Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.20.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74056	0.169
27DAP/17DAP	1.6839	0.714
39DAP/27DAP	1.02508	0.82
41DAP/39DAP	0.94447	0.694
42DAP/41DAP	1.06382	0.978
43DAP/42DAP	1.05915	0.937
47DAP/43DAP	1.76205	0.448
52DAP/47DAP	0.98123	0.812
57DAP/52DAP	1.37266	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.58373	0.024
17DAP/reference	0.54001
27DAP/reference	0.49015	0.03
39DAP/reference	N/A	N/A
41DAP/reference	N/A	N/A
42DAP/reference	0.9523	0.501
43DAP/reference	0.37058	0.056
47DAP/reference	1.40492
52DAP/reference	0.55678	0.189
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00515	1
27DAP/17DAP	1.65082	0.541
39DAP/27DAP	0.78538	0.419
41DAP/39DAP	0.93992	0.875
42DAP/41DAP	1.56208	0.601
43DAP/42DAP	1.44497	0.664
47DAP/43DAP	1.22324	0.678
52DAP/47DAP	0.73829	0.247
57DAP/52DAP	1.20468	0.518
57DAP/7DAP	1.27191

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89052	0.122
17DAP/reference	0.98568	0.518
27DAP/reference	0.91771	0.062
39DAP/reference	0.66082	0.014
41DAP/reference	0.61566	0.016
42DAP/reference	0.59544	0.01
43DAP/reference	0.75462	0.023
47DAP/reference	0.93625	0.504
52DAP/reference	0.74439	0.015
57DAP/reference	0.82755	0.056

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07522	0.626
17DAP/reference	0.81475	0.009
27DAP/reference	0.71434	0.033
39DAP/reference	0.75965	0.093
41DAP/reference	0.80132	0.094
42DAP/reference	0.62385
43DAP/reference	0.83694	0.128
47DAP/reference	0.86722
52DAP/reference	0.89654	0.093
57DAP/reference	0.96457	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79006	0.059
17DAP/reference	0.87463	0.144
27DAP/reference	1.07013	0.487
39DAP/reference	0.97645	0.544
41DAP/reference	0.83046	0.046
42DAP/reference	0.74528	0.025
43DAP/reference	0.73346	0.029
47DAP/reference	0.90362	0.161
52DAP/reference	3.03456	0.349
57DAP/reference	1.22793	0.66

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97751	1
26DAP/20DAP	1.64281	0.312
34DAP/26DAP	0.65414	0.267
51DAP/34DAP	0.66827	0.197
52DAP/51DAP	1.30606	0.439
53DAP/52DAP	1.23704	0.806
55DAP/53DAP	1.05975	1
57DAP/55DAP	1.01994	0.902
62DAP/57DAP	1.36423	0.723
68DAP/62DAP	1.06785	1
68DAP/14DAP	1.18275	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.24095	0.74

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	11.042	0.058
Mature Green Tomato/Ripe Tomato	0.20981	0.017
Immature Eggplant/Mature Eggplant	2.699	0.05
Ripe Pepper/Ripe Tomato	1.40826	1
Mature Eggplant/Ripe Tomato	0.29802	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.93846	1
12-2/M82	1.36025
12-4/M82	1.19156
1-3/M82	0.4688
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.94773
3-2/M82	0.92283	1
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.99582	1
6-2/M82	N/A	N/A
6-3/M82	1.13751	1
7-1/M82	1.13055
7-2/M82	0.79638
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09938
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.66684
IL1-4/WTpooled	0.93458	0.834
WT/WTpooled	1.62116	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	0.8262	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12092	0.921
DC3000/delta hrp 6h	0.97604	0.95
DC3000/delta hrp 12h	1.38117	1
DC3000/delta hrp 24h	1.29167	0.151

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
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	1.28898	1
Exp 36h	1.52829	1
Exp 60h	1.03332	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94702	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.98777	0.565
Var 12h NI row2-row1	1.26328	0.649
Var 36h I row2-row1	1.20869	0.339
Var 36h NI row2-row1	1.838	1
Var 60h I row2-row1	0.67308	0.293
Var 60h NI row2-row1	0.75419	0.756
Time course 0hI-0hNI	1.09177	0.852
Time course 12hI-12hNI	2.02903	0.493
Time course 36hI-36hNI	1.41885	0.056
Time course 60hI-60hNI	10.2675	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)	0.89596	0.246
transgenic ySAMdc/azygous control (breaker)	1.33901	0.248
transgenic ySAMdc/azygous control (red)	1.21071	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.68605	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98728	1
Manapal/WT (break)	0.85986	1
Manapal/WT (red)	0.65881	0.424