Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.15.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13039	0.588
27DAP/17DAP	1.29806	0.798
39DAP/27DAP	0.94105	0.641
41DAP/39DAP	1.03203	0.921
42DAP/41DAP	0.95283	1
43DAP/42DAP	1.13182	0.809
47DAP/43DAP	1.19821	0.497
52DAP/47DAP	0.85511	0.612
57DAP/52DAP	1.14878	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99669	0.756
17DAP/reference	1.07939	0.021
27DAP/reference	1.08689	0.057
39DAP/reference	1.03194	0.465
41DAP/reference	1.03443	0.451
42DAP/reference	1.01859	0.504
43DAP/reference	1.00002	0.942
47DAP/reference	1.05752	0.05
52DAP/reference	0.98538	0.515
57DAP/reference	0.91938	0.262

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98766	0.782
27DAP/17DAP	0.96909	0.648
39DAP/27DAP	0.98338	0.87
41DAP/39DAP	1.03868	0.735
42DAP/41DAP	0.95589	0.595
43DAP/42DAP	1.04529	0.122
47DAP/43DAP	1.00784	0.969
52DAP/47DAP	0.95796	0.763
57DAP/52DAP	0.96081	0.558
57DAP/7DAP	0.99333	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89178	0.157
17DAP/reference	0.92729	0.124
27DAP/reference	0.86023	0.082
39DAP/reference	0.98785	0.64
41DAP/reference	0.94004	0.259
42DAP/reference	0.94195	0.355
43DAP/reference	0.98369	0.48
47DAP/reference	0.89176	0.222
52DAP/reference	0.93067	0.278
57DAP/reference	0.96873	0.382

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90893	0.043
17DAP/reference	0.90867	0.025
27DAP/reference	0.86953	0.06
39DAP/reference	0.93737	0.195
41DAP/reference	0.98174	0.481
42DAP/reference	1.00439	1
43DAP/reference	0.96386	0.478
47DAP/reference	1.05959	0.282
52DAP/reference	1.009	1
57DAP/reference	1.02939	0.771

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05121	0.659
17DAP/reference	0.98392	0.681
27DAP/reference	0.94051	0.376
39DAP/reference	0.97569	0.544
41DAP/reference	1.02777	0.889
42DAP/reference	0.96326	0.671
43DAP/reference	0.90456	0.15
47DAP/reference	1.07992	0.239
52DAP/reference	0.907	0.395
57DAP/reference	0.76962	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01526	0.966
26DAP/20DAP	0.99761	1
34DAP/26DAP	1.01919	0.819
51DAP/34DAP	0.99937	0.967
52DAP/51DAP	0.97964	1
53DAP/52DAP	1.02333	0.944
55DAP/53DAP	0.92922	0.478
57DAP/55DAP	1.16241	0.067
62DAP/57DAP	0.94881	0.681
68DAP/62DAP	1.07218	0.984
68DAP/14DAP	0.9839	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93132	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70993	0.261
Mature Green Tomato/Ripe Tomato	0.82293	0.055
Immature Eggplant/Mature Eggplant	1.30271	0.239
Ripe Pepper/Ripe Tomato	3.64389	1
Mature Eggplant/Ripe Tomato	2.01348

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97693	0.961
1-1-2/M82	0.96089	1
12-2/M82	0.96851	0.955
12-4/M82	0.93444	0.619
1-3/M82	1.01639	1
2-1-1/M82	1.022	1
2-1/M82	1.22849	1
2-6/M82	0.98683	1
3-2/M82	1.03524	0.388
4-1-1/M82	1.11731	1
4-1/M82	0.99493	1
4-3-2/M82	0.96085	1
4-3/M82	1.01157	1
5-3/M82	0.97403	1
6-2/M82	1.0169	1
6-3/M82	1.06155	1
7-1/M82	0.91918	0.509
7-2/M82	0.92019	0.796
9-3-2/M82	0.80735	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.05314	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.12039	1
IL12-4/WTpooled	1.17562	0.525
IL1-4/WTpooled	1.49034
WT/WTpooled	0.98104	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	1.07327

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03728	0.921
DC3000/delta hrp 6h	1.12015	1
DC3000/delta hrp 12h	0.9456	1
DC3000/delta hrp 24h	1.04547	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09741	0.076
DC3000 delta B/DC3000 delta AB	1.21875	0.181

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04844	1
Exp 36h	1.58567	0.693
Exp 60h	1.56837	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02315	1
Var 0h	1.92835	1
Var 12h I row2-row1	1.12829	0.379
Var 12h NI row2-row1	0.97871	0.713
Var 36h I row2-row1	1.09851	1
Var 36h NI row2-row1	0.92057	0.421
Var 60h I row2-row1	1.19855	1
Var 60h NI row2-row1	1.07889	0.904
Time course 0hI-0hNI	1.01231	1
Time course 12hI-12hNI	1.02557	0.816
Time course 36hI-36hNI	1.07871	0.128
Time course 60hI-60hNI	1.52752	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)	0.94686	0.662
transgenic ySAMdc/azygous control (breaker)	1.35297	1
transgenic ySAMdc/azygous control (red)	1.31652	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97757	0.313

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.18729	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00706	1
Manapal/WT (break)	1.01504	1
Manapal/WT (red)	0.75483	0.181