Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27177	0.485
27DAP/17DAP	0.56822	0.038
39DAP/27DAP	0.9841	0.749
41DAP/39DAP	0.67226	0.087
42DAP/41DAP	0.8094	0.774
43DAP/42DAP	1.17485	0.816
47DAP/43DAP	0.8332	0.492
52DAP/47DAP	0.80118	0.507
57DAP/52DAP	1.0219	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80381	0.121
17DAP/reference	0.53818	0.008
27DAP/reference	0.55849	0.013
39DAP/reference	0.58138	0.018
41DAP/reference	0.41351	0.008
42DAP/reference	0.47806	0.001
43DAP/reference	0.42129	0.014
47DAP/reference	0.32423	0.001
52DAP/reference	0.32233	0.013
57DAP/reference	0.45622	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.93445	0.041
27DAP/17DAP	0.73046	0.131
39DAP/27DAP	0.38239	0.029
41DAP/39DAP	1.47457	0.042
42DAP/41DAP	0.82904	0.123
43DAP/42DAP	0.64375	0.025
47DAP/43DAP	0.93111	0.543
52DAP/47DAP	0.90952	0.397
57DAP/52DAP	0.78227	0.187
57DAP/7DAP	0.33777	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96875	0.495
17DAP/reference	0.69622	0.012
27DAP/reference	0.52824	0.01
39DAP/reference	0.38564	0.011
41DAP/reference	0.29956	0.009
42DAP/reference	0.30374	0.01
43DAP/reference	0.23837	0.008
47DAP/reference	0.22866	0.026
52DAP/reference	0.28638	0.01
57DAP/reference	0.28138	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.53056	0.008
17DAP/reference	0.60409	0.019
27DAP/reference	0.70812	0.087
39DAP/reference	0.43795	0.011
41DAP/reference	0.53292	0.005
42DAP/reference	0.48125	0.01
43DAP/reference	0.26295	0.002
47DAP/reference	0.39377	0.007
52DAP/reference	0.23115	0.003
57DAP/reference	0.18516	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.80832	0.016
17DAP/reference	1.64736	0.129
27DAP/reference	1.21224	0.179
39DAP/reference	0.96367	0.464
41DAP/reference	0.68213	0.019
42DAP/reference	0.55623	0.019
43DAP/reference	0.49383	0.016
47DAP/reference	0.42677	0.005
52DAP/reference	0.33332	0.043
57DAP/reference	1.52495	0.153

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9337	1
26DAP/20DAP	1.16334	0.654
34DAP/26DAP	0.78224	0.093
51DAP/34DAP	0.37202	0.049
52DAP/51DAP	1.01594	0.954
53DAP/52DAP	0.61499	0.049
55DAP/53DAP	0.61385	0.021
57DAP/55DAP	1.09498	0.841
62DAP/57DAP	1.76715	0.04
68DAP/62DAP	1.02752	0.914
68DAP/14DAP	1.19196	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90038	0.341

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.12297	0.058
Mature Green Tomato/Ripe Tomato	6.25774	0.018
Immature Eggplant/Mature Eggplant	0.51586	0.057
Ripe Pepper/Ripe Tomato	9.47443	0.256
Mature Eggplant/Ripe Tomato	19.2924	0.26

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	1.122
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	0.90742	1
4-3/M82	N/A	N/A
5-3/M82	1.27876	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.39733

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90959
IL2-6/WTpooled	0.96158	1
IL7-5/WTpooled	1.44513	1
IL7-3/WTpooled	1.01435	1
IL12-4/WTpooled	0.90882	1
IL1-4/WTpooled	0.80787	0.444
WT/WTpooled	1.07776	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	1.08418	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96642	1
DC3000/delta hrp 6h	1.00058	0.95
DC3000/delta hrp 12h	1.22315	1
DC3000/delta hrp 24h	0.93311	0.629

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.7637	0.065
DC3000 delta B/DC3000 delta AB	0.55078	0.036

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0465	1
Exp 36h	0.94858	0.879
Exp 60h	0.90407	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97623	1
Var 0h	0.52455	0.782
Var 12h I row2-row1	1.00647	1
Var 12h NI row2-row1	0.99349	1
Var 36h I row2-row1	0.99419	1
Var 36h NI row2-row1	0.97862	0.584
Var 60h I row2-row1	1.39703	0.543
Var 60h NI row2-row1	1.03022	0.904
Time course 0hI-0hNI	1.01306	1
Time course 12hI-12hNI	1.08823	0.49
Time course 36hI-36hNI	1.10369	0.128
Time course 60hI-60hNI	0.54773	0.015

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)	1.13361	0.748
transgenic ySAMdc/azygous control (breaker)	2.31904	0.178
transgenic ySAMdc/azygous control (red)	1.20831	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.54296	0.075

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07552	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	18.0903	0.087
Manapal/WT (break)	8.62493	0.126
Manapal/WT (red)	2.12464	0.413