Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.11.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.48778	0.014
27DAP/17DAP	0.41648	0.027
39DAP/27DAP	1.06241	0.769
41DAP/39DAP	0.51821	0.049
42DAP/41DAP	0.8109	0.774
43DAP/42DAP	1.26923	0.69
47DAP/43DAP	0.87478	0.562
52DAP/47DAP	1.17866	0.786
57DAP/52DAP	0.84043	0.82

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.73212	0.007
17DAP/reference	2.05225	0.016
27DAP/reference	2.46435	0.014
39DAP/reference	0.73466	0.015
41DAP/reference	0.62691	0.009
42DAP/reference	0.84234	0.005
43DAP/reference	0.46293	0.012
47DAP/reference	0.43436	0.001
52DAP/reference	0.52043	0.012
57DAP/reference	0.53037	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.27901	0.025
27DAP/17DAP	2.23019	0.02
39DAP/27DAP	0.47556	0.032
41DAP/39DAP	0.31135	0.013
42DAP/41DAP	0.98177	0.753
43DAP/42DAP	1.49965	0.018
47DAP/43DAP	0.67452	0.021
52DAP/47DAP	0.90953	0.634
57DAP/52DAP	1.11225	0.851
57DAP/7DAP	0.07374	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.73344	0.05
17DAP/reference	1.31878	0.01
27DAP/reference	1.32148	0.012
39DAP/reference	0.97272	0.354
41DAP/reference	0.87087	0.029
42DAP/reference	1.0694	0.405
43DAP/reference	0.89851	0.151
47DAP/reference	0.64603	0.066
52DAP/reference	1.0813	0.428
57DAP/reference	0.94537	0.123

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.94384	0.063
17DAP/reference	1.92975	0.018
27DAP/reference	1.56295	0.149
39DAP/reference	0.38962	0.007
41DAP/reference	0.64041	0.006
42DAP/reference	1.25295	0.369
43DAP/reference	0.57844	0.005
47DAP/reference	0.70805	0.027
52DAP/reference	0.40785	0.004
57DAP/reference	0.34517	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.74895	0.017
17DAP/reference	1.80702	0.046
27DAP/reference	1.68286	0.02
39DAP/reference	1.04597	0.752
41DAP/reference	1.06872	0.57
42DAP/reference	1.01047	1
43DAP/reference	0.7216	0.084
47DAP/reference	0.34868	0.004
52DAP/reference	0.71566	0.223
57DAP/reference	0.50239	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.27556	0.43
26DAP/20DAP	1.29994	0.394
34DAP/26DAP	0.75208	0.286
51DAP/34DAP	0.5396	0.049
52DAP/51DAP	1.04205	0.708
53DAP/52DAP	0.64232	0.049
55DAP/53DAP	0.42192	0.016
57DAP/55DAP	0.77294	0.246
62DAP/57DAP	1.12019	0.767
68DAP/62DAP	0.6736	0.177
68DAP/14DAP	0.17726	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.11131	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.73099	0.058
Mature Green Tomato/Ripe Tomato	3.73819	0.016
Immature Eggplant/Mature Eggplant	0.5907	0.07
Ripe Pepper/Ripe Tomato	23.1395	0.258
Mature Eggplant/Ripe Tomato	45.0388	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01556	1
1-1-2/M82	0.99236	1
12-2/M82	1.57635
12-4/M82	0.95875	1
1-3/M82	0.82267	0.501
2-1-1/M82	1.21171
2-1/M82	N/A	N/A
2-6/M82	1.16908	0.594
3-2/M82	1.04385
4-1-1/M82	0.9674	1
4-1/M82	0.90736	1
4-3-2/M82	0.77521	0.698
4-3/M82	0.92693	1
5-3/M82	0.90143	0.642
6-2/M82	0.68089
6-3/M82	0.95171	1
7-1/M82	N/A	N/A
7-2/M82	0.94252	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.29264	0.365
IL2-6/WTpooled	0.94066	1
IL7-5/WTpooled	0.99912	1
IL7-3/WTpooled	1.47347	0.362
IL12-4/WTpooled	1.21031	0.538
IL1-4/WTpooled	1.20736	1
WT/WTpooled	0.95246	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	0.91385	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97102	1
DC3000/delta hrp 6h	0.9576	0.95
DC3000/delta hrp 12h	0.76014	1
DC3000/delta hrp 24h	0.80222	0.246

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.68323	0.041
DC3000 delta B/DC3000 delta AB	0.53695	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01073	1
Exp 36h	0.91922	0.504
Exp 60h	0.91088	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03877	1
Var 0h	0.93009	0.933
Var 12h I row2-row1	0.93511	0.77
Var 12h NI row2-row1	0.91659	0.713
Var 36h I row2-row1	1.11492	0.41
Var 36h NI row2-row1	1.18976	1
Var 60h I row2-row1	1.00984	1
Var 60h NI row2-row1	1.00125	1
Time course 0hI-0hNI	1.102	0.413
Time course 12hI-12hNI	0.98611	0.931
Time course 36hI-36hNI	0.87408	0.076
Time course 60hI-60hNI	0.49154	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)	0.84741	0.454
transgenic ySAMdc/azygous control (breaker)	2.17934	1
transgenic ySAMdc/azygous control (red)	1.01825	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.70568	0.064

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.11489	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.25422	0.14
Manapal/WT (break)	1.79284	1
Manapal/WT (red)	1.28586	1