Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.17.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72511	0.232
27DAP/17DAP	1.46287	0.625
39DAP/27DAP	1.09069	0.992
41DAP/39DAP	0.85261	0.453
42DAP/41DAP	1.28116	0.582
43DAP/42DAP	1.24148	1
47DAP/43DAP	0.75253	0.276
52DAP/47DAP	1.63146	0.307
57DAP/52DAP	0.91184	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26937	0.05
17DAP/reference	1.05915	0.585
27DAP/reference	1.21778	0.15
39DAP/reference	1.14122	0.236
41DAP/reference	1.12462	0.393
42DAP/reference	1.24082	0.002
43DAP/reference	0.98022	0.708
47DAP/reference	1.04342	0.433
52DAP/reference	1.03825	0.695
57DAP/reference	0.99582	0.701

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82469	0.277
27DAP/17DAP	0.88139	0.748
39DAP/27DAP	1.08537	0.581
41DAP/39DAP	1.18058	0.531
42DAP/41DAP	0.64918	0.009
43DAP/42DAP	1.17568	0.042
47DAP/43DAP	1.08325	0.822
52DAP/47DAP	1.35795	0.19
57DAP/52DAP	1.14577	0.745
57DAP/7DAP	1.09469	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70565	0.077
17DAP/reference	0.82503	0.019
27DAP/reference	1.07094	0.804
39DAP/reference	0.66937	0.011
41DAP/reference	0.82431	0.039
42DAP/reference	0.77798	0.012
43DAP/reference	0.86559	0.095
47DAP/reference	0.87124	0.222
52DAP/reference	0.88813	0.126
57DAP/reference	1.2269	0.035

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03922	0.926
17DAP/reference	1.33412	0.027
27DAP/reference	1.15965	0.31
39DAP/reference	1.26303	0.056
41DAP/reference	1.32623	0.035
42DAP/reference	1.3264	0.053
43DAP/reference	1.53158	0.027
47DAP/reference	1.33462	0.008
52DAP/reference	1.40765	0.006
57DAP/reference	1.45775	0.025

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80014	0.071
17DAP/reference	1.00119	0.739
27DAP/reference	0.80138	0.063
39DAP/reference	1.07534	0.422
41DAP/reference	1.05227	0.961
42DAP/reference	1.1942	0.3
43DAP/reference	1.22424	0.139
47DAP/reference	1.09846	0.265
52DAP/reference	1.07159	0.979
57DAP/reference	1.39045	0.141

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09147	0.966
26DAP/20DAP	0.98645	1
34DAP/26DAP	1.25592	0.819
51DAP/34DAP	0.59441	0.072
52DAP/51DAP	0.88607	0.151
53DAP/52DAP	0.89509	0.621
55DAP/53DAP	0.82836	0.389
57DAP/55DAP	0.81663	0.268
62DAP/57DAP	1.0157	1
68DAP/62DAP	1.13762	1
68DAP/14DAP	0.8477	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.58067	0.052

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.09761	0.06
Mature Green Tomato/Ripe Tomato	0.60187	0.033
Immature Eggplant/Mature Eggplant	6.39576	0.066
Ripe Pepper/Ripe Tomato	0.66319	1
Mature Eggplant/Ripe Tomato	0.36129	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.02025
12-2/M82	1.98306	0.519
12-4/M82	0.97314
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
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	1.08257	1
5-3/M82	0.50839	0.364
6-2/M82	1.31392
6-3/M82	N/A	N/A
7-1/M82	1.32567
7-2/M82	N/A	N/A
9-3-2/M82	1.00238

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01635	0.277
IL2-6/WTpooled	1.06559	0.395
IL7-5/WTpooled	1.01867	1
IL7-3/WTpooled	0.90003	0.31
IL12-4/WTpooled	0.94917	1
IL1-4/WTpooled	1.10857	0.426
WT/WTpooled	1.01599	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	1.00481	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13377	0.846
DC3000/delta hrp 6h	0.95985	0.95
DC3000/delta hrp 12h	1.07591	1
DC3000/delta hrp 24h	1.09678	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.52663	0.023
DC3000 delta B/DC3000 delta AB	0.4382	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17022	0.254
Exp 36h	1.28204	0.409
Exp 60h	1.15321	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02799	1
Var 0h	1.18648	0.259
Var 12h I row2-row1	1.10637	0.324
Var 12h NI row2-row1	0.85864	0.494
Var 36h I row2-row1	1.03814	0.489
Var 36h NI row2-row1	0.96686	0.791
Var 60h I row2-row1	0.97846	1
Var 60h NI row2-row1	1.03892	0.904
Time course 0hI-0hNI	1.042	0.833
Time course 12hI-12hNI	1.2721	0.012
Time course 36hI-36hNI	1.1393	0.063
Time course 60hI-60hNI	0.33862	0.005

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)	1.61541	0.321
transgenic ySAMdc/azygous control (breaker)	0.52839	0.132
transgenic ySAMdc/azygous control (red)	1.31926	0.92

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	0.58236	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0431	1
Manapal/WT (break)	0.90358	1
Manapal/WT (red)	2.14113	1