Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.15.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.55552	0.05
27DAP/17DAP	2.29917	0.353
39DAP/27DAP	0.94663	0.67
41DAP/39DAP	0.68977	0.145
42DAP/41DAP	1.09132	0.983
43DAP/42DAP	1.15555	0.974
47DAP/43DAP	1.10899	0.647
52DAP/47DAP	1.14021	0.937
57DAP/52DAP	1.08104	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95162	0.205
17DAP/reference	1.01528	0.907
27DAP/reference	1.02079	0.806
39DAP/reference	0.99678	0.957
41DAP/reference	0.932	0.267
42DAP/reference	0.86979	0.009
43DAP/reference	0.9358	0.148
47DAP/reference	1.00557	1
52DAP/reference	0.96498	0.393
57DAP/reference	1.01917	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8614	0.402
27DAP/17DAP	0.98414	0.943
39DAP/27DAP	1.36127	0.505
41DAP/39DAP	1.17328	0.612
42DAP/41DAP	0.65075	0.104
43DAP/42DAP	1.27345	0.162
47DAP/43DAP	0.94925	0.843
52DAP/47DAP	1.18347	0.558
57DAP/52DAP	0.9169	0.695
57DAP/7DAP	0.9998	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13105	0.444
17DAP/reference	1.1787	0.269
27DAP/reference	1.03137	0.804
39DAP/reference	1.09001	0.391
41DAP/reference	1.01729	1
42DAP/reference	1.16443	0.308
43DAP/reference	1.13044	0.188
47DAP/reference	0.89845	0.168
52DAP/reference	0.90072	0.213
57DAP/reference	1.01114	0.775

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95087	0.441
17DAP/reference	0.93283	0.037
27DAP/reference	0.82182	0.062
39DAP/reference	0.89642	0.085
41DAP/reference	0.9901	0.57
42DAP/reference	0.88435	0.035
43DAP/reference	0.94661	0.378
47DAP/reference	0.93394	0.062
52DAP/reference	0.97388	0.38
57DAP/reference	0.95072	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0569	0.775
17DAP/reference	1.05876	0.712
27DAP/reference	1.02282	0.934
39DAP/reference	0.97867	0.544
41DAP/reference	0.89789	0.264
42DAP/reference	0.78517	0.019
43DAP/reference	0.82934	0.137
47DAP/reference	0.96488	0.259
52DAP/reference	1.16794	0.566
57DAP/reference	0.77312	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05905	1
26DAP/20DAP	0.97005	1
34DAP/26DAP	1.07247	1
51DAP/34DAP	1.69724	0.281
52DAP/51DAP	1.11405	0.783
53DAP/52DAP	1.25994	0.104
55DAP/53DAP	0.99676	0.886
57DAP/55DAP	0.84953	0.313
62DAP/57DAP	1.12522	0.569
68DAP/62DAP	1.05252	1
68DAP/14DAP	1.10531	0.236

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.13229	0.635

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.35408
Mature Green Tomato/Ripe Tomato	0.35389
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.53225
Mature Eggplant/Ripe Tomato	0.85863

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.14172
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.95904
1-3/M82	0.68526
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.08506	0.695
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	N/A	N/A
5-3/M82	0.85352	0.642
6-2/M82	1.02897
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.99164
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.71833	0.243
IL2-6/WTpooled	1.03384	1
IL7-5/WTpooled	1.64855	0.792
IL7-3/WTpooled	0.72705	0.294
IL12-4/WTpooled	1.20687	0.595
IL1-4/WTpooled	1.07329	1
WT/WTpooled	1.11775	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	1.82049

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05638	0.921
DC3000/delta hrp 6h	1.07907	0.95
DC3000/delta hrp 12h	1.21472	1
DC3000/delta hrp 24h	1.38713	0.059

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.5472	0.371
Exp 60h	1.23228	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99486	1
Var 0h	0.52366	0.457
Var 12h I row2-row1	1.1458	0.348
Var 12h NI row2-row1	0.96293	0.906
Var 36h I row2-row1	0.81052	1
Var 36h NI row2-row1	0.64996	0.645
Var 60h I row2-row1	1.13963	0.523
Var 60h NI row2-row1	0.93128	0.904
Time course 0hI-0hNI	1.07003	0.985
Time course 12hI-12hNI	1.18225	0.242
Time course 36hI-36hNI	2.14218	0.006
Time course 60hI-60hNI	1.92483	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)	0.77791	0.3
transgenic ySAMdc/azygous control (breaker)	1.11461	1
transgenic ySAMdc/azygous control (red)	1.27126	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95927	0.172

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96509	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99512	1
Manapal/WT (break)	0.63913	0.333
Manapal/WT (red)	0.57941	0.181