Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.11.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85533	0.098
27DAP/17DAP	1.10984	0.881
39DAP/27DAP	0.96472	0.719
41DAP/39DAP	1.38856	0.553
42DAP/41DAP	1.13156	0.971
43DAP/42DAP	0.82818	0.627
47DAP/43DAP	1.15618	0.756
52DAP/47DAP	1.85357	0.202
57DAP/52DAP	0.91547	0.7

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01365	0.928
17DAP/reference	1.00105	1
27DAP/reference	0.96979	0.349
39DAP/reference	0.97454	0.587
41DAP/reference	0.96086	0.154
42DAP/reference	0.9016	0.011
43DAP/reference	0.95998	0.36
47DAP/reference	0.91651	0.023
52DAP/reference	0.85404	0.099
57DAP/reference	0.85094	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06577	0.525
27DAP/17DAP	0.98379	0.919
39DAP/27DAP	1.06908	0.615
41DAP/39DAP	1.10115	0.861
42DAP/41DAP	1.01914	1
43DAP/42DAP	1.00512	1
47DAP/43DAP	1.01771	0.973
52DAP/47DAP	1.01181	1
57DAP/52DAP	1.04728	0.8
57DAP/7DAP	1.1382	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92689	0.157
17DAP/reference	0.94936	0.064
27DAP/reference	0.94758	0.03
39DAP/reference	0.89978	0.011
41DAP/reference	0.89404	0.042
42DAP/reference	0.87592	0.019
43DAP/reference	0.89417	0.091
47DAP/reference	0.88006	0.033
52DAP/reference	0.89467	0.072
57DAP/reference	0.81045	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98209	0.706
17DAP/reference	0.97925	0.499
27DAP/reference	0.93311	0.317
39DAP/reference	0.93356	0.214
41DAP/reference	0.83074	0.024
42DAP/reference	0.90824	0.073
43DAP/reference	1.07435	0.485
47DAP/reference	0.87515	0.012
52DAP/reference	0.97789	0.38
57DAP/reference	1.03732	0.538

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.898	0.082
17DAP/reference	1.00425	1
27DAP/reference	0.9061	0.085
39DAP/reference	0.98947	0.693
41DAP/reference	0.94603	0.064
42DAP/reference	0.94044	0.361
43DAP/reference	0.86582	0.106
47DAP/reference	0.9769	0.465
52DAP/reference	0.97399	0.637
57DAP/reference	0.74445	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00209	1
26DAP/20DAP	0.97065	1
34DAP/26DAP	1.12008	0.819
51DAP/34DAP	0.89293	0.317
52DAP/51DAP	0.98106	1
53DAP/52DAP	1.04305	0.845
55DAP/53DAP	1.09675	0.534
57DAP/55DAP	1.07821	0.906
62DAP/57DAP	1.10106	0.723
68DAP/62DAP	0.84638	0.641
68DAP/14DAP	0.93025	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91769	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.01162	1
Mature Green Tomato/Ripe Tomato	0.99865	0.835
Immature Eggplant/Mature Eggplant	1.16025	0.248
Ripe Pepper/Ripe Tomato	1.68984	1
Mature Eggplant/Ripe Tomato	1.96997	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08035	1
1-1-2/M82	0.92491	0.958
12-2/M82	1.07866	1
12-4/M82	0.95111	1
1-3/M82	0.92312	0.501
2-1-1/M82	1.09392	0.375
2-1/M82	1.28854	1
2-6/M82	0.99945	1
3-2/M82	0.96903
4-1-1/M82	1.04722	0.915
4-1/M82	0.91132	1
4-3-2/M82	0.7865	0.445
4-3/M82	0.91105	1
5-3/M82	1.03962	1
6-2/M82	0.95181	1
6-3/M82	N/A	N/A
7-1/M82	0.9579	1
7-2/M82	1.0055	1
9-3-2/M82	0.72614	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.61235	0.243
IL2-6/WTpooled	1.06904	1
IL7-5/WTpooled	0.70755	1
IL7-3/WTpooled	0.68978	0.31
IL12-4/WTpooled	0.93022	0.71
IL1-4/WTpooled	0.9389	1
WT/WTpooled	1.07366	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	0.85777	0.226

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04574	0.894
DC3000/delta hrp 6h	1.07755	1
DC3000/delta hrp 12h	0.99998	1
DC3000/delta hrp 24h	1.03655	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03569	0.648
DC3000 delta B/DC3000 delta AB	1.04779	0.593

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.22929	1
Exp 36h	1.32265	0.489
Exp 60h	0.98882	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95224	1
Var 0h	1.00691	1
Var 12h I row2-row1	1.21366	0.222
Var 12h NI row2-row1	1.09675	1
Var 36h I row2-row1	0.91863	1
Var 36h NI row2-row1	0.78891	0.522
Var 60h I row2-row1	1.39994	0.562
Var 60h NI row2-row1	1.25556	0.904
Time course 0hI-0hNI	1.14232	0.764
Time course 12hI-12hNI	0.99723	1
Time course 36hI-36hNI	0.97711	0.514
Time course 60hI-60hNI	1.60574	0.053

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)	1.00637	0.798
transgenic ySAMdc/azygous control (breaker)	1.06083	1
transgenic ySAMdc/azygous control (red)	0.92143	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08152	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96611	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01221	1
Manapal/WT (break)	0.96635	1
Manapal/WT (red)	1.11303	0.413