Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.7.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30183	0.901
27DAP/17DAP	0.77292	0.438
39DAP/27DAP	1.02742	0.769
41DAP/39DAP	0.80158	0.357
42DAP/41DAP	1.04823	0.997
43DAP/42DAP	0.9998	0.93
47DAP/43DAP	0.87967	0.609
52DAP/47DAP	1.22538	0.518
57DAP/52DAP	0.83377	0.849

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97108	0.539
17DAP/reference	0.95614	0.567
27DAP/reference	0.84933	0.083
39DAP/reference	0.94747	0.487
41DAP/reference	0.83981	0.154
42DAP/reference	0.93946	0.169
43DAP/reference	1.1706	0.217
47DAP/reference	0.99779	0.602
52DAP/reference	0.88882	0.275
57DAP/reference	1.0249	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2398	0.482
27DAP/17DAP	1.07424	0.909
39DAP/27DAP	0.7045	0.181
41DAP/39DAP	1.20042	0.315
42DAP/41DAP	0.91065	0.579
43DAP/42DAP	0.86843	0.28
47DAP/43DAP	0.99236	0.985
52DAP/47DAP	0.71903	0.498
57DAP/52DAP	1.4776	0.674
57DAP/7DAP	0.84468

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84543	0.108
17DAP/reference	1.18702	0.574
27DAP/reference	1.11159	0.664
39DAP/reference	1.51976	0.033
41DAP/reference	1.32223	1
42DAP/reference	1.30576	0.686
43DAP/reference	1.61099	0.457
47DAP/reference	0.94089	0.504
52DAP/reference	1.31871	0.081
57DAP/reference	1.01662	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9505	0.607
17DAP/reference	0.96619	0.548
27DAP/reference	1.01335	0.735
39DAP/reference	0.73672	0.034
41DAP/reference	0.85632	0.148
42DAP/reference	0.86697	0.189
43DAP/reference	0.8087	0.114
47DAP/reference	1.01219	0.833
52DAP/reference	0.94008	0.28
57DAP/reference	0.98218	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22555	0.444
17DAP/reference	0.92356	0.417
27DAP/reference	1.45365	0.052
39DAP/reference	1.06761	0.813
41DAP/reference	1.03641	1
42DAP/reference	0.9907	0.816
43DAP/reference	1.06492	0.734
47DAP/reference	0.89006	0.278
52DAP/reference	1.1329	0.714
57DAP/reference	0.92762	0.242

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20637	0.966
26DAP/20DAP	1.03423	1
34DAP/26DAP	1.03316	1
51DAP/34DAP	1.14636	0.677
52DAP/51DAP	0.81251	1
53DAP/52DAP	1.06778	0.806
55DAP/53DAP	1.04881	0.848
57DAP/55DAP	0.93173	0.76
62DAP/57DAP	0.69635	0.004
68DAP/62DAP	1.14703	0.17
68DAP/14DAP	0.96213	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.36973	0.026

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	4.92383	0.017
Immature Eggplant/Mature Eggplant	1.0259	1
Ripe Pepper/Ripe Tomato	51.5708
Mature Eggplant/Ripe Tomato	7.7016	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09827	0.877
1-1-2/M82	1.23255
12-2/M82	1.3485	0.61
12-4/M82	0.72929	0.282
1-3/M82	1.50434
2-1-1/M82	1.03902	0.439
2-1/M82	N/A	N/A
2-6/M82	0.82668	1
3-2/M82	N/A	N/A
4-1-1/M82	0.80637	1
4-1/M82	N/A	N/A
4-3-2/M82	0.659	0.487
4-3/M82	0.91832	1
5-3/M82	1.14421	0.572
6-2/M82	0.82825
6-3/M82	1.14968	1
7-1/M82	0.90602	0.452
7-2/M82	0.92636
9-3-2/M82	1.17787	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.47154	0.277
IL2-6/WTpooled	1.01571	1
IL7-5/WTpooled	1.04846	0.75
IL7-3/WTpooled	1.03833	1
IL12-4/WTpooled	1.07819	0.503
IL1-4/WTpooled	0.99561	1
WT/WTpooled	1.00957	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	0.89763	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.78685	0.95
DC3000/delta hrp 12h	0.97507	1
DC3000/delta hrp 24h	1.39123	0.202

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.39822	0.055
DC3000 delta B/DC3000 delta AB	2.17822	0.141

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.56566	1
Exp 36h	0.93711	0.879
Exp 60h	0.56804	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00405	1
Var 0h	0.79281	0.933
Var 12h I row2-row1	1.2953	0.473
Var 12h NI row2-row1	1.27368	0.649
Var 36h I row2-row1	0.96239	1
Var 36h NI row2-row1	0.94928	0.791
Var 60h I row2-row1	0.80094	0.374
Var 60h NI row2-row1	0.89149	0.932
Time course 0hI-0hNI	1.06158	0.764
Time course 12hI-12hNI	0.9637	0.742
Time course 36hI-36hNI	1.23708	0.007
Time course 60hI-60hNI	1.67756	0.008

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)	1.00281	1
transgenic ySAMdc/azygous control (breaker)	1.256	0.248
transgenic ySAMdc/azygous control (red)	1.06646	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10363	0.061

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96742	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91688	1
Manapal/WT (break)	1.48892	0.381
Manapal/WT (red)	0.77109	0.229