Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.9.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15079	0.656
27DAP/17DAP	1.08316	0.92
39DAP/27DAP	1.66681	0.82
41DAP/39DAP	1.49049	0.372
42DAP/41DAP	1.4094	0.894
43DAP/42DAP	1.16075	1
47DAP/43DAP	0.89927	0.58
52DAP/47DAP	2.04628	0.227
57DAP/52DAP	0.9495	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9465	0.246
17DAP/reference	1.10428	0.066
27DAP/reference	1.02358	0.548
39DAP/reference	1.01295	0.816
41DAP/reference	1.0975	0.171
42DAP/reference	0.92236	0.099
43DAP/reference	1.06322	0.569
47DAP/reference	0.86872	0.032
52DAP/reference	0.7592	0.028
57DAP/reference	0.752	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18784	0.247
27DAP/17DAP	1.06847	0.924
39DAP/27DAP	1.06473	0.663
41DAP/39DAP	1.06859	0.887
42DAP/41DAP	1.03234	0.929
43DAP/42DAP	0.91577	0.137
47DAP/43DAP	0.99043	0.947
52DAP/47DAP	0.9441	0.807
57DAP/52DAP	0.98434	0.798
57DAP/7DAP	1.06716	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89788	0.246
17DAP/reference	0.837	0.013
27DAP/reference	0.80319	0.016
39DAP/reference	0.79587	0.011
41DAP/reference	0.78579	0.047
42DAP/reference	0.76453	0.011
43DAP/reference	0.74484	0.02
47DAP/reference	0.86289	0.293
52DAP/reference	0.65413	0.012
57DAP/reference	0.67212	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20776	0.139
17DAP/reference	1.1693	0.139
27DAP/reference	0.90575	0.257
39DAP/reference	0.81606	0.152
41DAP/reference	0.79283	0.058
42DAP/reference	0.83874	0.042
43DAP/reference	1.10321	0.641
47DAP/reference	0.88096	0.038
52DAP/reference	1.04424	0.747
57DAP/reference	1.39066	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88607	0.158
17DAP/reference	0.99234	0.778
27DAP/reference	0.82802	0.085
39DAP/reference	0.90341	0.054
41DAP/reference	0.84739	0.055
42DAP/reference	0.74549	0.02
43DAP/reference	0.79305	0.088
47DAP/reference	1.05953	0.901
52DAP/reference	1.1276	0.871
57DAP/reference	0.59759	0.024

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.44659	0.945
26DAP/20DAP	0.79797	0.317
34DAP/26DAP	1.1459	1
51DAP/34DAP	1.15154	0.898
52DAP/51DAP	1.05525	0.776
53DAP/52DAP	1.00237	0.998
55DAP/53DAP	1.10946	0.712
57DAP/55DAP	0.96961	0.825
62DAP/57DAP	1.35138	0.158
68DAP/62DAP	0.80027	0.227
68DAP/14DAP	0.64114	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.74734	0.097

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.15408	0.632
Immature Eggplant/Mature Eggplant	2.87207
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.6412
1-1-2/M82	1.12089
12-2/M82	1.5833
12-4/M82	1.16919
1-3/M82	0.64268	0.378
2-1-1/M82	1.10248
2-1/M82	N/A	N/A
2-6/M82	1.19932	0.425
3-2/M82	N/A	N/A
4-1-1/M82	1.09559	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.54486
5-3/M82	0.86325	0.642
6-2/M82	0.85229	0.497
6-3/M82	1.02885	1
7-1/M82	N/A	N/A
7-2/M82	0.91259	0.796
9-3-2/M82	N/A	N/A

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	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.83378	0.201

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02177	0.921
DC3000/delta hrp 6h	1.67251	1
DC3000/delta hrp 12h	1.24229	1
DC3000/delta hrp 24h	0.92319	0.575

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	0.99048	1
Exp 36h	N/A	N/A
Exp 60h	0.75783	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.08793	1
Var 0h	0.39085	0.332
Var 12h I row2-row1	0.93718	0.77
Var 12h NI row2-row1	0.83836	0.488
Var 36h I row2-row1	0.82861	0.805
Var 36h NI row2-row1	1.04734	1
Var 60h I row2-row1	1.49581	0.562
Var 60h NI row2-row1	1.28833	0.904
Time course 0hI-0hNI	1.0751	0.574
Time course 12hI-12hNI	1.02338	0.818
Time course 36hI-36hNI	0.91519	0.049
Time course 60hI-60hNI	0.82546	0.161

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)	0.81815	0.377
transgenic ySAMdc/azygous control (breaker)	1.45077	1
transgenic ySAMdc/azygous control (red)	1.19613	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01403	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.00735	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.61048	0.083
Manapal/WT (break)	0.98307	1
Manapal/WT (red)	0.82202	0.607