Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.3.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.53896	0.062
27DAP/17DAP	0.55161	0.062
39DAP/27DAP	0.78208	0.522
41DAP/39DAP	0.60775	0.075
42DAP/41DAP	1.01795	1
43DAP/42DAP	1.26153	0.726
47DAP/43DAP	0.8644	0.54
52DAP/47DAP	1.06821	0.945
57DAP/52DAP	0.88697	0.889

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.58829	0.006
17DAP/reference	0.88556	0.393
27DAP/reference	1.12194	0.285
39DAP/reference	0.56198	0.009
41DAP/reference	0.58025	0.008
42DAP/reference	1.36363	0.003
43DAP/reference	1.22716
47DAP/reference	1.043	0.593
52DAP/reference	0.9146	0.086
57DAP/reference	0.49077

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.55549	0.047
27DAP/17DAP	1.4137	0.283
39DAP/27DAP	0.67614	0.046
41DAP/39DAP	1.02995	1
42DAP/41DAP	0.90316	0.541
43DAP/42DAP	1.49153	0.25
47DAP/43DAP	1.26715	0.193
52DAP/47DAP	1.4137	0.276
57DAP/52DAP	3.24724	0.091
57DAP/7DAP	1.24167	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95483	0.168
17DAP/reference	0.87132	0.167
27DAP/reference	0.78075	0.159
39DAP/reference	0.67131	0.095
41DAP/reference	0.81319	0.073
42DAP/reference	0.78237	0.077
43DAP/reference	1.12426	0.188
47DAP/reference	0.9022	0.222
52DAP/reference	0.75895	0.021
57DAP/reference	1.10518	0.536

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.49573	0.127
17DAP/reference	1.27218	0.32
27DAP/reference	0.9859	0.598
39DAP/reference	0.79079	0.091
41DAP/reference	0.91614	0.112
42DAP/reference	1.01405	1
43DAP/reference	0.74733	0.039
47DAP/reference	0.87357	0.025
52DAP/reference	0.64266	0.004
57DAP/reference	0.82831	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05585	0.397
17DAP/reference	1.04825	0.9
27DAP/reference	1.02526	0.834
39DAP/reference	0.8906	0.299
41DAP/reference	0.85834	0.185
42DAP/reference	0.89978	0.361
43DAP/reference	0.99526	0.685
47DAP/reference	1.15569	0.562
52DAP/reference	1.50131	0.216
57DAP/reference	1.61312	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.48009	0.786
26DAP/20DAP	1.79981	0.099
34DAP/26DAP	1.0157	1
51DAP/34DAP	0.72398	0.286
52DAP/51DAP	0.969	1
53DAP/52DAP	0.88978	0.723
55DAP/53DAP	0.73367	0.417
57DAP/55DAP	0.73238	0.21
62DAP/57DAP	0.80924	0.162
68DAP/62DAP	1.77098
68DAP/14DAP	1.10661	0.636

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.56865	0.068

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.55715	0.058
Mature Green Tomato/Ripe Tomato	4.7038	0.017
Immature Eggplant/Mature Eggplant	0.45258	0.062
Ripe Pepper/Ripe Tomato	1.15308	1
Mature Eggplant/Ripe Tomato	2.57027	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.80685
1-1-2/M82	1.16879	1
12-2/M82	N/A	N/A
12-4/M82	1.02167	1
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	N/A	N/A
3-2/M82	N/A	N/A
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	1.04732
5-3/M82	0.70105	0.49
6-2/M82	0.99821	1
6-3/M82	1.00155	1
7-1/M82	N/A	N/A
7-2/M82	0.89235	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.79905	0.243
IL2-6/WTpooled	1.09583	1
IL7-5/WTpooled	0.48332
IL7-3/WTpooled	1.07143
IL12-4/WTpooled	1.09547	0.839
IL1-4/WTpooled	0.85351	0.562
WT/WTpooled	1.17976	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	0.52939	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98176	1
DC3000/delta hrp 6h	1.12884	1
DC3000/delta hrp 12h	1.37784	1
DC3000/delta hrp 24h	0.35564	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.48774	0.023
DC3000 delta B/DC3000 delta AB	0.55607	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05443	1
Exp 36h	0.87782	0.589
Exp 60h	0.80221	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04833
Var 0h	0.48945	1
Var 12h I row2-row1	0.85585	0.705
Var 12h NI row2-row1	1.0158	1
Var 36h I row2-row1	0.81625	1
Var 36h NI row2-row1	1.53739	1
Var 60h I row2-row1	1.12221	0.288
Var 60h NI row2-row1	0.99602	1
Time course 0hI-0hNI	1.05881	0.833
Time course 12hI-12hNI	0.86803	0.208
Time course 36hI-36hNI	0.76686	0.023
Time course 60hI-60hNI	0.13223	0.005

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)	0.84571	0.309
transgenic ySAMdc/azygous control (breaker)	0.729	0.15
transgenic ySAMdc/azygous control (red)	1.04964	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.74667	0.168

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.24928	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.14022	0.307
Manapal/WT (break)	1.44551	0.381
Manapal/WT (red)	0.86007	0.229