Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.4.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92556	0.496
27DAP/17DAP	1.03689	0.892
39DAP/27DAP	0.98853	0.782
41DAP/39DAP	1.07621	0.88
42DAP/41DAP	0.97192	1
43DAP/42DAP	0.92259	0.736
47DAP/43DAP	1.13596	0.809
52DAP/47DAP	1.13844	0.676
57DAP/52DAP	1.09764	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05385	0.403
17DAP/reference	N/A	N/A
27DAP/reference	0.96721	0.683
39DAP/reference	1.01137	0.8
41DAP/reference	0.76566	0.154
42DAP/reference	0.99851	0.517
43DAP/reference	N/A	N/A
47DAP/reference	1.03828	1
52DAP/reference	0.86951	0.35
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02587	0.749
27DAP/17DAP	1.02431	0.924
39DAP/27DAP	0.98642	0.887
41DAP/39DAP	0.91976	0.481
42DAP/41DAP	1.01377	0.976
43DAP/42DAP	1.00448	0.788
47DAP/43DAP	0.99783	0.998
52DAP/47DAP	0.96075	0.797
57DAP/52DAP	0.98798	0.784
57DAP/7DAP	0.96317	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04588	0.613
17DAP/reference	1.02456	0.627
27DAP/reference	0.99712	0.748
39DAP/reference	1.03786	0.252
41DAP/reference	1.06564	0.121
42DAP/reference	1.14919	0.021
43DAP/reference	0.96672	0.292
47DAP/reference	0.96764	0.383
52DAP/reference	1.07618	0.066
57DAP/reference	0.97569	0.25

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07193	0.642
17DAP/reference	1.01121	1
27DAP/reference	1.16455	0.404
39DAP/reference	0.98147	0.586
41DAP/reference	1.04434	0.688
42DAP/reference	1.0613	0.532
43DAP/reference	1.04009	0.509
47DAP/reference	1.06401	0.124
52DAP/reference	0.97802	0.537
57DAP/reference	0.99205	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04939	0.775
17DAP/reference	0.99355	0.81
27DAP/reference	0.9714	0.49
39DAP/reference	0.97763	0.591
41DAP/reference	0.96942	0.209
42DAP/reference	1.04993	0.408
43DAP/reference	1.09358	0.254
47DAP/reference	0.99946	0.754
52DAP/reference	1.00554	1
57DAP/reference	1.16218	0.079

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97676	1
26DAP/20DAP	1.02572	0.988
34DAP/26DAP	0.9277	0.509
51DAP/34DAP	1.01011	0.949
52DAP/51DAP	0.98431	1
53DAP/52DAP	1.01786	0.921
55DAP/53DAP	0.96826	0.796
57DAP/55DAP	0.99848	0.935
62DAP/57DAP	0.71144
68DAP/62DAP	0.79752	0.747
68DAP/14DAP	1.22956	0.153

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.10987	0.055

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.02827	1
Mature Green Tomato/Ripe Tomato	0.88596	0.287
Immature Eggplant/Mature Eggplant	1.24802	0.311
Ripe Pepper/Ripe Tomato	0.59355	0.293
Mature Eggplant/Ripe Tomato	0.55689	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9969	1
1-1-2/M82	0.85376	1
12-2/M82	0.94299	0.955
12-4/M82	1.02692	1
1-3/M82	0.95159	0.441
2-1-1/M82	0.84723	0.465
2-1/M82	1.08337	1
2-6/M82	0.95643	0.501
3-2/M82	0.97554	1
4-1-1/M82	1.00006	1
4-1/M82	0.99644	1
4-3-2/M82	0.86853	1
4-3/M82	0.93653	1
5-3/M82	1.00323	1
6-2/M82	1.07377	1
6-3/M82	0.98929	1
7-1/M82	0.96081	0.509
7-2/M82	0.9201	0.796
9-3-2/M82	0.80408	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	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.67342	0.426
WT/WTpooled	0.53352

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	0.89682	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05232	0.921
DC3000/delta hrp 6h	1.2199	1
DC3000/delta hrp 12h	1.06244	1
DC3000/delta hrp 24h	1.0604	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13666	0.049
DC3000 delta B/DC3000 delta AB	1.19905	0.181

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86351	1
Exp 36h	0.69917	0.434
Exp 60h	0.71693	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98627	1
Var 0h	1.57276	0.98
Var 12h I row2-row1	0.94211	0.565
Var 12h NI row2-row1	1.25857	0.281
Var 36h I row2-row1	2.17922	0.908
Var 36h NI row2-row1	0.94095	0.706
Var 60h I row2-row1	0.64518	0.374
Var 60h NI row2-row1	1.08396	1
Time course 0hI-0hNI	0.9583	0.791
Time course 12hI-12hNI	0.98162	0.897
Time course 36hI-36hNI	1.18454	0.016
Time course 60hI-60hNI	3.8552	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)	0.94848	0.567
transgenic ySAMdc/azygous control (breaker)	0.81476	0.251
transgenic ySAMdc/azygous control (red)	1.12201	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04479	0.273

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90901	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.41869	0.14
Manapal/WT (break)	0.69508	1
Manapal/WT (red)	0.81848	0.183