Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.7.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88476	0.464
27DAP/17DAP	0.84965	0.604
39DAP/27DAP	1.44278	0.391
41DAP/39DAP	0.79752	0.33
42DAP/41DAP	0.95738	1
43DAP/42DAP	1.25586	0.507
47DAP/43DAP	0.9677	0.868
52DAP/47DAP	1.49347	0.538
57DAP/52DAP	1.28991	0.93

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92319	0.182
17DAP/reference	0.84667	0.046
27DAP/reference	0.93534	0.304
39DAP/reference	0.85824	0.09
41DAP/reference	0.84419	0.154
42DAP/reference	0.84179	0.007
43DAP/reference	0.96146	0.594
47DAP/reference	0.97458	0.392
52DAP/reference	1.01282	0.689
57DAP/reference	1.05115	0.344

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77795	0.211
27DAP/17DAP	1.23381	0.593
39DAP/27DAP	0.94403	0.703
41DAP/39DAP	0.90094	0.63
42DAP/41DAP	1.42625	0.327
43DAP/42DAP	0.9286	0.665
47DAP/43DAP	0.89798	0.41
52DAP/47DAP	0.77197	0.512
57DAP/52DAP	1.22226	0.718
57DAP/7DAP	0.41518	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08525	0.564
17DAP/reference	1.18228	0.07
27DAP/reference	1.19579	0.131
39DAP/reference	0.97426	0.474
41DAP/reference	1.16553	0.09
42DAP/reference	0.93957	0.304
43DAP/reference	1.10343	0.2
47DAP/reference	0.96542	0.504
52DAP/reference	1.04378	0.459
57DAP/reference	1.31421	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80401	0.064
17DAP/reference	1.02579	0.824
27DAP/reference	1.18543	0.217
39DAP/reference	1.01394	0.702
41DAP/reference	1.1519	0.301
42DAP/reference	1.06929	0.509
43DAP/reference	1.03652	0.692
47DAP/reference	0.89861	0.039
52DAP/reference	0.9489	0.187
57DAP/reference	0.94294	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12769	0.07
17DAP/reference	0.99583	0.825
27DAP/reference	1.13679	0.237
39DAP/reference	1.16195	0.094
41DAP/reference	1.17554	0.108
42DAP/reference	1.06788	0.671
43DAP/reference	1.34747	0.079
47DAP/reference	0.83439	0.093
52DAP/reference	1.11529	0.724
57DAP/reference	1.26937	0.113

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.76349	0.981
26DAP/20DAP	0.88136	1
34DAP/26DAP	N/A	N/A
51DAP/34DAP	0.73928	0.436
52DAP/51DAP	1.22249	0.783
53DAP/52DAP	0.85029	0.336
55DAP/53DAP	0.67329	0.163
57DAP/55DAP	0.66058	0.03
62DAP/57DAP	0.7443	0.28
68DAP/62DAP	1.05019	0.977
68DAP/14DAP	1.17629	0.739

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.69496	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	3.02968	0.237
Immature Eggplant/Mature Eggplant	6.95184	0.074
Ripe Pepper/Ripe Tomato	0.74322	1
Mature Eggplant/Ripe Tomato	0.43518

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.06917
12-2/M82	1.17108
12-4/M82	0.80485
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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.351	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87807	0.321
IL2-6/WTpooled	1.11882	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10838	0.362
IL12-4/WTpooled	0.87776	0.478
IL1-4/WTpooled	0.82514	0.435
WT/WTpooled	0.9421	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	1.321	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11725	0.921
DC3000/delta hrp 6h	0.88825	0.95
DC3000/delta hrp 12h	1.08925	1
DC3000/delta hrp 24h	0.90316	0.464

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.53375	0.025
DC3000 delta B/DC3000 delta AB	0.50965	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9566	1
Var 0h	0.47141	1
Var 12h I row2-row1	0.71296	0.338
Var 12h NI row2-row1	0.8645	0.494
Var 36h I row2-row1	1.07419	0.368
Var 36h NI row2-row1	1.25443	0.482
Var 60h I row2-row1	0.87129	0.292
Var 60h NI row2-row1	1.05216	1
Time course 0hI-0hNI	0.94146	0.683
Time course 12hI-12hNI	1.00231	1
Time course 36hI-36hNI	0.8686	0.084
Time course 60hI-60hNI	0.31087	0.005

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)	1.21968	0.347
transgenic ySAMdc/azygous control (breaker)	0.92572	0.251
transgenic ySAMdc/azygous control (red)	1.08615	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.18351	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95814	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05274	1
Manapal/WT (break)	1.17286	1
Manapal/WT (red)	N/A	N/A