Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.17.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15961	0.912
27DAP/17DAP	1.0995	1
39DAP/27DAP	0.76592	0.512
41DAP/39DAP	0.87742	0.681
42DAP/41DAP	1.3403	0.792
43DAP/42DAP	1.08918	1
47DAP/43DAP	1.33385	0.825
52DAP/47DAP	0.86678	0.694
57DAP/52DAP	1.18691	0.972

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85797	0.027
17DAP/reference	0.91635	0.097
27DAP/reference	0.99324	0.779
39DAP/reference	0.95476	0.292
41DAP/reference	0.85613	0.065
42DAP/reference	0.91086	0.005
43DAP/reference	0.89258	0.148
47DAP/reference	0.93709	0.055
52DAP/reference	1.04296	0.73
57DAP/reference	1.1102	0.054

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.13252	0.099
27DAP/17DAP	0.70197	0.58
39DAP/27DAP	0.83025	0.251
41DAP/39DAP	1.02392
42DAP/41DAP	1.34561	0.401
43DAP/42DAP	0.84787	0.576
47DAP/43DAP	1.1215	1
52DAP/47DAP	0.63209	0.222
57DAP/52DAP	1.8752	0.175
57DAP/7DAP	0.51351

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82056	0.129
17DAP/reference	0.93614	0.389
27DAP/reference	0.80416	0.03
39DAP/reference	0.95626	0.411
41DAP/reference	0.97226	0.489
42DAP/reference	0.89647	0.189
43DAP/reference	0.83201	0.022
47DAP/reference	1.03166	1
52DAP/reference	1.10019	0.401
57DAP/reference	0.99781	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96391	0.607
17DAP/reference	0.89844	0.153
27DAP/reference	0.92566	0.317
39DAP/reference	0.93811	0.126
41DAP/reference	0.99305	0.584
42DAP/reference	0.90522	0.039
43DAP/reference	0.96624	0.527
47DAP/reference	0.86616	0.012
52DAP/reference	0.99738	0.713
57DAP/reference	0.84751	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04908	1
17DAP/reference	0.93898	0.499
27DAP/reference	1.18174	0.357
39DAP/reference	0.98302	0.643
41DAP/reference	1.1273	0.588
42DAP/reference	1.22799	0.3
43DAP/reference	1.46366	0.137
47DAP/reference	1.00954	1
52DAP/reference	1.05457	0.779
57DAP/reference	1.34822	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22513	0.916
26DAP/20DAP	1.93336
34DAP/26DAP	0.97654	0.988
51DAP/34DAP	0.92306	0.714
52DAP/51DAP	2.14318	0.032
53DAP/52DAP	1.16559	0.83
55DAP/53DAP	1.11139	0.813
57DAP/55DAP	1.00023	0.93
62DAP/57DAP	0.92232	0.871
68DAP/62DAP	1.40102	0.035
68DAP/14DAP	1.35518	0.099

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90708	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.99612	0.886
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.7036	0.092
Ripe Pepper/Ripe Tomato	0.76693
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.33727
3-2/M82	N/A	N/A
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	1.11965
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.28471
IL2-6/WTpooled	1.22785	0.531
IL7-5/WTpooled	1.35647
IL7-3/WTpooled	0.96114	1
IL12-4/WTpooled	1.14604	0.532
IL1-4/WTpooled	1.07886	0.421
WT/WTpooled	0.94093	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	0.80946	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92832	1
DC3000/delta hrp 6h	0.98128	0.95
DC3000/delta hrp 12h	1.05652	1
DC3000/delta hrp 24h	0.86657	0.098

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	0.93364	1
Exp 36h	0.79605	0.406
Exp 60h	0.81822	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99422	1
Var 0h	0.0536	1
Var 12h I row2-row1	0.93178	0.705
Var 12h NI row2-row1	0.898	0.488
Var 36h I row2-row1	0.88595	0.805
Var 36h NI row2-row1	1.50415	1
Var 60h I row2-row1	1.01974
Var 60h NI row2-row1	1.01075	1
Time course 0hI-0hNI	0.98925	1
Time course 12hI-12hNI	0.95274	0.357
Time course 36hI-36hNI	0.86252	0.15
Time course 60hI-60hNI	0.17103	0.006

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)	1.03882	0.331
transgenic ySAMdc/azygous control (breaker)	1.21276	0.178
transgenic ySAMdc/azygous control (red)	0.99015	1

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	1.07844	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.24877	0.096
Manapal/WT (break)	1.0588	1
Manapal/WT (red)	1.10319	0.413