Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.3.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.978	0.77
27DAP/17DAP	1.01437	1
39DAP/27DAP	1.4728	0.312
41DAP/39DAP	1.03741	0.701
42DAP/41DAP	1.24618	0.806
43DAP/42DAP	1.24498	0.861
47DAP/43DAP	1.17171	0.727
52DAP/47DAP	0.84905	0.618
57DAP/52DAP	0.90461	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76341	0.064
17DAP/reference	0.70711	0.035
27DAP/reference	0.78384	0.048
39DAP/reference	0.49821	0.005
41DAP/reference	0.52337	0.009
42DAP/reference	0.70563	0.001
43DAP/reference	0.70839
47DAP/reference	0.69652	0.004
52DAP/reference	1.07903	0.607
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07053	0.91
27DAP/17DAP	1.15295	0.719
39DAP/27DAP	0.91867	0.712
41DAP/39DAP	0.92054	0.893
42DAP/41DAP	1.32043	0.622
43DAP/42DAP	0.93538	0.597
47DAP/43DAP	0.9665	0.877
52DAP/47DAP	1.24421	0.573
57DAP/52DAP	1.52791	0.175
57DAP/7DAP	4.13107

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38345	0.115
17DAP/reference	1.50125	0.008
27DAP/reference	1.47242	0.041
39DAP/reference	1.77157	0.006
41DAP/reference	1.41646	0.083
42DAP/reference	1.66013	0.007
43DAP/reference	1.82475	0.011
47DAP/reference	1.02821	0.901
52DAP/reference	1.39122	0.076
57DAP/reference	1.41817	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80401	0.072
17DAP/reference	0.61571	0.004
27DAP/reference	0.98496	0.554
39DAP/reference	1.04641	1
41DAP/reference	1.04308	0.91
42DAP/reference	0.85759	0.067
43DAP/reference	0.67534	0.028
47DAP/reference	0.79834	0.017
52DAP/reference	0.97796	0.5
57DAP/reference	0.78739	0.05

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35367	0.079
17DAP/reference	1.12205	0.854
27DAP/reference	1.43062	0.039
39DAP/reference	1.5591	0.078
41DAP/reference	1.64373	0.027
42DAP/reference	1.63719	0.013
43DAP/reference	1.31716	0.037
47DAP/reference	0.95766	0.434
52DAP/reference	1.51498	0.144
57DAP/reference	1.75961	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0938	1
26DAP/20DAP	0.84018	1
34DAP/26DAP	0.60032	0.078
51DAP/34DAP	0.95893	0.77
52DAP/51DAP	1.58377
53DAP/52DAP	0.99076	0.902
55DAP/53DAP	0.58035	0.233
57DAP/55DAP	0.75555	0.133
62DAP/57DAP	17.4483	0.445
68DAP/62DAP	1.94515	0.027
68DAP/14DAP	3.14275	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.26447	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.00046
Immature Eggplant/Mature Eggplant	1.1607	0.348
Ripe Pepper/Ripe Tomato	0.8489	0.293
Mature Eggplant/Ripe Tomato	2.32733	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15113
IL2-6/WTpooled	1.11753	0.531
IL7-5/WTpooled	1.18978
IL7-3/WTpooled	1.19268	0.362
IL12-4/WTpooled	1.02686	0.891
IL1-4/WTpooled	0.81401	0.457
WT/WTpooled	0.97563	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	0.79388	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.78009	0.642
DC3000/delta hrp 6h	1.18379	1
DC3000/delta hrp 12h	0.81914
DC3000/delta hrp 24h	0.13724	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.66218	0.024
DC3000 delta B/DC3000 delta AB	0.46252	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.87055	0.24
Exp 36h	1.117	1
Exp 60h	0.83449	0.586

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	1.53787	0.98
Var 12h I row2-row1	0.78529	0.338
Var 12h NI row2-row1	0.48511	1
Var 36h I row2-row1	0.87434	1
Var 36h NI row2-row1	1.43955	0.482
Var 60h I row2-row1	1.02668
Var 60h NI row2-row1	1.24367	0.691
Time course 0hI-0hNI	1.03992	0.833
Time course 12hI-12hNI	0.95565	0.687
Time course 36hI-36hNI	0.7825	0.03
Time course 60hI-60hNI	0.11944	0.006

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)	1.10424	0.292
transgenic ySAMdc/azygous control (breaker)	0.87123	0.251
transgenic ySAMdc/azygous control (red)	0.98355	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.49078	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0321	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90536	1
Manapal/WT (break)	1.0534	1
Manapal/WT (red)	1.48171	0.133