0.837
42DAP/41DAP	0.98394	1
43DAP/42DAP	0.95569	0.89
47DAP/43DAP	0.83924	0.504
52DAP/47DAP	0.94376	0.746
57DAP/52DAP	1.10402	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07072	0.403
17DAP/reference	0.92319	0.208
27DAP/reference	1.00595	0.797
39DAP/reference	0.84128	0.072
41DAP/reference	0.88814	0.201
42DAP/reference	0.98645	0.44
43DAP/reference	1.15059	0.287
47DAP/reference	0.96755	0.207
52DAP/reference	1.01389	0.73
57DAP/reference	1.06899	0.511

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8126	0.087
27DAP/17DAP	0.93661	0.748
39DAP/27DAP	1.16522	0.249
41DAP/39DAP	0.78973	0.018
42DAP/41DAP	1.42944	0.007
43DAP/42DAP	1.61985	0.019
47DAP/43DAP	0.97839	0.923
52DAP/47DAP	0.97952	0.907
57DAP/52DAP	0.90698	0.461
57DAP/7DAP	1.1704	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84884	0.062
17DAP/reference	0.92769	0.064
27DAP/reference	0.94093	0.125
39DAP/reference	0.91398	0.013
41DAP/reference	0.87597	0.09
42DAP/reference	0.84756	0.01
43DAP/reference	0.83398	0.016
47DAP/reference	1.04652	1
52DAP/reference	0.82692	0.021
57DAP/reference	0.87527	0.042

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1296	0.477
17DAP/reference	0.82516	0.089
27DAP/reference	0.91988	0.327
39DAP/reference	0.95846	0.485
41DAP/reference	1.14081	0.353
42DAP/reference	1.04226	0.759
43DAP/reference	0.92704	0.394
47DAP/reference	0.96213	0.5
52DAP/reference	0.88608	0.187
57DAP/reference	0.96251	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90143	0.135
17DAP/reference	0.91197	0.186
27DAP/reference	0.93719	0.067
39DAP/reference	0.90281	0.015
41DAP/reference	0.86648	0.05
42DAP/reference	0.95123	0.361
43DAP/reference	0.95128	0.106
47DAP/reference	0.83156	0.114
52DAP/reference	0.93828	0.376
57DAP/reference	0.90356	0.049

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1444	0.966
26DAP/20DAP	1.37825	0.265
34DAP/26DAP	0.86933	0.381
51DAP/34DAP	1.00859	0.978
52DAP/51DAP	1.07143	0.492
53DAP/52DAP	1.04348	0.91
55DAP/53DAP	0.89447	0.313
57DAP/55DAP	1.14683	0.805
62DAP/57DAP	N/A	N/A
68DAP/62DAP	0.98617	0.914
68DAP/14DAP	1.19229	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02419	0.855

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.98271	0.847
Mature Green Tomato/Ripe Tomato	1.4133
Immature Eggplant/Mature Eggplant	0.95545	0.808
Ripe Pepper/Ripe Tomato	2.08883	0.256
Mature Eggplant/Ripe Tomato	2.16824	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13466	0.742
1-1-2/M82	1.16565	1
12-2/M82	N/A	N/A
12-4/M82	1.04725	1
1-3/M82	1.09042	1
2-1-1/M82	0.73969	0.683
2-1/M82	1.04063
2-6/M82	N/A	N/A
3-2/M82	1.37928	0.463
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	1.45676	1
5-3/M82	0.92725	0.49
6-2/M82	N/A	N/A
6-3/M82	0.91688	1
7-1/M82	0.90986	1
7-2/M82	1.38483
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.21009	0.277
IL2-6/WTpooled	1.04727	0.788
IL7-5/WTpooled	1.12733	0.75
IL7-3/WTpooled	1.20136	1
IL12-4/WTpooled	0.95712	1
IL1-4/WTpooled	1.00215	1
WT/WTpooled	0.86191	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	0.84182	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01025	1
DC3000/delta hrp 6h	1.03489	0.95
DC3000/delta hrp 12h	0.90527	1
DC3000/delta hrp 24h	2.42139	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16982	0.134
DC3000 delta B/DC3000 delta AB	1.64768	0.156

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95422	1
Exp 36h	1.79936	0.693
Exp 60h	1.55225	0.563

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	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.00473	0.921
transgenic ySAMdc/azygous control (breaker)	1.07641	1
transgenic ySAMdc/azygous control (red)	1.03136	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02042	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.6543	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78273	1
Manapal/WT (break)	0.76772	0.333
Manapal/WT (red)	0.87827	0.315