Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.9.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98063	0.76
27DAP/17DAP	0.89286	0.751
39DAP/27DAP	1.28985	0.626
41DAP/39DAP	0.75	0.153
42DAP/41DAP	0.99134	1
43DAP/42DAP	1.08191	1
47DAP/43DAP	0.9574	0.799
52DAP/47DAP	1.35848	0.446
57DAP/52DAP	1.22788	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09254	0.278
17DAP/reference	1.25596	0.127
27DAP/reference	1.25788	0.069
39DAP/reference	1.49557	0.012
41DAP/reference	1.32405	0.03
42DAP/reference	1.09173	0.144
43DAP/reference	1.16923	0.089
47DAP/reference	1.68542	0.001
52DAP/reference	1.33929	0.021
57DAP/reference	1.44646	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.82126	0.111
27DAP/17DAP	1.31201	0.564
39DAP/27DAP	0.90962	0.594
41DAP/39DAP	1.11613	1
42DAP/41DAP	1.06977	0.825
43DAP/42DAP	0.87485	0.308
47DAP/43DAP	1.14681	0.788
52DAP/47DAP	1.26792	0.563
57DAP/52DAP	1.45434	0.106
57DAP/7DAP	1.23448	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.67413	0.032
17DAP/reference	1.53952	0.007
27DAP/reference	1.42782	0.007
39DAP/reference	1.80719	0.005
41DAP/reference	1.54877	0.028
42DAP/reference	1.77295	0.006
43DAP/reference	2.05895	0.01
47DAP/reference	1.62024	0.04
52DAP/reference	1.75105	0.011
57DAP/reference	1.85029	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92696	0.399
17DAP/reference	1.15336	0.139
27DAP/reference	1.39338	0.053
39DAP/reference	1.31726	0.025
41DAP/reference	1.31364	0.036
42DAP/reference	1.27766	0.015
43DAP/reference	1.01142	0.801
47DAP/reference	1.3691	0.019
52DAP/reference	1.13161	0.124
57DAP/reference	0.94068	0.408

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23889	0.122
17DAP/reference	0.99653	0.792
27DAP/reference	1.55508	0.02
39DAP/reference	1.44081	0.019
41DAP/reference	1.06454	0.357
42DAP/reference	1.11513	0.347
43DAP/reference	1.1262	0.285
47DAP/reference	1.09734	0.372
52DAP/reference	1.50169	0.033
57DAP/reference	1.8347	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.953	1
26DAP/20DAP	3.1953	0.099
34DAP/26DAP	0.62897	0.111
51DAP/34DAP	1.60198	0.092
52DAP/51DAP	0.85271	1
53DAP/52DAP	1.17662	0.678
55DAP/53DAP	0.55061	0.017
57DAP/55DAP	0.97604	0.859
62DAP/57DAP	0.88711	0.681
68DAP/62DAP	1.30942	0.36
68DAP/14DAP	2.1199	0.025

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.32303	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.83576	0.318
Mature Green Tomato/Ripe Tomato	1.29498
Immature Eggplant/Mature Eggplant	1.0281	0.606
Ripe Pepper/Ripe Tomato	0.91522	1
Mature Eggplant/Ripe Tomato	1.17748	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.77774	0.605
1-1-2/M82	1.11623	1
12-2/M82	1.15997	1
12-4/M82	1.1521	1
1-3/M82	1.40694	0.277
2-1-1/M82	0.73329	0.465
2-1/M82	0.80495	0.74
2-6/M82	0.73931	1
3-2/M82	0.95578	1
4-1-1/M82	0.96205	1
4-1/M82	0.90225
4-3-2/M82	0.91579	1
4-3/M82	1.25548	1
5-3/M82	0.95426	1
6-2/M82	0.95109	1
6-3/M82	1.04567	1
7-1/M82	0.93769	1
7-2/M82	1.2632	0.324
9-3-2/M82	1.10783	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.13717	0.365
IL2-6/WTpooled	1.24595	0.395
IL7-5/WTpooled	2.02663	0.6
IL7-3/WTpooled	0.88809	0.31
IL12-4/WTpooled	0.81828	0.484
IL1-4/WTpooled	1.24736	1
WT/WTpooled	0.98641	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	1.19188	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9897	1
DC3000/delta hrp 6h	0.81749	0.95
DC3000/delta hrp 12h	1.07084	1
DC3000/delta hrp 24h	1.01493	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07683	0.355
DC3000 delta B/DC3000 delta AB	1.13624	0.302

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0071	1
Exp 36h	1.57121	1
Exp 60h	1.36998	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0011	1
Var 0h	1.12231	0.782
Var 12h I row2-row1	1.12935	0.654
Var 12h NI row2-row1	1.24356	0.649
Var 36h I row2-row1	0.95714	1
Var 36h NI row2-row1	0.92742	0.743
Var 60h I row2-row1	0.65636	0.285
Var 60h NI row2-row1	0.9244	0.977
Time course 0hI-0hNI	0.97751	0.892
Time course 12hI-12hNI	1.07729	0.55
Time course 36hI-36hNI	1.34291	0.01
Time course 60hI-60hNI	1.89071	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)	1.26837	0.261
transgenic ySAMdc/azygous control (breaker)	0.68845	0.15
transgenic ySAMdc/azygous control (red)	0.95741	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12502	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.62697	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85379	1
Manapal/WT (break)	1.28127	0.381
Manapal/WT (red)	1.00718	1