Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.7.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26712	0.303
27DAP/17DAP	0.79392	0.397
39DAP/27DAP	0.89237	0.529
41DAP/39DAP	0.95049	0.727
42DAP/41DAP	0.91339	1
43DAP/42DAP	0.84511	0.467
47DAP/43DAP	0.69606	0.165
52DAP/47DAP	0.93162	0.742
57DAP/52DAP	1.24095	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2133	0.033
17DAP/reference	1.09275	0.442
27DAP/reference	1.32819	0.043
39DAP/reference	1.24563	0.023
41DAP/reference	1.12906	0.516
42DAP/reference	1.03123	0.565
43DAP/reference	1.01374	0.982
47DAP/reference	0.99573	0.636
52DAP/reference	1.06798	0.951
57DAP/reference	1.12622	0.211

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98356	0.732
27DAP/17DAP	0.97282	0.887
39DAP/27DAP	0.79406	0.074
41DAP/39DAP	0.88723	0.31
42DAP/41DAP	1.06787	0.694
43DAP/42DAP	0.85731	0.024
47DAP/43DAP	0.88483	0.272
52DAP/47DAP	0.939	0.645
57DAP/52DAP	0.91607	0.591
57DAP/7DAP	0.79024	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28548	0.043
17DAP/reference	1.36721	0.064
27DAP/reference	1.20449	0.073
39DAP/reference	1.41248	0.02
41DAP/reference	1.13754	0.113
42DAP/reference	1.19908	0.018
43DAP/reference	1.47806	0.013
47DAP/reference	1.16335	0.561
52DAP/reference	1.58739	0.007
57DAP/reference	1.5308	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05975	0.832
17DAP/reference	1.35617	0.104
27DAP/reference	1.32421	0.028
39DAP/reference	1.00375	0.722
41DAP/reference	1.08909	0.406
42DAP/reference	1.18199	0.036
43DAP/reference	0.96398	0.494
47DAP/reference	1.13765	0.169
52DAP/reference	0.92143	0.093
57DAP/reference	0.75407	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25692	0.04
17DAP/reference	1.59752	0.043
27DAP/reference	1.36557	0.02
39DAP/reference	1.33831	0.006
41DAP/reference	1.50931	0.01
42DAP/reference	1.23989	0.099
43DAP/reference	1.44544	0.04
47DAP/reference	1.04001	1
52DAP/reference	1.05665	0.952
57DAP/reference	1.76206	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97988	1
26DAP/20DAP	0.72653	0.317
34DAP/26DAP	0.82888	0.693
51DAP/34DAP	1.01793	0.962
52DAP/51DAP	0.87119	1
53DAP/52DAP	1.0066	0.924
55DAP/53DAP	0.85447	0.195
57DAP/55DAP	0.96842	0.845
62DAP/57DAP	1.16297	0.445
68DAP/62DAP	0.89575	0.505
68DAP/14DAP	0.80594	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30414	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.11927	0.058
Mature Green Tomato/Ripe Tomato	4.17548	0.016
Immature Eggplant/Mature Eggplant	0.57913	0.066
Ripe Pepper/Ripe Tomato	0.9466	1
Mature Eggplant/Ripe Tomato	2.74587	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99089	0.961
1-1-2/M82	0.89137
12-2/M82	1.07805
12-4/M82	1.01481	1
1-3/M82	0.95859
2-1-1/M82	0.96949
2-1/M82	N/A	N/A
2-6/M82	1.07207	0.695
3-2/M82	N/A	N/A
4-1-1/M82	0.9219	1
4-1/M82	1.12034
4-3-2/M82	N/A	N/A
4-3/M82	1.14549	1
5-3/M82	1.03102	1
6-2/M82	1.03333	1
6-3/M82	1.00666	1
7-1/M82	1.00087
7-2/M82	1.05007	1
9-3-2/M82	1.59743	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.80615	0.243
IL2-6/WTpooled	1.07346	0.419
IL7-5/WTpooled	0.99878	1
IL7-3/WTpooled	1.02449	1
IL12-4/WTpooled	0.88943	0.566
IL1-4/WTpooled	0.95427	1
WT/WTpooled	1.05133	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	0.88109	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92936	0.868
DC3000/delta hrp 6h	1.0981
DC3000/delta hrp 12h	0.96232	1
DC3000/delta hrp 24h	0.96427	0.769

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.69286	0.026
DC3000 delta B/DC3000 delta AB	0.7091	0.048

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02854	1
Var 0h	0.45546	0.933
Var 12h I row2-row1	0.8654	0.338
Var 12h NI row2-row1	1.00981	1
Var 36h I row2-row1	0.95816	0.805
Var 36h NI row2-row1	1.03568	1
Var 60h I row2-row1	0.69998	0.285
Var 60h NI row2-row1	0.99521	1
Time course 0hI-0hNI	1.01499	0.852
Time course 12hI-12hNI	0.95031	0.597
Time course 36hI-36hNI	0.85175	0.035
Time course 60hI-60hNI	0.71575	0.026

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)	1.071	0.455
transgenic ySAMdc/azygous control (breaker)	1.66249	0.248
transgenic ySAMdc/azygous control (red)	0.98807	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02845	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.40832	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.92462	0.086
Manapal/WT (break)	3.9082	0.123
Manapal/WT (red)	3.6727	0.133