Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.17.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29246	0.205
27DAP/17DAP	1.04926	0.91
39DAP/27DAP	1.16688	0.643
41DAP/39DAP	1.02846	0.946
42DAP/41DAP	1.2087	0.871
43DAP/42DAP	1.23729	0.785
47DAP/43DAP	1.53761	0.555
52DAP/47DAP	1.08481	0.934
57DAP/52DAP	1.01689	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32048	0.179
17DAP/reference	1.34269	0.02
27DAP/reference	1.1695	0.179
39DAP/reference	1.22499	0.122
41DAP/reference	1.58191	0.012
42DAP/reference	1.0915	0.072
43DAP/reference	1.05545	0.866
47DAP/reference	1.10735	0.318
52DAP/reference	1.06614	0.633
57DAP/reference	0.84819	0.049

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04365	0.662
27DAP/17DAP	1.0262	0.909
39DAP/27DAP	1.02115	0.707
41DAP/39DAP	0.99861	1
42DAP/41DAP	1.02	0.947
43DAP/42DAP	1.02927	0.664
47DAP/43DAP	1.0301	0.678
52DAP/47DAP	1.02287	0.919
57DAP/52DAP	0.99355	0.845
57DAP/7DAP	1.15769	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95985	0.157
17DAP/reference	0.94701	0.021
27DAP/reference	0.96822	0.071
39DAP/reference	0.96955	0.073
41DAP/reference	0.9428	0.032
42DAP/reference	0.94396	0.038
43DAP/reference	0.93456	0.026
47DAP/reference	1.06724	0.996
52DAP/reference	0.89916	0.043
57DAP/reference	0.92073	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95228	0.592
17DAP/reference	1.43823	0.03
27DAP/reference	1.19751	0.116
39DAP/reference	1.31643	0.087
41DAP/reference	1.13714	0.129
42DAP/reference	0.97954	0.534
43DAP/reference	1.23611	0.142
47DAP/reference	1.11279	0.095
52DAP/reference	1.19486	0.471
57DAP/reference	1.34859	0.054

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99449	0.653
17DAP/reference	1.05169	0.253
27DAP/reference	0.96702	0.147
39DAP/reference	0.98633	0.544
41DAP/reference	1.01125	1
42DAP/reference	1.0151	0.979
43DAP/reference	1.12843	0.474
47DAP/reference	1.07607	0.61
52DAP/reference	0.91638	0.211
57DAP/reference	0.99578	0.572

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.4749
26DAP/20DAP	0.92632	0.244
34DAP/26DAP	0.97208	0.893
51DAP/34DAP	0.99957	0.96
52DAP/51DAP	1.04669	0.638
53DAP/52DAP	1.10035	0.274
55DAP/53DAP	0.99272	0.886
57DAP/55DAP	1.16658	0.818
62DAP/57DAP	1.20934	0.185
68DAP/62DAP	0.88404	0.641
68DAP/14DAP	1.1368

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02765	0.74

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.65125	0.095
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.31956
Mature Eggplant/Ripe Tomato	3.08793	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96444	0.944
1-1-2/M82	1.04174	1
12-2/M82	N/A	N/A
12-4/M82	0.87668	0.282
1-3/M82	N/A	N/A
2-1-1/M82	1.19203
2-1/M82	N/A	N/A
2-6/M82	1.1235
3-2/M82	N/A	N/A
4-1-1/M82	0.94841	1
4-1/M82	0.76761
4-3-2/M82	1.33899
4-3/M82	N/A	N/A
5-3/M82	0.96374	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	1.00974	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.80442	0.321
IL2-6/WTpooled	0.88173	1
IL7-5/WTpooled	0.50859	0.427
IL7-3/WTpooled	0.66962	0.294
IL12-4/WTpooled	0.79993	0.71
IL1-4/WTpooled	0.76019	0.457
WT/WTpooled	1.07792	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	0.84959	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99768	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.77545	1
DC3000/delta hrp 24h	1.24515	0.103

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03461	0.333
DC3000 delta B/DC3000 delta AB	0.99217	1

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	1.007	1
Var 0h	1.23826	0.421
Var 12h I row2-row1	1.03004	0.692
Var 12h NI row2-row1	1.05198	1
Var 36h I row2-row1	1.08381	1
Var 36h NI row2-row1	0.9264	0.478
Var 60h I row2-row1	1.15666	0.562
Var 60h NI row2-row1	0.95418	0.977
Time course 0hI-0hNI	1.08993	0.63
Time course 12hI-12hNI	1.0247	0.811
Time course 36hI-36hNI	1.0144	0.975
Time course 60hI-60hNI	1.12068	0.009

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)	1.82759	1
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.32148	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.66589	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.18979	0.413