Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.2.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95528	0.713
27DAP/17DAP	0.99955	0.996
39DAP/27DAP	1.23393	0.675
41DAP/39DAP	0.85001	0.483
42DAP/41DAP	1.10988	0.888
43DAP/42DAP	0.92303	0.877
47DAP/43DAP	0.98702	0.828
52DAP/47DAP	1.09126	0.906
57DAP/52DAP	1.36462	0.948

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95941	0.344
17DAP/reference	0.98547	0.737
27DAP/reference	0.89398	0.223
39DAP/reference	1.03962	0.497
41DAP/reference	1.00501	1
42DAP/reference	1.02243	0.901
43DAP/reference	1.09956	0.042
47DAP/reference	1.05869	0.708
52DAP/reference	1.19366	0.011
57DAP/reference	0.96853	0.503

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11756	0.23
27DAP/17DAP	0.95103	0.782
39DAP/27DAP	1.13926	0.471
41DAP/39DAP	1.00244	1
42DAP/41DAP	1.0301	1
43DAP/42DAP	0.88804	0.197
47DAP/43DAP	1.03173	0.95
52DAP/47DAP	0.97882	0.919
57DAP/52DAP	1.07161	0.783
57DAP/7DAP	1.31845	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20954	0.09
17DAP/reference	1.36505	0.007
27DAP/reference	1.19082	0.088
39DAP/reference	1.64012	0.011
41DAP/reference	1.49378	0.011
42DAP/reference	1.54043	0.008
43DAP/reference	1.322	0.007
47DAP/reference	1.34504	0.145
52DAP/reference	1.41165	0.007
57DAP/reference	1.58097	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02257	0.832
17DAP/reference	1.01023	1
27DAP/reference	1.0582	0.629
39DAP/reference	1.02349	1
41DAP/reference	1.13637	0.327
42DAP/reference	0.96717	0.392
43DAP/reference	0.86456	0.132
47DAP/reference	1.04829	0.712
52DAP/reference	1.00005	0.761
57DAP/reference	0.96204	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21349	0.022
17DAP/reference	1.09683	0.685
27DAP/reference	1.29164	0.051
39DAP/reference	1.28197	0.055
41DAP/reference	1.26901	0.031
42DAP/reference	1.25121	0.204
43DAP/reference	1.173	0.445
47DAP/reference	1.11281	0.042
52DAP/reference	1.42197	0.128
57DAP/reference	1.23222	0.064

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16352	0.966
26DAP/20DAP	1.1447	0.504
34DAP/26DAP	1.00853	1
51DAP/34DAP	1.55811	0.281
52DAP/51DAP	0.92369	1
53DAP/52DAP	0.74195	0.25
55DAP/53DAP	1.12684	0.948
57DAP/55DAP	2.53563	0.694
62DAP/57DAP	1.23704	0.723
68DAP/62DAP	0.98922	0.885
68DAP/14DAP	1.00255	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.6007	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.65498	0.182
Immature Eggplant/Mature Eggplant	0.79584
Ripe Pepper/Ripe Tomato	0.69058	1
Mature Eggplant/Ripe Tomato	0.55609	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.24936	1
12-2/M82	N/A	N/A
12-4/M82	0.9344
1-3/M82	N/A	N/A
2-1-1/M82	0.86831
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	0.97967
5-3/M82	0.98838	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.84226
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.47224	0.456
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.88245	1
IL12-4/WTpooled	0.97992	1
IL1-4/WTpooled	0.79559
WT/WTpooled	1.00786	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	0.84788	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.18341	0.921
DC3000/delta hrp 6h	0.95965	0.95
DC3000/delta hrp 12h	1.02506	1
DC3000/delta hrp 24h	0.7794	0.174

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	0.94712	0.787

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89628	1
Exp 36h	1.14231	1
Exp 60h	1.09817	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99443	1
Var 0h	1.03532	1
Var 12h I row2-row1	0.89202	0.353
Var 12h NI row2-row1	1.01994	1
Var 36h I row2-row1	1.02536	1
Var 36h NI row2-row1	0.67111	1
Var 60h I row2-row1	1.09368	1
Var 60h NI row2-row1	1.17696	0.793
Time course 0hI-0hNI	0.96258	0.817
Time course 12hI-12hNI	0.94263	0.255
Time course 36hI-36hNI	0.89057	0.047
Time course 60hI-60hNI	0.68722	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)	1.08288	0.286
transgenic ySAMdc/azygous control (breaker)	1.14475	0.248
transgenic ySAMdc/azygous control (red)	1.15413	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0178	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83305	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02533	1
Manapal/WT (break)	1.07075	1
Manapal/WT (red)	0.91128	0.503