Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.4.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81958	0.405
27DAP/17DAP	0.99247	0.947
39DAP/27DAP	1.28719	0.397
41DAP/39DAP	1.05765	0.758
42DAP/41DAP	1.2171	0.644
43DAP/42DAP	1.02507	1
47DAP/43DAP	1.202	0.659
52DAP/47DAP	0.98461	0.89
57DAP/52DAP	0.91246	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04043	1
17DAP/reference	1.04912	0.843
27DAP/reference	0.95878	0.581
39DAP/reference	1.0916	0.243
41DAP/reference	1.01521	1
42DAP/reference	0.9491	0.218
43DAP/reference	1.12135	0.189
47DAP/reference	0.99461	0.568
52DAP/reference	0.83021	0.036
57DAP/reference	0.85751	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95005	0.509
27DAP/17DAP	0.99622	0.943
39DAP/27DAP	1.01505	0.793
41DAP/39DAP	1.03196	0.735
42DAP/41DAP	0.97825	0.777
43DAP/42DAP	1.06531	0.079
47DAP/43DAP	0.96801	0.75
52DAP/47DAP	1.00786	0.979
57DAP/52DAP	0.9565	0.528
57DAP/7DAP	0.94299	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14931	0.205
17DAP/reference	1.11525	0.049
27DAP/reference	1.21315	0.131
39DAP/reference	1.28998	0.035
41DAP/reference	1.06352	0.655
42DAP/reference	1.22245	0.132
43DAP/reference	1.22346	0.111
47DAP/reference	0.91	0.035
52DAP/reference	0.95178	0.332
57DAP/reference	0.94472	0.176

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04626	0.65
17DAP/reference	1.20036	0.496
27DAP/reference	0.96319	0.501
39DAP/reference	0.98994	0.621
41DAP/reference	0.93923	0.098
42DAP/reference	0.7695	0.028
43DAP/reference	1.06947	0.885
47DAP/reference	0.90796	0.075
52DAP/reference	0.98463	0.619
57DAP/reference	1.32476	0.101

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18063	0.28
17DAP/reference	1.03143	0.72
27DAP/reference	0.95161	0.442
39DAP/reference	1.1094	0.307
41DAP/reference	0.98343	0.618
42DAP/reference	0.9433	0.445
43DAP/reference	0.8528	0.294
47DAP/reference	0.97695	0.509
52DAP/reference	1.17565	0.592
57DAP/reference	0.87967	0.097

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04168	1
26DAP/20DAP	0.94952	1
34DAP/26DAP	1.00736	1
51DAP/34DAP	0.99411	0.927
52DAP/51DAP	0.98599	1
53DAP/52DAP	1.05752	0.697
55DAP/53DAP	0.97945	0.698
57DAP/55DAP	1.11093	0.793
62DAP/57DAP	0.83167	0.28
68DAP/62DAP	0.90109	0.429
68DAP/14DAP	1.05992	0.826

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88141	0.057

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.57867	0.177
Mature Green Tomato/Ripe Tomato	0.42692
Immature Eggplant/Mature Eggplant	1.63663	0.198
Ripe Pepper/Ripe Tomato	2.56327	1
Mature Eggplant/Ripe Tomato	0.59333

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.86289
12-2/M82	0.58764
12-4/M82	1.0065
1-3/M82	N/A	N/A
2-1-1/M82	0.58934
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.049
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	1.56079	1
5-3/M82	0.75536	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.93031	1
7-2/M82	0.79828
9-3-2/M82	1.01204

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87972	0.321
IL2-6/WTpooled	1.6591
IL7-5/WTpooled	0.67499	1
IL7-3/WTpooled	1.37953
IL12-4/WTpooled	1.06752	0.785
IL1-4/WTpooled	0.80005
WT/WTpooled	1.15774	0.789

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	0.92767	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89794	1
DC3000/delta hrp 6h	0.99255	0.95
DC3000/delta hrp 12h	1.14533	1
DC3000/delta hrp 24h	0.46592	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97763	0.92
DC3000 delta B/DC3000 delta AB	1.01808	0.694

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93118	1
Exp 36h	0.71624	0.456
Exp 60h	0.70721	0.29

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	1.04246	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
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)	0.97377	0.567
transgenic ySAMdc/azygous control (breaker)	0.85649	0.173
transgenic ySAMdc/azygous control (red)	1.00223	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03432	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09329	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.29033	0.093
Manapal/WT (break)	1.43389	0.14
Manapal/WT (red)	0.98875	0.863