Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.6.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81728	0.238
27DAP/17DAP	0.8815	0.704
39DAP/27DAP	1.30958	0.433
41DAP/39DAP	0.98452	0.918
42DAP/41DAP	1.57987	0.143
43DAP/42DAP	1.1436	0.968
47DAP/43DAP	1.21362	0.527
52DAP/47DAP	0.91141	0.724
57DAP/52DAP	1.34301	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.34761	0.024
17DAP/reference	0.38213	0.006
27DAP/reference	0.47733	0.012
39DAP/reference	1.07955	0.75
41DAP/reference	0.68418	0.021
42DAP/reference	2.37965	0.001
43DAP/reference	6.06986	0.006
47DAP/reference	5.46256	0.001
52DAP/reference	2.87211	0.009
57DAP/reference	3.52499	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91673	0.496
27DAP/17DAP	1.04281	0.909
39DAP/27DAP	1.10542	0.534
41DAP/39DAP	1.08567	0.612
42DAP/41DAP	1.1387	0.495
43DAP/42DAP	0.91768	0.367
47DAP/43DAP	1.05701	0.779
52DAP/47DAP	0.83285	0.107
57DAP/52DAP	0.97341	0.637
57DAP/7DAP	1.12343	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89848	0.326
17DAP/reference	0.93106	0.295
27DAP/reference	0.97643	0.53
39DAP/reference	1.12092	0.186
41DAP/reference	0.97054	0.512
42DAP/reference	1.13217	0.174
43DAP/reference	0.98969	0.608
47DAP/reference	0.91471	0.293
52DAP/reference	1.04713	0.832
57DAP/reference	1.05632	0.654

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.37066	0.004
17DAP/reference	0.29832	0.003
27DAP/reference	0.4476	0.013
39DAP/reference	0.48088	0.01
41DAP/reference	0.42965	0.006
42DAP/reference	0.52028	0.016
43DAP/reference	0.66565	0.027
47DAP/reference	1.17131	0.943
52DAP/reference	0.30298	0.009
57DAP/reference	0.69299	0.04

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00684	1
17DAP/reference	0.77316	0.221
27DAP/reference	0.92975	0.397
39DAP/reference	0.85196	0.133
41DAP/reference	1.01297	1
42DAP/reference	1.33751	0.233
43DAP/reference	2.41954	0.074
47DAP/reference	5.28918	0.004
52DAP/reference	1.90123	0.237
57DAP/reference	2.36205	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10417	0.966
26DAP/20DAP	1.28721	0.235
34DAP/26DAP	0.92035	0.584
51DAP/34DAP	1.55044	0.032
52DAP/51DAP	0.80765	0.151
53DAP/52DAP	1.43667	0.044
55DAP/53DAP	0.90001	0.273
57DAP/55DAP	1.18874	0.728
62DAP/57DAP	N/A	N/A
68DAP/62DAP	0.86729	0.668
68DAP/14DAP	1.37672	0.153

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.84631	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.39842	0.078
Mature Green Tomato/Ripe Tomato	0.66296	0.107
Immature Eggplant/Mature Eggplant	1.93483	0.05
Ripe Pepper/Ripe Tomato	0.91007	1
Mature Eggplant/Ripe Tomato	0.85353	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88412	0.512
1-1-2/M82	1.00766	1
12-2/M82	0.92325	0.955
12-4/M82	0.79042	0.319
1-3/M82	1.25661	1
2-1-1/M82	1.00418	1
2-1/M82	1.09029	1
2-6/M82	0.93338	1
3-2/M82	0.74048	1
4-1-1/M82	0.82483	0.962
4-1/M82	0.9436
4-3-2/M82	0.98041	1
4-3/M82	0.94933	1
5-3/M82	1.31821	0.378
6-2/M82	0.94372
6-3/M82	1.00422	1
7-1/M82	0.87529	0.803
7-2/M82	0.96586	1
9-3-2/M82	1.15128	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.17308	0.659
IL7-5/WTpooled	1.69543
IL7-3/WTpooled	0.93328	0.294
IL12-4/WTpooled	0.97063	1
IL1-4/WTpooled	0.88534	0.562
WT/WTpooled	0.81887	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	1.12756	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94864	1
DC3000/delta hrp 6h	1.05646	1
DC3000/delta hrp 12h	0.94235	1
DC3000/delta hrp 24h	1.1504	0.174

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.78154	0.25
DC3000 delta B/DC3000 delta AB	1.34435	0.186

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02373	1
Exp 36h	1.06663	1
Exp 60h	1.12995	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01007	1
Var 0h	0.8155	0.339
Var 12h I row2-row1	0.90274	0.514
Var 12h NI row2-row1	1.2237	0.34
Var 36h I row2-row1	1.37633	0.489
Var 36h NI row2-row1	0.67576	0.329
Var 60h I row2-row1	0.8969	0.374
Var 60h NI row2-row1	0.79049	0.292
Time course 0hI-0hNI	0.98837	0.991
Time course 12hI-12hNI	1.08459	0.26
Time course 36hI-36hNI	1.72964	0.004
Time course 60hI-60hNI	4.45544	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)	0.86227	0.454
transgenic ySAMdc/azygous control (breaker)	1.12014	1
transgenic ySAMdc/azygous control (red)	1.05722	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06603	0.039

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.16362	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.36864	0.14
Manapal/WT (break)	1.04417	0.381
Manapal/WT (red)	0.83027	0.503