Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.1.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.85482	0.033
27DAP/17DAP	1.27494	0.735
39DAP/27DAP	1.28361	0.277
41DAP/39DAP	1.04146	0.748
42DAP/41DAP	1.14307	0.933
43DAP/42DAP	0.82733	0.705
47DAP/43DAP	1.30795	0.438
52DAP/47DAP	0.93228	0.765
57DAP/52DAP	1.61426	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48109	0.007
17DAP/reference	1.11191	0.239
27DAP/reference	1.08231	0.623
39DAP/reference	1.25164	0.243
41DAP/reference	1.10071	0.516
42DAP/reference	1.30842	0.001
43DAP/reference	1.10255	0.34
47DAP/reference	1.24972	0.031
52DAP/reference	0.95606	0.371
57DAP/reference	1.17988	0.05

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.47978
27DAP/17DAP	0.43139
39DAP/27DAP	1.41224
41DAP/39DAP	2.23896	0.005
42DAP/41DAP	1.37819	1
43DAP/42DAP	0.89944	0.641
47DAP/43DAP	0.96176	0.911
52DAP/47DAP	2.03354	0.048
57DAP/52DAP	0.47593	0.223
57DAP/7DAP	1.40859	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00637	0.758
17DAP/reference	1.40346	0.006
27DAP/reference	1.69531	0.006
39DAP/reference	1.4685	0.005
41DAP/reference	1.21439	0.077
42DAP/reference	1.21301	0.174
43DAP/reference	1.19522	0.241
47DAP/reference	1.20912	0.149
52DAP/reference	1.37167	0.098
57DAP/reference	1.29402	0.053

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41639	0.22
17DAP/reference	1.52001	0.058
27DAP/reference	1.68714	0.015
39DAP/reference	1.61551	0.011
41DAP/reference	1.26682	0.015
42DAP/reference	1.58063	0.008
43DAP/reference	1.22407	0.021
47DAP/reference	1.34135	0.011
52DAP/reference	1.19883	0.559
57DAP/reference	1.29177	0.101

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0543	0.809
17DAP/reference	1.1998	0.169
27DAP/reference	1.17157	0.026
39DAP/reference	1.21914	0.009
41DAP/reference	1.32777	0.012
42DAP/reference	1.39016	0.018
43DAP/reference	1.17659	0.164
47DAP/reference	0.95999	0.296
52DAP/reference	1.29842	0.289
57DAP/reference	1.26387	0.043

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.40464	0.85
26DAP/20DAP	1.30972
34DAP/26DAP	1.08293	1
51DAP/34DAP	0.74117	0.084
52DAP/51DAP	0.559	1
53DAP/52DAP	1.02428	0.951
55DAP/53DAP	1.40179	0.236
57DAP/55DAP	0.94307	0.845
62DAP/57DAP	0.84991	0.681
68DAP/62DAP	0.77218	0.641
68DAP/14DAP	0.72407	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.94636	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.27604	0.075
Mature Green Tomato/Ripe Tomato	1.39102	0.086
Immature Eggplant/Mature Eggplant	0.96552	0.808
Ripe Pepper/Ripe Tomato	1.27504	1
Mature Eggplant/Ripe Tomato	2.92233	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.79575	0.651
1-1-2/M82	1.15076	1
12-2/M82	0.90158	0.955
12-4/M82	0.93642	1
1-3/M82	1.50913	0.479
2-1-1/M82	1.00275	1
2-1/M82	0.83419	0.322
2-6/M82	0.64399	0.501
3-2/M82	0.9982	1
4-1-1/M82	0.8421	0.962
4-1/M82	1.15257	1
4-3-2/M82	1.28174
4-3/M82	1.04418	1
5-3/M82	1.25869	0.496
6-2/M82	0.97762
6-3/M82	0.9867
7-1/M82	1.35223	0.587
7-2/M82	0.88246	0.578
9-3-2/M82	0.58869	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.65186	0.243
IL2-6/WTpooled	0.77489	0.383
IL7-5/WTpooled	0.62364	1
IL7-3/WTpooled	0.57428	0.31
IL12-4/WTpooled	0.98704	1
IL1-4/WTpooled	0.78674	0.457
WT/WTpooled	1.18236	0.855

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04343	0.921
DC3000/delta hrp 6h	1.28127	0.777
DC3000/delta hrp 12h	0.94243	1
DC3000/delta hrp 24h	1.04527	0.779

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	0.8172	0.242
Exp 36h	0.62232	0.406
Exp 60h	0.65688	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	1.2762
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	1.44243
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.77024
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.87115	0.314
transgenic ySAMdc/azygous control (breaker)	1.14369	1
transgenic ySAMdc/azygous control (red)	0.99323	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.1681	0.061

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.45809	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86732	0.172
Manapal/WT (break)	0.92606	1
Manapal/WT (red)	1.23841	0.133