Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.19.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3249	0.893
27DAP/17DAP	1.30294	0.688
39DAP/27DAP	2.22988	0.03
41DAP/39DAP	0.64534	0.075
42DAP/41DAP	1.18511	0.978
43DAP/42DAP	1.04563	0.948
47DAP/43DAP	1.01905	1
52DAP/47DAP	1.23157	0.624
57DAP/52DAP	1.22628	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04438	0.96
17DAP/reference	1.30946	0.045
27DAP/reference	1.14454	0.15
39DAP/reference	1.33121	0.076
41DAP/reference	1.61869	0.014
42DAP/reference	1.23471	0.002
43DAP/reference	1.44281	0.018
47DAP/reference	2.16984	0.001
52DAP/reference	1.52544	0.008
57DAP/reference	1.35113	0.019

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.07284	0.036
27DAP/17DAP	0.93974	0.648
39DAP/27DAP	1.0498	0.646
41DAP/39DAP	1.17961	1
42DAP/41DAP	1.11697	0.425
43DAP/42DAP	0.90532	0.149
47DAP/43DAP	0.94443	0.647
52DAP/47DAP	1.12421	0.66
57DAP/52DAP	1.16019	0.708
57DAP/7DAP	1.44248	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98275	0.495
17DAP/reference	0.92776	0.039
27DAP/reference	0.86918	0.01
39DAP/reference	1.00268	1
41DAP/reference	1.00739	1
42DAP/reference	1.01858	0.889
43DAP/reference	0.98827	0.527
47DAP/reference	1.02929	0.791
52DAP/reference	0.99836	0.74
57DAP/reference	0.97442	0.314

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98712	0.77
17DAP/reference	1.07889	1
27DAP/reference	1.00059	0.686
39DAP/reference	1.1011	0.912
41DAP/reference	1.20962	0.362
42DAP/reference	1.10913	0.621
43DAP/reference	1.04463	0.735
47DAP/reference	1.17455	0.105
52DAP/reference	0.82352	0.203
57DAP/reference	0.96352	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01944	1
17DAP/reference	0.96794	0.601
27DAP/reference	0.99458	0.763
39DAP/reference	0.98312	0.544
41DAP/reference	0.94045	0.077
42DAP/reference	0.89742	0.087
43DAP/reference	1.06809	0.7
47DAP/reference	1.71365	0.021
52DAP/reference	0.98226	0.663
57DAP/reference	1.05619	0.636

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.53304
26DAP/20DAP	2.33858	0.097
34DAP/26DAP	1.08083	1
51DAP/34DAP	1.45954	0.055
52DAP/51DAP	0.61958	0.151
53DAP/52DAP	1.30933	0.065
55DAP/53DAP	0.86469	0.07
57DAP/55DAP	1.19431	0.898
62DAP/57DAP	0.52606	0.004
68DAP/62DAP	1.05441	0.914
68DAP/14DAP	1.2923	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.10723	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.40486	0.267
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.50483	1
Mature Eggplant/Ripe Tomato	2.15646	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97317	0.961
1-1-2/M82	1.08753	0.977
12-2/M82	0.48255
12-4/M82	0.82068	0.619
1-3/M82	2.0431	0.248
2-1-1/M82	0.83305	0.465
2-1/M82	0.41278
2-6/M82	0.87251	1
3-2/M82	1.06366	0.84
4-1-1/M82	0.97078	1
4-1/M82	0.55869
4-3-2/M82	1.17207
4-3/M82	1.59716	1
5-3/M82	1.13538	1
6-2/M82	0.88499
6-3/M82	0.63225	0.637
7-1/M82	1.07025
7-2/M82	1.53769	0.324
9-3-2/M82	0.96492

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.23335
IL2-6/WTpooled	1.04105	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.44363	0.553
IL1-4/WTpooled	1.16897	1
WT/WTpooled	0.93983	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	1.11305	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08922	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.98542	0.934

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16876	0.073
DC3000 delta B/DC3000 delta AB	1.15903	0.272

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	1.02122	1
Var 0h	1.09466	1
Var 12h I row2-row1	0.92479	0.418
Var 12h NI row2-row1	0.99021	1
Var 36h I row2-row1	1.15984	0.298
Var 36h NI row2-row1	1.0352	1
Var 60h I row2-row1	0.72696	0.582
Var 60h NI row2-row1	0.85989	0.572
Time course 0hI-0hNI	1.00217	1
Time course 12hI-12hNI	0.99202	0.994
Time course 36hI-36hNI	1.10722	0.056
Time course 60hI-60hNI	1.48239	0.008

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)	1.46442	0.798
transgenic ySAMdc/azygous control (breaker)	0.54458	0.15
transgenic ySAMdc/azygous control (red)	0.69931	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.46415	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.46753	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.5808	0.172
Manapal/WT (break)	1.26091	0.183
Manapal/WT (red)	1.10796	1