Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.7.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22412	0.588
27DAP/17DAP	1.26331	0.845
39DAP/27DAP	1.31434	0.444
41DAP/39DAP	0.78911	0.281
42DAP/41DAP	1.66161	0.481
43DAP/42DAP	0.79614	0.454
47DAP/43DAP	0.93903	0.746
52DAP/47DAP	0.93381	0.783
57DAP/52DAP	1.10167	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00426	0.756
17DAP/reference	1.11906	0.185
27DAP/reference	1.01509	1
39DAP/reference	1.12822	0.486
41DAP/reference	1.0982	0.093
42DAP/reference	0.91799	0.103
43DAP/reference	0.95062	0.448
47DAP/reference	0.92756	0.174
52DAP/reference	1.0039	0.749
57DAP/reference	1.10716	0.433

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.66218	0.164
27DAP/17DAP	1.09755	0.699
39DAP/27DAP	1.16946	0.3
41DAP/39DAP	1.25524	0.393
42DAP/41DAP	0.91066	0.365
43DAP/42DAP	0.89517	0.28
47DAP/43DAP	1.09294	0.234
52DAP/47DAP	1.06046	0.804
57DAP/52DAP	0.87089	0.324
57DAP/7DAP	1.17464	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01286	1
17DAP/reference	0.89345	0.167
27DAP/reference	1.25211	0.551
39DAP/reference	0.95291	0.354
41DAP/reference	1.07977	0.977
42DAP/reference	0.86866	0.151
43DAP/reference	0.8744	0.151
47DAP/reference	1.02522	1
52DAP/reference	1.20128	0.066
57DAP/reference	1.10783	0.468

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06126	0.712
17DAP/reference	0.9686	0.434
27DAP/reference	1.11813	0.265
39DAP/reference	1.13934	0.556
41DAP/reference	0.95534	0.373
42DAP/reference	0.98497	0.594
43DAP/reference	0.75775	0.017
47DAP/reference	1.0035	0.77
52DAP/reference	0.9552	0.407
57DAP/reference	0.94091	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09287	0.06
17DAP/reference	1.22432	0.179
27DAP/reference	1.47022
39DAP/reference	1.03423	0.578
41DAP/reference	1.13316	0.383
42DAP/reference	1.27017	0.06
43DAP/reference	1.21199	0.275
47DAP/reference	0.99032	0.61
52DAP/reference	0.97615	0.821
57DAP/reference	1.23391	0.187

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95183	1
26DAP/20DAP	1.2324	0.558
34DAP/26DAP	0.86255	0.575
51DAP/34DAP	1.41322	0.084
52DAP/51DAP	0.89834	1
53DAP/52DAP	1.22353	0.458
55DAP/53DAP	0.80179	0.293
57DAP/55DAP	1.18722	0.745
62DAP/57DAP	1.45529	0.158
68DAP/62DAP	1.57041	0.597
68DAP/14DAP	1.10724	0.295

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.17747	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.29562	0.113
Mature Green Tomato/Ripe Tomato	1.02175	1
Immature Eggplant/Mature Eggplant	0.76325	0.159
Ripe Pepper/Ripe Tomato	1.3946	1
Mature Eggplant/Ripe Tomato	0.70186	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0656	0.742
1-1-2/M82	1.27114	1
12-2/M82	0.90751	0.955
12-4/M82	1.25262	1
1-3/M82	N/A	N/A
2-1-1/M82	1.09585	0.689
2-1/M82	0.75694	0.74
2-6/M82	1.15743
3-2/M82	1.23272
4-1-1/M82	0.59492	1
4-1/M82	N/A	N/A
4-3-2/M82	1.15892	0.508
4-3/M82	1.58706	1
5-3/M82	1.19629	0.572
6-2/M82	1.25682
6-3/M82	1.94883
7-1/M82	1.23515
7-2/M82	1.08001	0.385
9-3-2/M82	1.16545	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.71987
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.1059	1
IL12-4/WTpooled	1.0614	1
IL1-4/WTpooled	1.28919
WT/WTpooled	0.87781	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	0.99871	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0857	0.921
DC3000/delta hrp 6h	1.17229	1
DC3000/delta hrp 12h	0.83246	1
DC3000/delta hrp 24h	0.88167	0.43

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.18658	0.476
DC3000 delta B/DC3000 delta AB	2.07636	0.081

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.64697	1
Exp 36h	0.66203	0.539
Exp 60h	0.75632	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.018	1
Var 0h	1.03521	1
Var 12h I row2-row1	1.08272	0.272
Var 12h NI row2-row1	1.31014	0.281
Var 36h I row2-row1	1.14732	0.908
Var 36h NI row2-row1	0.84344	0.706
Var 60h I row2-row1	0.73217	0.285
Var 60h NI row2-row1	0.75527	0.38
Time course 0hI-0hNI	1.0352	0.852
Time course 12hI-12hNI	1.23417	0.058
Time course 36hI-36hNI	1.99612	0.005
Time course 60hI-60hNI	4.82053	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)	0.95505	0.529
transgenic ySAMdc/azygous control (breaker)	1.12679	0.248
transgenic ySAMdc/azygous control (red)	1.11858	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11568	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.12237	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.23963	0.096
Manapal/WT (break)	0.99973	1
Manapal/WT (red)	1.38869	0.222