Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.3.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87236	0.381
27DAP/17DAP	0.91904	0.833
39DAP/27DAP	1.13796	0.944
41DAP/39DAP	1.02374	0.883
42DAP/41DAP	0.8266	0.774
43DAP/42DAP	1.03558	1
47DAP/43DAP	1.01464	0.979
52DAP/47DAP	1.64311	0.851
57DAP/52DAP	1.05818	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2982	0.028
17DAP/reference	0.86095	0.031
27DAP/reference	0.88442	0.359
39DAP/reference	0.66609	0.025
41DAP/reference	0.7597	0.085
42DAP/reference	0.89338	0.218
43DAP/reference	N/A	N/A
47DAP/reference	0.57989
52DAP/reference	0.99616	0.709
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99559	0.782
27DAP/17DAP	1.13186	0.863
39DAP/27DAP	0.9515	0.712
41DAP/39DAP	0.94549	0.822
42DAP/41DAP	1.00438	0.85
43DAP/42DAP	1.07956	0.746
47DAP/43DAP	1.16338	0.262
52DAP/47DAP	0.9418	0.777
57DAP/52DAP	1.29681	0.188
57DAP/7DAP	0.75365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91489	0.224
17DAP/reference	0.89856	0.108
27DAP/reference	0.93847	0.231
39DAP/reference	0.9838	0.552
41DAP/reference	1.05729	0.637
42DAP/reference	0.95921	0.32
43DAP/reference	0.9879	0.58
47DAP/reference	0.846	0.168
52DAP/reference	0.85249	0.031
57DAP/reference	0.80405	0.021

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20897	0.102
17DAP/reference	1.12502	0.06
27DAP/reference	1.22945	0.116
39DAP/reference	1.22759	0.109
41DAP/reference	1.17143	0.072
42DAP/reference	1.09043	0.715
43DAP/reference	0.8073	0.117
47DAP/reference	0.96508	0.359
52DAP/reference	1.18178	0.079
57DAP/reference	1.06896	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91052	0.049
17DAP/reference	0.95261	0.499
27DAP/reference	0.86869	0.067
39DAP/reference	0.86967	0.063
41DAP/reference	0.8685	0.107
42DAP/reference	0.96654	0.671
43DAP/reference	1.16107	0.369
47DAP/reference	0.97503	0.525
52DAP/reference	1.09675	0.705
57DAP/reference	2.13005	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.23415	0.966
26DAP/20DAP	2.38986	0.098
34DAP/26DAP	0.70679	0.148
51DAP/34DAP	1.21976	0.339
52DAP/51DAP	N/A	N/A
53DAP/52DAP	1.21476	0.274
55DAP/53DAP	0.94588	0.807
57DAP/55DAP	1.11439	0.817
62DAP/57DAP	0.96486	0.994
68DAP/62DAP	1.12387	0.759
68DAP/14DAP	1.46322	0.453

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.18995	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.27138	0.363
Immature Eggplant/Mature Eggplant	3.81775
Ripe Pepper/Ripe Tomato	0.23854	0.224
Mature Eggplant/Ripe Tomato	0.82364	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9951
1-1-2/M82	1.49696	1
12-2/M82	N/A	N/A
12-4/M82	0.9563	1
1-3/M82	1.22129
2-1-1/M82	1.24435	0.764
2-1/M82	N/A	N/A
2-6/M82	0.94037
3-2/M82	0.99957
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.78904
4-3/M82	1.1139
5-3/M82	0.83632	0.49
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.38723
7-2/M82	1.17931	0.302
9-3-2/M82	1.23121	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09041	0.493
IL2-6/WTpooled	1.0115	1
IL7-5/WTpooled	0.8848	1
IL7-3/WTpooled	1.23988	1
IL12-4/WTpooled	1.27205	0.624
IL1-4/WTpooled	1.1955	1
WT/WTpooled	0.70124	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	0.91949	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.15465	0.692
DC3000/delta hrp 6h	1.06869	1
DC3000/delta hrp 12h	0.89037	1
DC3000/delta hrp 24h	1.00403	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.26412
DC3000 delta B/DC3000 delta AB	1.23811	0.181

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99357	1
Exp 36h	0.85661	0.661
Exp 60h	0.7386	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01086	1
Var 0h	0.72321
Var 12h I row2-row1	1.34197	0.58
Var 12h NI row2-row1	1.20968	0.161
Var 36h I row2-row1	1.13901	0.601
Var 36h NI row2-row1	1.16098	1
Var 60h I row2-row1	0.76804
Var 60h NI row2-row1	0.95033	1
Time course 0hI-0hNI	0.97247	0.9
Time course 12hI-12hNI	1.12	0.287
Time course 36hI-36hNI	1.18365	0.218
Time course 60hI-60hNI	1.34552	0.037

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)	1.30525	0.372
transgenic ySAMdc/azygous control (breaker)	0.83307	0.251
transgenic ySAMdc/azygous control (red)	1.01007	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9948	0.806

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.29488	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0241	1
Manapal/WT (break)	1.07426	1
Manapal/WT (red)	1.11491	0.413