Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.19.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01937	0.876
27DAP/17DAP	1.12539	0.849
39DAP/27DAP	1.63636	0.83
41DAP/39DAP	0.96227	0.798
42DAP/41DAP	1.27557	0.871
43DAP/42DAP	1.30257	0.985
47DAP/43DAP	1.30407	0.633
52DAP/47DAP	1.417	0.67
57DAP/52DAP	1.15441	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83552	0.083
17DAP/reference	1.11848	0.22
27DAP/reference	1.22973	0.018
39DAP/reference	1.14709	0.032
41DAP/reference	1.02282	0.91
42DAP/reference	0.9701	0.151
43DAP/reference	0.9653	0.555
47DAP/reference	1.02937	0.593
52DAP/reference	0.95545	0.35
57DAP/reference	1.00817	0.984

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00246	0.871
27DAP/17DAP	1.06686	0.794
39DAP/27DAP	1.13351	0.296
41DAP/39DAP	1.0196	1
42DAP/41DAP	0.96961	0.737
43DAP/42DAP	1.06444	0.351
47DAP/43DAP	1.01979	0.95
52DAP/47DAP	0.94044	0.655
57DAP/52DAP	0.93939	0.415
57DAP/7DAP	1.17705	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13238	0.377
17DAP/reference	0.92582	0.192
27DAP/reference	0.97238	0.494
39DAP/reference	1.13389	0.333
41DAP/reference	1.13251	0.655
42DAP/reference	1.15426	0.308
43DAP/reference	1.07421	0.707
47DAP/reference	1.06516	0.647
52DAP/reference	1.21414	0.066
57DAP/reference	1.00346	0.694

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84569	0.017
17DAP/reference	0.92891	0.253
27DAP/reference	1.1276	0.23
39DAP/reference	1.12845	0.085
41DAP/reference	0.9762	0.459
42DAP/reference	1.02099	0.915
43DAP/reference	0.94981	0.459
47DAP/reference	1.00381	0.833
52DAP/reference	1.18068	0.009
57DAP/reference	0.79096	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00686	1
17DAP/reference	1.03769	0.685
27DAP/reference	1.00798	0.763
39DAP/reference	1.03456	0.691
41DAP/reference	1.02004	1
42DAP/reference	1.09303	0.433
43DAP/reference	1.21674	0.071
47DAP/reference	1.53574	0.032
52DAP/reference	1.0069	0.888
57DAP/reference	2.12945	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97706	1
26DAP/20DAP	0.90202	0.228
34DAP/26DAP	1.01446	1
51DAP/34DAP	1.13303	0.909
52DAP/51DAP	0.99065	1
53DAP/52DAP	1.02205	0.921
55DAP/53DAP	0.96634	0.735
57DAP/55DAP	1.13313	0.826
62DAP/57DAP	0.91256	0.088
68DAP/62DAP	1.18953	0.616
68DAP/14DAP	1.11839	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94797	0.115

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.00616	0.058
Mature Green Tomato/Ripe Tomato	0.45405	0.021
Immature Eggplant/Mature Eggplant	0.66468	0.063
Ripe Pepper/Ripe Tomato	1.00062	1
Mature Eggplant/Ripe Tomato	0.6654	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9817	0.503
1-1-2/M82	0.8995
12-2/M82	1.15827
12-4/M82	1.17315
1-3/M82	N/A	N/A
2-1-1/M82	1.42175
2-1/M82	N/A	N/A
2-6/M82	0.62803
3-2/M82	N/A	N/A
4-1-1/M82	0.94784
4-1/M82	0.75298
4-3-2/M82	0.82363
4-3/M82	N/A	N/A
5-3/M82	1.09392	0.467
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.29584
7-2/M82	0.99855
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	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.87319	0.71
IL1-4/WTpooled	1.10071	1
WT/WTpooled	N/A	N/A

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	1.21883	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88535	0.868
DC3000/delta hrp 6h	1.07377	1
DC3000/delta hrp 12h	0.99754	1
DC3000/delta hrp 24h	1.10076	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.98697
DC3000 delta B/DC3000 delta AB	1.14659	0.256

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1226	1
Exp 36h	0.93497	0.82
Exp 60h	0.92522	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04155	1
Var 0h	1.12607	0.325
Var 12h I row2-row1	1.10515	0.22
Var 12h NI row2-row1	1.08604	0.649
Var 36h I row2-row1	1.05187	0.368
Var 36h NI row2-row1	0.8463	0.645
Var 60h I row2-row1	0.92247	0.285
Var 60h NI row2-row1	0.87834	0.866
Time course 0hI-0hNI	1.16884	0.189
Time course 12hI-12hNI	1.29013	0.012
Time course 36hI-36hNI	1.6796	0.005
Time course 60hI-60hNI	2.06607	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)	1.02505	0.748
transgenic ySAMdc/azygous control (breaker)	1.29491	0.248
transgenic ySAMdc/azygous control (red)	1.02626	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.32568	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.35121	0.086
Manapal/WT (break)	4.46516	0.123
Manapal/WT (red)	1.72043	0.413