Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.19.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11824	0.477
27DAP/17DAP	1.03458	0.905
39DAP/27DAP	1.04167	0.769
41DAP/39DAP	1.34019	0.286
42DAP/41DAP	0.96351	1
43DAP/42DAP	1.07072	1
47DAP/43DAP	1.22225	0.569
52DAP/47DAP	1.45856	0.325
57DAP/52DAP	0.85383	0.74

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0747	0.403
17DAP/reference	1.05374	0.585
27DAP/reference	0.92344	0.124
39DAP/reference	0.98123	0.734
41DAP/reference	1.12092	0.05
42DAP/reference	1.0438	0.166
43DAP/reference	1.07329	0.306
47DAP/reference	0.99313	0.568
52DAP/reference	1.02389	0.951
57DAP/reference	0.95956	0.395

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97775	0.716
27DAP/17DAP	1.12729	0.645
39DAP/27DAP	1.31077	0.173
41DAP/39DAP	0.7368	0.013
42DAP/41DAP	1.5882	0.003
43DAP/42DAP	2.44135	0.013
47DAP/43DAP	0.94834	0.687
52DAP/47DAP	1.16234	0.66
57DAP/52DAP	1.03141	0.913
57DAP/7DAP	2.29806	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93987	0.296
17DAP/reference	0.80405	0.02
27DAP/reference	0.81421	0.017
39DAP/reference	0.96093	0.264
41DAP/reference	0.93775	0.046
42DAP/reference	0.9827	0.506
43DAP/reference	0.8487	0.027
47DAP/reference	0.86718	0.066
52DAP/reference	0.83222	0.024
57DAP/reference	0.81127	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11858	0.246
17DAP/reference	1.13597	0.396
27DAP/reference	1.17257	0.09
39DAP/reference	1.07471	0.502
41DAP/reference	1.0614	0.814
42DAP/reference	1.00788	1
43DAP/reference	1.40283	0.03
47DAP/reference	0.92574	0.099
52DAP/reference	1.11435	0.074
57DAP/reference	1.19087	0.374

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85836	0.052
17DAP/reference	0.99329	0.792
27DAP/reference	0.85842	0.033
39DAP/reference	0.90701	0.163
41DAP/reference	0.91702	0.07
42DAP/reference	1.04966	1
43DAP/reference	1.05684	0.961
47DAP/reference	1.15805	0.063
52DAP/reference	0.90894	0.433
57DAP/reference	0.99283	0.73

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97353	1
26DAP/20DAP	0.95955	1
34DAP/26DAP	0.92676	0.619
51DAP/34DAP	1.07745	0.692
52DAP/51DAP	1.06927	0.758
53DAP/52DAP	1.51612	0.049
55DAP/53DAP	1.07299	0.29
57DAP/55DAP	0.8176	0.253
62DAP/57DAP	0.95615	0.994
68DAP/62DAP	0.94933	0.787
68DAP/14DAP	0.86814	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.2353	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.34074	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.96935
Mature Eggplant/Ripe Tomato	0.409

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90596	0.944
1-1-2/M82	0.90807	0.804
12-2/M82	1.13738
12-4/M82	1.38223	1
1-3/M82	0.81922	0.501
2-1-1/M82	1.24818	0.689
2-1/M82	N/A	N/A
2-6/M82	1.08554	0.594
3-2/M82	N/A	N/A
4-1-1/M82	1.0913
4-1/M82	1.2408
4-3-2/M82	0.95965	1
4-3/M82	N/A	N/A
5-3/M82	0.99505	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.05896	1
9-3-2/M82	1.35277	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01615	1
IL2-6/WTpooled	0.85728	1
IL7-5/WTpooled	1.20272
IL7-3/WTpooled	1.00711	1
IL12-4/WTpooled	1.0822	0.785
IL1-4/WTpooled	0.98756	1
WT/WTpooled	0.97156	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	0.99042	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02403	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.05622	1
DC3000/delta hrp 24h	1.05193	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.26959
DC3000 delta B/DC3000 delta AB	1.00505	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0174	1
Var 0h	0.81022	0.332
Var 12h I row2-row1	1.16781	0.254
Var 12h NI row2-row1	0.90085	0.546
Var 36h I row2-row1	0.97799	0.805
Var 36h NI row2-row1	0.94275	0.706
Var 60h I row2-row1	1.11776	1
Var 60h NI row2-row1	0.95134	1
Time course 0hI-0hNI	1.13947	0.574
Time course 12hI-12hNI	1.00968	0.867
Time course 36hI-36hNI	0.99117	0.68
Time course 60hI-60hNI	1.58693	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)	0.96393	0.454
transgenic ySAMdc/azygous control (breaker)	1.02277	1
transgenic ySAMdc/azygous control (red)	0.78511	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00744	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14957	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.67476	0.083
Manapal/WT (break)	1.52104	0.14
Manapal/WT (red)	3.02057	0.126