Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.6.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.87637	0.394
27DAP/17DAP	5.83652	0.034
39DAP/27DAP	4.25441	0.025
41DAP/39DAP	2.20517	0.285
42DAP/41DAP	1.61389	0.026
43DAP/42DAP	1.65734	0.445
47DAP/43DAP	0.95253	0.825
52DAP/47DAP	0.38835	0.033
57DAP/52DAP	0.59618	0.513

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04653	0.814
17DAP/reference	1.50751	0.014
27DAP/reference	1.16431	0.109
39DAP/reference	1.30631	0.132
41DAP/reference	1.45076	0.012
42DAP/reference	0.83007	0.007
43DAP/reference	0.89843	0.093
47DAP/reference	0.79193	0.003
52DAP/reference	0.75421	0.038
57DAP/reference	0.74839	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75295	0.26
27DAP/17DAP	1.17513	0.872
39DAP/27DAP	5.91601	0.039
41DAP/39DAP	2.02359	0.119
42DAP/41DAP	0.95348	0.484
43DAP/42DAP	0.8349	0.308
47DAP/43DAP	2.51534	0.019
52DAP/47DAP	0.68473	0.254
57DAP/52DAP	1.08599	0.628
57DAP/7DAP	4.22856	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54802	0.033
17DAP/reference	1.18107	0.014
27DAP/reference	1.51413	0.131
39DAP/reference	2.59406	0.005
41DAP/reference	1.45023	0.022
42DAP/reference	3.3355	0.012
43DAP/reference	2.4987	0.014
47DAP/reference	2.41669	0.018
52DAP/reference	5.69588	0.007
57DAP/reference	5.39135	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84218	0.17
17DAP/reference	1.63282	0.015
27DAP/reference	1.47335	0.018
39DAP/reference	2.78484	0.011
41DAP/reference	1.62393	0.005
42DAP/reference	1.91718	0.008
43DAP/reference	1.5576	0.026
47DAP/reference	2.07955	0.008
52DAP/reference	2.6723	0.006
57DAP/reference	1.77577	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07687	0.75
17DAP/reference	1.51169	0.139
27DAP/reference	1.13608	0.34
39DAP/reference	1.80924	0.006
41DAP/reference	1.82782	0.008
42DAP/reference	1.32004	0.313
43DAP/reference	1.49464	0.148
47DAP/reference	0.7518	0.007
52DAP/reference	0.91218	0.424
57DAP/reference	0.75071	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11927	0.916
26DAP/20DAP	1.14001	0.608
34DAP/26DAP	1.23835	0.819
51DAP/34DAP	0.89576	0.546
52DAP/51DAP	1.04822	1
53DAP/52DAP	1.09818	0.858
55DAP/53DAP	0.93364	0.675
57DAP/55DAP	0.87468	0.539
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.04605	1
68DAP/14DAP	0.67035	0.054

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	10.2017	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	8.40353	0.058
Mature Green Tomato/Ripe Tomato	0.238	0.017
Immature Eggplant/Mature Eggplant	0.16837	0.057
Ripe Pepper/Ripe Tomato	1.19788	1
Mature Eggplant/Ripe Tomato	2.56148	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.2686	0.591
1-1-2/M82	1.41803	1
12-2/M82	0.60706
12-4/M82	1.06344	0.655
1-3/M82	3.47782	0.248
2-1-1/M82	0.97126	1
2-1/M82	1.20552	0.345
2-6/M82	1.93987	0.395
3-2/M82	1.00486	1
4-1-1/M82	1.48102	1
4-1/M82	1.90739	0.512
4-3-2/M82	3.2108	0.246
4-3/M82	1.26346	0.268
5-3/M82	1.56121	0.572
6-2/M82	3.26074	0.253
6-3/M82	0.96911	1
7-1/M82	1.49081	0.741
7-2/M82	2.24568	0.385
9-3-2/M82	2.74698

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.44545
IL12-4/WTpooled	0.89192	0.71
IL1-4/WTpooled	0.95051	0.476
WT/WTpooled	0.89865

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	0.84349	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9992
DC3000/delta hrp 6h	0.98308	0.95
DC3000/delta hrp 12h	0.82794	1
DC3000/delta hrp 24h	0.72777	0.071

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.5216	0.408
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	0.66178	0.265
Exp 36h	0.61614	0.321
Exp 60h	0.33161	0.258

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99695	1
Var 0h	1.11791	0.98
Var 12h I row2-row1	1.11201	0.224
Var 12h NI row2-row1	1.11704	0.235
Var 36h I row2-row1	1.11411	1
Var 36h NI row2-row1	1.08439	1
Var 60h I row2-row1	0.9323	0.952
Var 60h NI row2-row1	1.18768	0.904
Time course 0hI-0hNI	0.87392	0.144
Time course 12hI-12hNI	1.02371	0.818
Time course 36hI-36hNI	0.8488	0.045
Time course 60hI-60hNI	0.6429	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)	1.1743	0.612
transgenic ySAMdc/azygous control (breaker)	0.57819	0.173
transgenic ySAMdc/azygous control (red)	1.62641	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00514	0.909

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.4872	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.07135	1
Manapal/WT (break)	0.66199	0.333
Manapal/WT (red)	0.57534	0.188