Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.9.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97105	0.722
27DAP/17DAP	1.17741	0.883
39DAP/27DAP	1.78428	0.287
41DAP/39DAP	0.89765	0.65
42DAP/41DAP	1.1417	0.92
43DAP/42DAP	0.88953	0.799
47DAP/43DAP	1.14628	0.825
52DAP/47DAP	0.62488	0.184
57DAP/52DAP	1.12091	0.995

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03428	0.994
17DAP/reference	1.07851	0.154
27DAP/reference	1.07112	0.52
39DAP/reference	1.10391	0.108
41DAP/reference	1.24657	0.014
42DAP/reference	1.0264	0.869
43DAP/reference	1.08649	0.133
47DAP/reference	1.07249	0.295
52DAP/reference	0.92446	0.237
57DAP/reference	0.82188	0.071

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88746	0.277
27DAP/17DAP	1.11577	0.639
39DAP/27DAP	1.50658	0.067
41DAP/39DAP	0.75741	0.013
42DAP/41DAP	1.06876	0.753
43DAP/42DAP	1.51319	0.013
47DAP/43DAP	1.06167	0.744
52DAP/47DAP	0.93806	0.634
57DAP/52DAP	0.87013	0.457
57DAP/7DAP	1.33632	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03815	0.927
17DAP/reference	1.04576	0.627
27DAP/reference	1.34451	0.02
39DAP/reference	1.09423	0.333
41DAP/reference	1.01057	0.811
42DAP/reference	1.23502	0.059
43DAP/reference	1.49263	0.018
47DAP/reference	1.65635	0.048
52DAP/reference	1.688	0.023
57DAP/reference	1.13258	0.125

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09012	0.238
17DAP/reference	1.12518	0.066
27DAP/reference	0.98902	0.598
39DAP/reference	1.08142	0.514
41DAP/reference	0.90689	0.145
42DAP/reference	1.01525	1
43DAP/reference	1.36715	0.029
47DAP/reference	1.08144	0.256
52DAP/reference	1.02619	0.789
57DAP/reference	1.23291	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0597	0.659
17DAP/reference	0.95908	0.499
27DAP/reference	0.96224	0.49
39DAP/reference	1.06148	0.342
41DAP/reference	1.1015	0.286
42DAP/reference	1.18592	0.239
43DAP/reference	0.88924	0.197
47DAP/reference	0.98956	0.593
52DAP/reference	1.25471	0.257
57DAP/reference	1.94977	0.939

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17187	0.735
26DAP/20DAP	0.81309	0.512
34DAP/26DAP	1.08186	0.819
51DAP/34DAP	1.19081	0.326
52DAP/51DAP	0.71013	0.151
53DAP/52DAP	1.23981	0.117
55DAP/53DAP	1.0782	0.622
57DAP/55DAP	1.02365	0.975
62DAP/57DAP	0.99418	0.994
68DAP/62DAP	0.80783	0.118
68DAP/14DAP	0.85244	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.30062	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.68844	0.181
Mature Green Tomato/Ripe Tomato	0.84133	0.096
Immature Eggplant/Mature Eggplant	1.42737	0.05
Ripe Pepper/Ripe Tomato	0.79259	0.293
Mature Eggplant/Ripe Tomato	0.38215	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02474	1
1-1-2/M82	1.13665	1
12-2/M82	1.4175	1
12-4/M82	1.31816	1
1-3/M82	2.78279	0.248
2-1-1/M82	0.96443	0.465
2-1/M82	0.80317	0.345
2-6/M82	0.77215	1
3-2/M82	1.27565	0.84
4-1-1/M82	0.71368	0.959
4-1/M82	N/A	N/A
4-3-2/M82	1.22272
4-3/M82	1.55123	1
5-3/M82	0.99507	1
6-2/M82	1.04392	1
6-3/M82	1.17111	1
7-1/M82	0.54732	0.408
7-2/M82	1.12053	0.291
9-3-2/M82	1.4498	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.74892	0.365
IL2-6/WTpooled	1.53448	0.395
IL7-5/WTpooled	2.25128	0.635
IL7-3/WTpooled	1.33039	1
IL12-4/WTpooled	1.28463	0.49
IL1-4/WTpooled	1.19372	1
WT/WTpooled	0.93324	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	1.14023	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14344	0.846
DC3000/delta hrp 6h	1.28666	1
DC3000/delta hrp 12h	0.86939	1
DC3000/delta hrp 24h	1.30585	0.057

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.24979	0.042
DC3000 delta B/DC3000 delta AB	1.06774	0.535

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.19807	0.254
Exp 36h	1.52842	0.326
Exp 60h	1.41534	0.226

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

hybridization	ratio	FDR (corrected p value)
self-self	0.92247	1
Var 0h	1.10329	0.936
Var 12h I row2-row1	1.14341	0.406
Var 12h NI row2-row1	1.06555	1
Var 36h I row2-row1	1.07809	1
Var 36h NI row2-row1	0.80085	0.645
Var 60h I row2-row1	0.85332	0.285
Var 60h NI row2-row1	0.9432	0.932
Time course 0hI-0hNI	1.03455	0.852
Time course 12hI-12hNI	1.50632	0.067
Time course 36hI-36hNI	2.61731	0.005
Time course 60hI-60hNI	10.6174	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)	0.85591	0.285
transgenic ySAMdc/azygous control (breaker)	1.59266	0.248
transgenic ySAMdc/azygous control (red)	1.43698	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07882	0.061

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.17515	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92109	1
Manapal/WT (break)	1.19084	0.381
Manapal/WT (red)	0.89297	0.503