Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.9.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15993	0.545
27DAP/17DAP	1.12558	0.845
39DAP/27DAP	0.89018	0.573
41DAP/39DAP	1.18018	0.468
42DAP/41DAP	1.103	0.938
43DAP/42DAP	1.04169	1
47DAP/43DAP	1.22824	0.412
52DAP/47DAP	0.81632	0.54
57DAP/52DAP	1.00532	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1444	0.334
17DAP/reference	0.96701	0.597
27DAP/reference	0.98114	0.668
39DAP/reference	0.95825	0.575
41DAP/reference	1.00057	1
42DAP/reference	1.13126	0.002
43DAP/reference	1.01311	0.957
47DAP/reference	1.04583	0.34
52DAP/reference	1.21847	0.012
57DAP/reference	1.0981	0.321

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97797	0.644
27DAP/17DAP	0.98935	0.919
39DAP/27DAP	0.96939	0.768
41DAP/39DAP	1.02985	0.774
42DAP/41DAP	0.98603	0.825
43DAP/42DAP	1.05025	0.25
47DAP/43DAP	0.97536	0.815
52DAP/47DAP	1.02564	0.892
57DAP/52DAP	0.92359	0.298
57DAP/7DAP	0.9864	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96954	0.402
17DAP/reference	1.09768	0.054
27DAP/reference	1.16741	0.041
39DAP/reference	1.00433	1
41DAP/reference	0.92722	0.153
42DAP/reference	0.90199	0.011
43DAP/reference	0.90742	0.091
47DAP/reference	0.96001	0.383
52DAP/reference	0.81969	0.053
57DAP/reference	1.02299	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17981	0.035
17DAP/reference	1.16918	0.127
27DAP/reference	1.12637	0.092
39DAP/reference	1.06751	0.22
41DAP/reference	0.98923	0.545
42DAP/reference	1.09422	0.105
43DAP/reference	1.2298	0.154
47DAP/reference	1.04277	0.256
52DAP/reference	1.09176	0.029
57DAP/reference	1.11111	0.049

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.89306	0.422
17DAP/reference	1.55499	0.602
27DAP/reference	1.73897	0.156
39DAP/reference	0.90564	0.101
41DAP/reference	1.03438	0.796
42DAP/reference	1.02716	0.818
43DAP/reference	0.96022	0.568
47DAP/reference	0.91008
52DAP/reference	0.94423	0.596
57DAP/reference	1.10749	0.401

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02013	0.966
26DAP/20DAP	0.99793	1
34DAP/26DAP	1.00459	1
51DAP/34DAP	1.0708	0.581
52DAP/51DAP	0.98134	1
53DAP/52DAP	1.03886	0.783
55DAP/53DAP	1.04201	0.904
57DAP/55DAP	0.9838	0.911
62DAP/57DAP	0.96737	0.994
68DAP/62DAP	1.04273	0.944
68DAP/14DAP	1.08229	0.487

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00273	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.06365	1
Mature Green Tomato/Ripe Tomato	1.13655	0.577
Immature Eggplant/Mature Eggplant	1.39476	0.15
Ripe Pepper/Ripe Tomato	0.61526	0.293
Mature Eggplant/Ripe Tomato	0.81153	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05836	0.877
1-1-2/M82	0.9648	0.958
12-2/M82	0.85889
12-4/M82	1.01189	1
1-3/M82	1.08837
2-1-1/M82	1.15293
2-1/M82	N/A	N/A
2-6/M82	1.28906
3-2/M82	0.84775
4-1-1/M82	1.11244	1
4-1/M82	N/A	N/A
4-3-2/M82	0.86979	0.487
4-3/M82	1.31192	1
5-3/M82	1.09429	1
6-2/M82	0.80843
6-3/M82	0.8285
7-1/M82	N/A	N/A
7-2/M82	0.99035
9-3-2/M82	0.80809	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94891
IL2-6/WTpooled	1.03647	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.69965	0.31
IL12-4/WTpooled	0.99447	1
IL1-4/WTpooled	0.95018	0.562
WT/WTpooled	0.97561	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	1.11276	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06287	0.914
DC3000/delta hrp 6h	1.17056	1
DC3000/delta hrp 12h	1.04044	1
DC3000/delta hrp 24h	0.94577	0.543

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07547	0.11
DC3000 delta B/DC3000 delta AB	0.96115	0.47

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93484	1
Exp 36h	0.88202	0.82
Exp 60h	1.08319	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01194	1
Var 0h	1.0552	1
Var 12h I row2-row1	1.21547	0.613
Var 12h NI row2-row1	0.99884	1
Var 36h I row2-row1	1.11252	1
Var 36h NI row2-row1	0.9643	0.61
Var 60h I row2-row1	1.21384	0.562
Var 60h NI row2-row1	1.00407	1
Time course 0hI-0hNI	0.97851	0.93
Time course 12hI-12hNI	1.00582	1
Time course 36hI-36hNI	1.0544	0.316
Time course 60hI-60hNI	0.69727	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)	0.92053	0.428
transgenic ySAMdc/azygous control (breaker)	1.44689	0.248
transgenic ySAMdc/azygous control (red)	1.29011	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97169	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.46407	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92408	1
Manapal/WT (break)	1.00429	1
Manapal/WT (red)	1.49771	0.413