Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.7.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09848	0.798
27DAP/17DAP	1.15509	0.841
39DAP/27DAP	1.2404	0.725
41DAP/39DAP	0.87645	0.494
42DAP/41DAP	0.97367	1
43DAP/42DAP	1.08496	1
47DAP/43DAP	1.29706	0.609
52DAP/47DAP	0.88041	0.668
57DAP/52DAP	1.15987	0.93

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07989	0.806
17DAP/reference	1.12435	1
27DAP/reference	1.82127	0.018
39DAP/reference	1.27533	0.486
41DAP/reference	1.08776	0.855
42DAP/reference	1.77393	0.001
43DAP/reference	1.48617	0.007
47DAP/reference	1.91142	0.001
52DAP/reference	1.29509	0.186
57DAP/reference	1.44923	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85429	0.289
27DAP/17DAP	1.09321	0.686
39DAP/27DAP	0.94997	0.55
41DAP/39DAP	1.01509	0.914
42DAP/41DAP	1.0947	0.487
43DAP/42DAP	0.96644	0.522
47DAP/43DAP	1.00397	1
52DAP/47DAP	1.22585	0.367
57DAP/52DAP	1.34213	0.14
57DAP/7DAP	0.96241	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34821	0.058
17DAP/reference	1.2957	0.007
27DAP/reference	1.83708	0.007
39DAP/reference	2.86473	0.005
41DAP/reference	1.55284	0.021
42DAP/reference	3.0216	0.006
43DAP/reference	3.37807	0.006
47DAP/reference	2.24633	0.036
52DAP/reference	2.57075	0.007
57DAP/reference	1.96525	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65984	0.034
17DAP/reference	1.12689	0.739
27DAP/reference	1.47915	0.044
39DAP/reference	1.91809	0.015
41DAP/reference	1.2121	0.248
42DAP/reference	2.20855	0.01
43DAP/reference	1.20613	0.929
47DAP/reference	2.43416	0.008
52DAP/reference	1.15294	0.114
57DAP/reference	0.96976	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08751	0.505
17DAP/reference	1.15325	0.518
27DAP/reference	2.26454	0.014
39DAP/reference	2.41957	0.005
41DAP/reference	1.85829	0.007
42DAP/reference	2.28154	0.007
43DAP/reference	2.28005	0.017
47DAP/reference	1.44494	0.026
52DAP/reference	1.86358	0.046
57DAP/reference	3.06296	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20035	0.878
26DAP/20DAP	0.84154	0.317
34DAP/26DAP	1.19328	1
51DAP/34DAP	0.92343	0.546
52DAP/51DAP	1.32966	0.123
53DAP/52DAP	0.79201	0.085
55DAP/53DAP	1.1383	0.15
57DAP/55DAP	0.77399	0.112
62DAP/57DAP	0.91658	0.871
68DAP/62DAP	1.50246	0.185
68DAP/14DAP	0.83283	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.66037	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.76632	0.228
Mature Green Tomato/Ripe Tomato	0.81818
Immature Eggplant/Mature Eggplant	0.97565	0.912
Ripe Pepper/Ripe Tomato	0.68723	0.293
Mature Eggplant/Ripe Tomato	0.49731	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.70822	0.651
1-1-2/M82	1.18184	1
12-2/M82	0.87782	0.74
12-4/M82	0.97399	1
1-3/M82	2.83978	0.255
2-1-1/M82	0.80384	0.465
2-1/M82	0.88833	0.519
2-6/M82	1.03981	1
3-2/M82	N/A	N/A
4-1-1/M82	1.07826	1
4-1/M82	1.03651
4-3-2/M82	1.84908
4-3/M82	0.89297	1
5-3/M82	0.96645	1
6-2/M82	1.01006	1
6-3/M82	0.98236	1
7-1/M82	1.13146	0.598
7-2/M82	1.46625	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.54144	0.277
IL2-6/WTpooled	0.52101	0.348
IL7-5/WTpooled	1.11447	0.792
IL7-3/WTpooled	1.26422	0.362
IL12-4/WTpooled	1.23772	0.516
IL1-4/WTpooled	0.89678	0.834
WT/WTpooled	0.96085	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	0.9419	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96131	1
DC3000/delta hrp 6h	1.05584
DC3000/delta hrp 12h	1.21534	1
DC3000/delta hrp 24h	0.78418	0.14

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9901	1
DC3000 delta B/DC3000 delta AB	1.03596	0.646

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.45473	1
Exp 36h	1.36489	1
Exp 60h	1.15743	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00846	1
Var 0h	0.4829	1
Var 12h I row2-row1	0.92273	0.514
Var 12h NI row2-row1	0.99129	0.906
Var 36h I row2-row1	0.97157	1
Var 36h NI row2-row1	0.77157	1
Var 60h I row2-row1	1.0599	0.523
Var 60h NI row2-row1	1.01328	0.904
Time course 0hI-0hNI	0.99542	1
Time course 12hI-12hNI	0.99141	0.968
Time course 36hI-36hNI	0.86423	0.062
Time course 60hI-60hNI	0.48949	0.005

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)	1.02931	0.798
transgenic ySAMdc/azygous control (breaker)	1.08996	1
transgenic ySAMdc/azygous control (red)	1.31701	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.5748	0.054

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91105	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8059	1
Manapal/WT (break)	1.10572	1
Manapal/WT (red)	1.91793	0.15