Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.4.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97842	0.76
27DAP/17DAP	1.04447	0.928
39DAP/27DAP	1.16884	0.759
41DAP/39DAP	1.30898	0.676
42DAP/41DAP	0.89339	1
43DAP/42DAP	0.93802	0.877
47DAP/43DAP	0.84159	0.487
52DAP/47DAP	1.45651	0.804
57DAP/52DAP	0.85807	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91637	0.2
17DAP/reference	1.10491	0.092
27DAP/reference	1.06868	0.216
39DAP/reference	1.10806	0.343
41DAP/reference	0.98427	0.814
42DAP/reference	0.97236	0.242
43DAP/reference	0.95362	0.41
47DAP/reference	0.983	0.503
52DAP/reference	0.9671	0.416
57DAP/reference	0.96343	0.176

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98414	0.782
27DAP/17DAP	1.28314	0.264
39DAP/27DAP	1.0026	1
41DAP/39DAP	1.52184	0.336
42DAP/41DAP	1.00629	0.781
43DAP/42DAP	0.94058	0.618
47DAP/43DAP	1.15656	0.61
52DAP/47DAP	1.07897	0.789
57DAP/52DAP	1.02315	1
57DAP/7DAP	0.59867

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2741	0.042
17DAP/reference	1.51869	0.009
27DAP/reference	1.27922	0.041
39DAP/reference	1.12404	0.601
41DAP/reference	1.24733	0.069
42DAP/reference	0.99202	0.582
43DAP/reference	1.17922	0.603
47DAP/reference	1.15681	0.158
52DAP/reference	1.45126	0.13
57DAP/reference	1.23605	0.035

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3162	0.284
17DAP/reference	0.92555	0.41
27DAP/reference	1.1293	0.497
39DAP/reference	1.05665	0.935
41DAP/reference	1.03806	1
42DAP/reference	1.02197	1
43DAP/reference	1.08281	0.831
47DAP/reference	1.132	0.124
52DAP/reference	1.02155	0.838
57DAP/reference	1.48926	0.019

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26505	0.056
17DAP/reference	1.09528	0.595
27DAP/reference	1.19884	0.237
39DAP/reference	1.23382	0.034
41DAP/reference	1.25758	0.048
42DAP/reference	1.26231	0.082
43DAP/reference	1.18358	0.547
47DAP/reference	0.85255	0.145
52DAP/reference	1.21418	0.42
57DAP/reference	1.20839	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17015	0.966
26DAP/20DAP	1.01026	1
34DAP/26DAP	1.34551	1
51DAP/34DAP	1.06824	0.785
52DAP/51DAP	0.99074	1
53DAP/52DAP	1.02076	0.983
55DAP/53DAP	1.04824	0.955
57DAP/55DAP	0.96841	0.817
62DAP/57DAP	1.04791	1
68DAP/62DAP	1.19145	0.549
68DAP/14DAP	0.52967	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.23523	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.13318	0.577
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.08771	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9259	0.944
1-1-2/M82	1.07499	1
12-2/M82	N/A	N/A
12-4/M82	0.80737	1
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	1.20499
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	0.92677
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.99725	1
9-3-2/M82	0.61799

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.75635	0.243
IL2-6/WTpooled	0.78911	0.473
IL7-5/WTpooled	0.68409	1
IL7-3/WTpooled	0.77312	0.31
IL12-4/WTpooled	0.89677	1
IL1-4/WTpooled	0.83993	0.699
WT/WTpooled	1.10389	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	1.17053	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97404	1
DC3000/delta hrp 6h	0.73099	0.95
DC3000/delta hrp 12h	1.13692	1
DC3000/delta hrp 24h	1.05394	0.633

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	1.04857	1
Exp 36h	1.81185	0.489
Exp 60h	1.49474	0.283

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	0.9362	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)	1.07425	0.571
transgenic ySAMdc/azygous control (breaker)	0.99885	1
transgenic ySAMdc/azygous control (red)	0.95407	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00798	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81202	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92638	1
Manapal/WT (break)	0.95672	1
Manapal/WT (red)	0.85858	0.274