Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.9.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81936	0.265
27DAP/17DAP	0.94794	0.898
39DAP/27DAP	1.75397	0.068
41DAP/39DAP	0.74793	0.215
42DAP/41DAP	1.39342	0.672
43DAP/42DAP	1.01001	0.932
47DAP/43DAP	0.74589	0.231
52DAP/47DAP	1.021	0.886
57DAP/52DAP	1.25761	0.76

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.50282	0.012
17DAP/reference	0.99891	0.819
27DAP/reference	0.83526	0.059
39DAP/reference	1.03883	0.92
41DAP/reference	0.89657	0.201
42DAP/reference	1.21339	0.007
43DAP/reference	1.26485	0.008
47DAP/reference	1.09566	0.329
52DAP/reference	1.0486	0.371
57DAP/reference	1.15574	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22794	0.04
27DAP/17DAP	0.90717	0.614
39DAP/27DAP	0.83436	0.063
41DAP/39DAP	1.18341	0.641
42DAP/41DAP	0.94018	0.61
43DAP/42DAP	0.79743	0.043
47DAP/43DAP	1.00501	1
52DAP/47DAP	0.77418	0.098
57DAP/52DAP	0.97239	0.697
57DAP/7DAP	0.58739	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.8177	0.036
17DAP/reference	1.25737	0.007
27DAP/reference	1.17476	0.011
39DAP/reference	1.04355	0.779
41DAP/reference	0.96894	0.469
42DAP/reference	0.9522	0.371
43DAP/reference	0.81128	0.025
47DAP/reference	1.24366	0.304
52DAP/reference	1.18548	0.491
57DAP/reference	1.09641	0.746

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12294	0.43
17DAP/reference	1.17907	0.045
27DAP/reference	1.2162	0.178
39DAP/reference	1.14105	0.62
41DAP/reference	1.41802	0.011
42DAP/reference	1.2342	0.064
43DAP/reference	0.89015	0.25
47DAP/reference	1.34539	0.061
52DAP/reference	1.00211	0.761
57DAP/reference	0.84766	0.125

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.7615	0.027
17DAP/reference	1.58082	0.258
27DAP/reference	1.34074	0.021
39DAP/reference	1.38748	0.011
41DAP/reference	1.11827	0.306
42DAP/reference	1.17499	0.391
43DAP/reference	1.00314	0.858
47DAP/reference	1.0695	0.877
52DAP/reference	1.17563	0.405
57DAP/reference	1.38756	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.67122	0.328
26DAP/20DAP	1.31518	0.558
34DAP/26DAP	0.81496	0.783
51DAP/34DAP	0.66275	0.095
52DAP/51DAP	0.81964	1
53DAP/52DAP	0.89179	0.297
55DAP/53DAP	0.63555	0.016
57DAP/55DAP	1.2876	0.793
62DAP/57DAP	1.64796	0.303
68DAP/62DAP	1.32059	0.074
68DAP/14DAP	3.36621	0.094

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.76863	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.96575	0.692
Mature Green Tomato/Ripe Tomato	1.72741	0.106
Immature Eggplant/Mature Eggplant	1.19744	0.061
Ripe Pepper/Ripe Tomato	1.66302	0.256
Mature Eggplant/Ripe Tomato	2.78282	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.83154	0.883
1-1-2/M82	1.12349	1
12-2/M82	0.96806	0.955
12-4/M82	1.10763	1
1-3/M82	2.56583
2-1-1/M82	1.16525	0.764
2-1/M82	0.56715	0.322
2-6/M82	0.9179	1
3-2/M82	1.04857	1
4-1-1/M82	1.02614	1
4-1/M82	1.36153	1
4-3-2/M82	1.36186	0.508
4-3/M82	1.13675	0.268
5-3/M82	1.30461	0.572
6-2/M82	1.01953
6-3/M82	1.06465	1
7-1/M82	0.81457	0.476
7-2/M82	1.26484	0.385
9-3-2/M82	1.19601	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.12231	0.365
IL2-6/WTpooled	0.83496	0.473
IL7-5/WTpooled	0.892	1
IL7-3/WTpooled	0.94797	1
IL12-4/WTpooled	0.98182	1
IL1-4/WTpooled	1.07337	1
WT/WTpooled	1.06224	0.874

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	1.0372	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08847	0.823
DC3000/delta hrp 6h	0.98276	0.95
DC3000/delta hrp 12h	1.21645	1
DC3000/delta hrp 24h	1.06637	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15651	0.229
DC3000 delta B/DC3000 delta AB	1.08863	0.403

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89366	1
Exp 36h	1.11261	1
Exp 60h	1.05619	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07463	1
Var 0h	1.18907	1
Var 12h I row2-row1	1.43784	0.692
Var 12h NI row2-row1	1.13349	1
Var 36h I row2-row1	0.88821	1
Var 36h NI row2-row1	0.88099	0.645
Var 60h I row2-row1	0.93691	0.952
Var 60h NI row2-row1	0.78587	0.292
Time course 0hI-0hNI	0.8772	0.188
Time course 12hI-12hNI	1.05907	0.554
Time course 36hI-36hNI	1.41955	0.05
Time course 60hI-60hNI	1.48046	0.009

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)	0.98792	0.454
transgenic ySAMdc/azygous control (breaker)	1.15756	1
transgenic ySAMdc/azygous control (red)	1.21121	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.16449	0.1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89059	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.58706	0.172
Manapal/WT (break)	0.82459	0.333
Manapal/WT (red)	1.11423	1