Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.18.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15549	0.646
27DAP/17DAP	1.26894	0.746
39DAP/27DAP	0.91114	0.641
41DAP/39DAP	1.06535	0.844
42DAP/41DAP	0.89254	1
43DAP/42DAP	0.97856	0.925
47DAP/43DAP	1.17074	0.444
52DAP/47DAP	1.08494	1
57DAP/52DAP	1.39979	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89079	0.068
17DAP/reference	0.84148	0.01
27DAP/reference	0.86082	0.04
39DAP/reference	0.90905	0.184
41DAP/reference	0.8515	0.049
42DAP/reference	0.84299	0.003
43DAP/reference	1.03886	0.596
47DAP/reference	0.90667	0.004
52DAP/reference	0.94961	0.177
57DAP/reference	1.09207	0.332

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01985	0.801
27DAP/17DAP	1.04096	0.9
39DAP/27DAP	1.21323	0.209
41DAP/39DAP	1.01771	1
42DAP/41DAP	1.01248	0.932
43DAP/42DAP	1.145	0.273
47DAP/43DAP	1.02534	0.93
52DAP/47DAP	0.9815	0.917
57DAP/52DAP	1.4163	0.051
57DAP/7DAP	1.48963	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2716	0.066
17DAP/reference	1.2529	0.18
27DAP/reference	1.05442	0.614
39DAP/reference	1.32414	0.04
41DAP/reference	1.60171	0.015
42DAP/reference	1.50942	0.021
43DAP/reference	1.71317	0.007
47DAP/reference	1.09043	0.549
52DAP/reference	1.57275	0.009
57DAP/reference	1.46486	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93151	0.248
17DAP/reference	0.84695	0.077
27DAP/reference	0.8985	0.119
39DAP/reference	0.83342	0.054
41DAP/reference	0.99117	0.557
42DAP/reference	0.85127	0.061
43DAP/reference	0.90537	0.217
47DAP/reference	0.91201	0.075
52DAP/reference	0.9508	0.072
57DAP/reference	1.01623	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11034	0.493
17DAP/reference	1.12405	0.689
27DAP/reference	1.24451	0.033
39DAP/reference	1.26509	0.218
41DAP/reference	1.31626	0.034
42DAP/reference	1.08635	0.6
43DAP/reference	1.06895	0.923
47DAP/reference	1.0132	1
52DAP/reference	1.56085	0.097
57DAP/reference	1.16666	0.57

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01219	1
26DAP/20DAP	0.91013	1
34DAP/26DAP	0.97015	0.909
51DAP/34DAP	1.18872	0.241
52DAP/51DAP	0.9158	1
53DAP/52DAP	1.04846	0.768
55DAP/53DAP	1.15374	0.261
57DAP/55DAP	1.00417	1
62DAP/57DAP	1.10535	0.515
68DAP/62DAP	1.07338	0.899
68DAP/14DAP	1.32491	0.419

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97715	0.607

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.67491	0.178
Mature Green Tomato/Ripe Tomato	1.07215	1
Immature Eggplant/Mature Eggplant	1.95799	0.069
Ripe Pepper/Ripe Tomato	0.9027	1
Mature Eggplant/Ripe Tomato	0.62219	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85216	0.944
1-1-2/M82	1.0833	1
12-2/M82	0.90431	0.955
12-4/M82	1.26217
1-3/M82	0.74555	0.376
2-1-1/M82	0.77251	0.784
2-1/M82	0.95712
2-6/M82	1.12449	0.695
3-2/M82	0.92902	1
4-1-1/M82	1.07732	1
4-1/M82	1.34303
4-3-2/M82	0.91509
4-3/M82	0.82759
5-3/M82	0.91766	0.49
6-2/M82	1.0124
6-3/M82	0.97325	1
7-1/M82	0.93269
7-2/M82	1.05198	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.72764	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.05236	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.72834
IL1-4/WTpooled	0.96134	1
WT/WTpooled	1.05174	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	1.08584	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02291	0.921
DC3000/delta hrp 6h	1.09225	1
DC3000/delta hrp 12h	1.73948	1
DC3000/delta hrp 24h	1.03803	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.52786	0.121
DC3000 delta B/DC3000 delta AB	1.07975	0.479

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93681	1
Exp 36h	1.15594	0.693
Exp 60h	0.99313	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99184	1
Var 0h	0.97513	1
Var 12h I row2-row1	1.14187	0.222
Var 12h NI row2-row1	0.88665	0.713
Var 36h I row2-row1	0.91298	0.805
Var 36h NI row2-row1	2.02146	1
Var 60h I row2-row1	1.06576	1
Var 60h NI row2-row1	0.97314	1
Time course 0hI-0hNI	1.01786	0.867
Time course 12hI-12hNI	1.08618	0.222
Time course 36hI-36hNI	1.18812	0.005
Time course 60hI-60hNI	2.03119	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)	1.20504	0.325
transgenic ySAMdc/azygous control (breaker)	0.87734	0.49
transgenic ySAMdc/azygous control (red)	0.76895	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01664	0.556

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.00804	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84137	0.172
Manapal/WT (break)	0.87778	1
Manapal/WT (red)	0.73256	0.184