Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.3.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70585	0.073
27DAP/17DAP	0.83939	0.363
39DAP/27DAP	0.98813	0.733
41DAP/39DAP	1.29379	0.268
42DAP/41DAP	1.14958	0.873
43DAP/42DAP	1.16474	0.91
47DAP/43DAP	1.59085	0.191
52DAP/47DAP	0.99031	0.92
57DAP/52DAP	1.07384	0.964

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12585	0.9
17DAP/reference	0.89203	0.342
27DAP/reference	0.97943	0.642
39DAP/reference	1.00882	0.747
41DAP/reference	0.96169	0.667
42DAP/reference	0.77155	0.023
43DAP/reference	0.90347
47DAP/reference	1.01454	1
52DAP/reference	0.73724	0.065
57DAP/reference	1.12565

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95812	0.526
27DAP/17DAP	1.07744	0.685
39DAP/27DAP	1.04829	0.643
41DAP/39DAP	0.97191	0.945
42DAP/41DAP	0.96061	0.679
43DAP/42DAP	1.09282	0.25
47DAP/43DAP	0.96412	0.764
52DAP/47DAP	1.00903	0.986
57DAP/52DAP	0.94105	0.466
57DAP/7DAP	1.02132	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91586	0.326
17DAP/reference	0.89208	0.108
27DAP/reference	0.87084	0.055
39DAP/reference	1.14087	0.314
41DAP/reference	1.01708	1
42DAP/reference	0.82744	0.053
43DAP/reference	0.9267	0.252
47DAP/reference	0.92684	0.293
52DAP/reference	0.92782	0.254
57DAP/reference	0.81499	0.069

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03874	0.66
17DAP/reference	1.05015	0.613
27DAP/reference	0.90231	0.317
39DAP/reference	1.25131	0.309
41DAP/reference	0.95289	0.384
42DAP/reference	1.12027	0.68
43DAP/reference	1.24716	0.38
47DAP/reference	0.95015	0.328
52DAP/reference	1.20109	0.168
57DAP/reference	0.93655	0.408

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05644	0.433
17DAP/reference	1.29274	0.1
27DAP/reference	1.04224	0.749
39DAP/reference	1.08798	0.275
41DAP/reference	1.00335	0.754
42DAP/reference	1.2531	0.042
43DAP/reference	1.27226	0.128
47DAP/reference	1.27057	0.007
52DAP/reference	1.05829	0.759
57DAP/reference	1.15991	0.394

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09434	0.966
26DAP/20DAP	0.88409	0.512
34DAP/26DAP	1.06131	1
51DAP/34DAP	0.98867	0.893
52DAP/51DAP	0.98818	1
53DAP/52DAP	1.04184	0.868
55DAP/53DAP	0.94914	0.592
57DAP/55DAP	1.11002	0.265
62DAP/57DAP	1.33566	0.217
68DAP/62DAP	1.1082	0.962
68DAP/14DAP	0.90763	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92859	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.54162
Mature Green Tomato/Ripe Tomato	1.11852	0.814
Immature Eggplant/Mature Eggplant	7.43128	0.05
Ripe Pepper/Ripe Tomato	0.14673	0.224
Mature Eggplant/Ripe Tomato	1.72039	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.25296	0.536
1-1-2/M82	N/A	N/A
12-2/M82	1.1697
12-4/M82	0.89818	1
1-3/M82	1.36656
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.54259	0.594
3-2/M82	0.74337
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.16832
4-3/M82	1.20821
5-3/M82	0.97951	1
6-2/M82	N/A	N/A
6-3/M82	0.69222
7-1/M82	1.01388
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93604	1
IL2-6/WTpooled	1.16611	1
IL7-5/WTpooled	0.81741	1
IL7-3/WTpooled	0.87129	0.31
IL12-4/WTpooled	0.9808	1
IL1-4/WTpooled	1.13	0.426
WT/WTpooled	0.98864	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	0.99329	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93241	1
DC3000/delta hrp 6h	1.0464	1
DC3000/delta hrp 12h	1.36982	1
DC3000/delta hrp 24h	0.74631	0.042

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95634	0.841
DC3000 delta B/DC3000 delta AB	0.94373	0.47

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94053	1
Exp 36h	0.74108	0.449
Exp 60h	0.69037	0.386

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	1.1417	0.258
Var 12h I row2-row1	0.71115	0.467
Var 12h NI row2-row1	1.11838
Var 36h I row2-row1	0.97608	1
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.49548
Var 60h NI row2-row1	0.67516	0.359
Time course 0hI-0hNI	1.14952	0.155
Time course 12hI-12hNI	1.21839	0.385
Time course 36hI-36hNI	2.12929	0.05
Time course 60hI-60hNI	5.33098	0.004

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)	1.10779	0.612
transgenic ySAMdc/azygous control (breaker)	1.28358	0.248
transgenic ySAMdc/azygous control (red)	1.68607	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92625	0.163

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	8.04799	0.083
Manapal/WT (break)	1.71256	0.183
Manapal/WT (red)	1.8187	0.133