Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.6.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78738	0.253
27DAP/17DAP	1.4481	0.62
39DAP/27DAP	1.10127	0.858
41DAP/39DAP	1.03819	0.859
42DAP/41DAP	0.89715	1
43DAP/42DAP	0.98953	0.934
47DAP/43DAP	1.26657	0.668
52DAP/47DAP	0.88897	0.668
57DAP/52DAP	1.14263	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8497	0.051
17DAP/reference	0.91762	0.194
27DAP/reference	0.96063	0.249
39DAP/reference	0.93437	0.118
41DAP/reference	0.80751	0.016
42DAP/reference	0.90583	0.014
43DAP/reference	0.97674	0.675
47DAP/reference	0.96629	0.3
52DAP/reference	1.10711	0.158
57DAP/reference	1.04	0.332

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96308	0.644
27DAP/17DAP	1.08273	0.932
39DAP/27DAP	1.26483	0.231
41DAP/39DAP	1.02382	1
42DAP/41DAP	1.07693	0.559
43DAP/42DAP	1.04205	0.664
47DAP/43DAP	1.14578	0.681
52DAP/47DAP	1.11607	0.696
57DAP/52DAP	0.95913	0.68
57DAP/7DAP	0.90222	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75913	0.129
17DAP/reference	1.03581	1
27DAP/reference	1.06117	0.804
39DAP/reference	1.05424	1
41DAP/reference	0.98589	0.619
42DAP/reference	0.86258	0.117
43DAP/reference	1.06493	0.727
47DAP/reference	1.00147	1
52DAP/reference	1.2352	0.401
57DAP/reference	1.03326	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76588	0.015
17DAP/reference	0.95188	0.378
27DAP/reference	0.958	0.407
39DAP/reference	1.00769	1
41DAP/reference	1.00397	0.683
42DAP/reference	0.88262	0.089
43DAP/reference	1.05091	0.835
47DAP/reference	0.90157	0.085
52DAP/reference	0.94346	0.239
57DAP/reference	0.79982	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32375	0.049
17DAP/reference	0.99811	0.9
27DAP/reference	0.71459
39DAP/reference	1.28177	0.189
41DAP/reference	1.08483	0.657
42DAP/reference	1.2628	0.057
43DAP/reference	1.43544	0.28
47DAP/reference	1.19352	0.034
52DAP/reference	1.05058	1
57DAP/reference	1.24912	0.078

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99457	1
26DAP/20DAP	0.92958	1
34DAP/26DAP	1.04512	1
51DAP/34DAP	1.09842	0.677
52DAP/51DAP	0.84481	1
53DAP/52DAP	2.35675	0.944
55DAP/53DAP	1.9823	0.394
57DAP/55DAP	0.89032	0.516
62DAP/57DAP	0.93467	0.871
68DAP/62DAP	0.99876	0.939
68DAP/14DAP	1.31893	0.453

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.76589	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.98461	0.745
Mature Green Tomato/Ripe Tomato	0.53068
Immature Eggplant/Mature Eggplant	1.3531	0.23
Ripe Pepper/Ripe Tomato	3.34262	1
Mature Eggplant/Ripe Tomato	1.56535

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.8909
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.93437	0.501
3-2/M82	1.36603
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.01543
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.9671
9-3-2/M82	1.23295

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.58779
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.8578	1
IL1-4/WTpooled	1.13133	1
WT/WTpooled	0.99144	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	1.15199	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07072	0.75
DC3000/delta hrp 6h	0.98623	0.95
DC3000/delta hrp 12h	1.30871	1
DC3000/delta hrp 24h	1.44424	0.054

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.74507	0.253

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10966	1
Exp 36h	0.93347	0.504
Exp 60h	1.07891	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00533	1
Var 0h	0.9021	0.933
Var 12h I row2-row1	0.96408	0.418
Var 12h NI row2-row1	1.04399	1
Var 36h I row2-row1	1.06719	1
Var 36h NI row2-row1	5.14459
Var 60h I row2-row1	0.52033
Var 60h NI row2-row1	0.92833	1
Time course 0hI-0hNI	0.97584	0.852
Time course 12hI-12hNI	0.94611	0.451
Time course 36hI-36hNI	0.83695	0.023
Time course 60hI-60hNI	0.58528	0.006

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)	0.9172	0.33
transgenic ySAMdc/azygous control (breaker)	1.14931	0.178
transgenic ySAMdc/azygous control (red)	1.07242	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02816	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86673	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.22242	0.14
Manapal/WT (break)	1.34113	0.183
Manapal/WT (red)	0.92243	0.607