Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.6.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80089	0.31
27DAP/17DAP	1.40851	0.793
39DAP/27DAP	1.01584	0.84
41DAP/39DAP	1.10684	0.949
42DAP/41DAP	1.20491	0.806
43DAP/42DAP	1.03253	0.937
47DAP/43DAP	0.84101	0.499
52DAP/47DAP	1.09777	0.883
57DAP/52DAP	1.06168	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9556	0.317
17DAP/reference	1.00494	0.813
27DAP/reference	0.99864	0.885
39DAP/reference	1.02115	1
41DAP/reference	0.9646	0.542
42DAP/reference	0.93654	0.052
43DAP/reference	1.03563	0.445
47DAP/reference	0.90306	0.046
52DAP/reference	0.99002	0.598
57DAP/reference	0.99283	0.61

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01796	0.899
27DAP/17DAP	0.93902	0.821
39DAP/27DAP	1.06012	0.698
41DAP/39DAP	0.90338	0.63
42DAP/41DAP	0.98113	0.757
43DAP/42DAP	0.98702	0.875
47DAP/43DAP	1.06453	0.906
52DAP/47DAP	1.00359	0.975
57DAP/52DAP	1.08523	0.759
57DAP/7DAP	1.36439

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06206	0.945
17DAP/reference	0.98858	0.518
27DAP/reference	1.0041	0.8
39DAP/reference	1.03051	0.819
41DAP/reference	1.10989	0.35
42DAP/reference	1.04224	0.828
43DAP/reference	1.05455	0.511
47DAP/reference	1.02495	1
52DAP/reference	1.23618	0.052
57DAP/reference	1.24187	0.158

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09038	0.55
17DAP/reference	1.08433	0.186
27DAP/reference	1.12819	0.12
39DAP/reference	1.07488	0.571
41DAP/reference	1.14712	0.138
42DAP/reference	1.03633	0.744
43DAP/reference	1.19835	0.466
47DAP/reference	1.11955	0.081
52DAP/reference	1.24662	0.008
57DAP/reference	1.18547	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0867	0.963
17DAP/reference	1.11228	0.376
27DAP/reference	1.26051	0.237
39DAP/reference	1.23093	0.163
41DAP/reference	1.05536	1
42DAP/reference	1.27378	0.3
43DAP/reference	1.32241	0.326
47DAP/reference	1.10542	0.089
52DAP/reference	1.31971	0.148
57DAP/reference	1.17725	0.081

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9548	1
26DAP/20DAP	1.04585	0.974
34DAP/26DAP	1.24498	1
51DAP/34DAP	1.12793	0.785
52DAP/51DAP	0.88122	0.079
53DAP/52DAP	0.85814	0.212
55DAP/53DAP	0.8007	0.478
57DAP/55DAP	1.39358	0.969
62DAP/57DAP	0.57144
68DAP/62DAP	2.10583	0.549
68DAP/14DAP	1.44032	0.676

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93889	0.341

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.90354	0.481
Mature Green Tomato/Ripe Tomato	0.79901	0.055
Immature Eggplant/Mature Eggplant	1.13217	0.174
Ripe Pepper/Ripe Tomato	0.73882	0.224
Mature Eggplant/Ripe Tomato	1.2806	1

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	0.78355	0.274
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	N/A	N/A
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	0.95295	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.33475
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	1.59814
IL2-6/WTpooled	1.19731	0.441
IL7-5/WTpooled	1.60452	1
IL7-3/WTpooled	1.39565	0.362
IL12-4/WTpooled	1.07161	0.737
IL1-4/WTpooled	1.12592	0.426
WT/WTpooled	0.9352	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	0.99406	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	5.33761
DC3000/delta hrp 6h	0.96652	0.95
DC3000/delta hrp 12h	0.96058	1
DC3000/delta hrp 24h	1.18621	0.797

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	0.88416	0.558

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.20569	0.228
Exp 36h	1.1039	1
Exp 60h	1.28896	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.09772	1
Var 0h	1.18276	0.594
Var 12h I row2-row1	0.87566	0.39
Var 12h NI row2-row1	1.02468	1
Var 36h I row2-row1	0.98578	1
Var 36h NI row2-row1	0.87154	0.706
Var 60h I row2-row1	0.94245
Var 60h NI row2-row1	1.08881	0.904
Time course 0hI-0hNI	0.96995	0.873
Time course 12hI-12hNI	1.0177	0.803
Time course 36hI-36hNI	1.02266	1
Time course 60hI-60hNI	1.30548	0.019

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)	1.06682	0.312
transgenic ySAMdc/azygous control (breaker)	1.04532	1
transgenic ySAMdc/azygous control (red)	0.93219	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05952	0.077

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.54135	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89883	1
Manapal/WT (break)	0.92848	1
Manapal/WT (red)	1.02568	1