Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.16.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01373	0.997
27DAP/17DAP	1.12678	0.881
39DAP/27DAP	0.93332	0.652
41DAP/39DAP	1.4039	0.494
42DAP/41DAP	1.08984	0.983
43DAP/42DAP	0.85811	0.705
47DAP/43DAP	1.21379	0.689
52DAP/47DAP	1.48964	0.385
57DAP/52DAP	0.94494	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04008	0.638
17DAP/reference	0.97089	0.419
27DAP/reference	0.93504	0.223
39DAP/reference	0.95706	0.404
41DAP/reference	0.973	0.542
42DAP/reference	0.97528	0.211
43DAP/reference	0.98754	0.728
47DAP/reference	0.92231	0.014
52DAP/reference	0.92535	0.125
57DAP/reference	0.93035	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03042	0.785
27DAP/17DAP	0.98167	0.919
39DAP/27DAP	1.03362	0.811
41DAP/39DAP	1.11447	0.921
42DAP/41DAP	0.99606	0.816
43DAP/42DAP	1.08768	0.478
47DAP/43DAP	1.05971	0.837
52DAP/47DAP	1.04386	0.907
57DAP/52DAP	0.88675	0.346
57DAP/7DAP	0.90411	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89239	0.066
17DAP/reference	0.90201	0.011
27DAP/reference	0.89587	0.011
39DAP/reference	0.91005	0.017
41DAP/reference	0.88666	0.017
42DAP/reference	0.91386	0.013
43DAP/reference	0.90249	0.02
47DAP/reference	0.8899	0.036
52DAP/reference	0.90145	0.046
57DAP/reference	0.89849	0.033

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02931	0.66
17DAP/reference	1.04067	0.496
27DAP/reference	0.93563	0.257
39DAP/reference	0.93047	0.105
41DAP/reference	1.05531	0.91
42DAP/reference	0.89223	0.023
43DAP/reference	1.1336	0.144
47DAP/reference	0.9462	0.188
52DAP/reference	1.02984	0.3
57DAP/reference	1.08702	0.409

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90993	0.098
17DAP/reference	0.96276	0.374
27DAP/reference	0.89589	0.029
39DAP/reference	0.91168	0.063
41DAP/reference	0.90989	0.07
42DAP/reference	0.91421	0.172
43DAP/reference	0.85946	0.054
47DAP/reference	0.94564	0.383
52DAP/reference	0.86388	0.144
57DAP/reference	0.80242	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97873	1
26DAP/20DAP	0.94723	1
34DAP/26DAP	0.98064	0.98
51DAP/34DAP	0.99961	0.927
52DAP/51DAP	0.99733	1
53DAP/52DAP	0.98489	0.917
55DAP/53DAP	0.99527	0.894
57DAP/55DAP	0.87047	0.568
62DAP/57DAP	0.99468	1
68DAP/62DAP	0.96834	0.787
68DAP/14DAP	0.94448	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82376	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.19013	0.632
Immature Eggplant/Mature Eggplant	1.61722	0.058
Ripe Pepper/Ripe Tomato	0.7411
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06617	1
1-1-2/M82	0.65025
12-2/M82	1.17422	0.61
12-4/M82	0.91626	1
1-3/M82	1.01607	1
2-1-1/M82	1.17681	0.764
2-1/M82	1.41578
2-6/M82	0.88308	1
3-2/M82	0.9837	1
4-1-1/M82	1.05536	1
4-1/M82	0.93913	0.867
4-3-2/M82	0.82607	0.487
4-3/M82	1.15503	1
5-3/M82	0.98797	1
6-2/M82	0.90738	1
6-3/M82	0.98855	1
7-1/M82	0.94203	0.509
7-2/M82	1.04999	1
9-3-2/M82	0.81655	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.68039
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.10624	1
WT/WTpooled	N/A	N/A

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	0.84618	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07591	0.846
DC3000/delta hrp 6h	1.08638	1
DC3000/delta hrp 12h	0.99024	1
DC3000/delta hrp 24h	1.01025	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.11257	0.29
DC3000 delta B/DC3000 delta AB	0.98852	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03794	1
Exp 36h	1.0057	1
Exp 60h	0.88968	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95956	1
Var 0h	0.63667	0.933
Var 12h I row2-row1	1.10169	0.254
Var 12h NI row2-row1	1.13167	1
Var 36h I row2-row1	0.85255	1
Var 36h NI row2-row1	0.92419	0.706
Var 60h I row2-row1	1.42607	1
Var 60h NI row2-row1	1.04433	1
Time course 0hI-0hNI	1.08745	0.719
Time course 12hI-12hNI	1.02227	0.85
Time course 36hI-36hNI	0.89172	0.114
Time course 60hI-60hNI	0.96081	0.646

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)	1.46375	0.36
transgenic ySAMdc/azygous control (breaker)	0.68772	0.134
transgenic ySAMdc/azygous control (red)	1.24617	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03575	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07411	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.15772	0.307
Manapal/WT (break)	0.93635	1
Manapal/WT (red)	1.24838	0.164