Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.6.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13972	0.67
27DAP/17DAP	1.31442	0.699
39DAP/27DAP	0.82672	0.507
41DAP/39DAP	1.35302	0.339
42DAP/41DAP	1.06364	0.938
43DAP/42DAP	0.99621	0.937
47DAP/43DAP	1.32589	0.438
52DAP/47DAP	1.02633	0.927
57DAP/52DAP	1.19306	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60544	0.043
17DAP/reference	0.70282	0.009
27DAP/reference	0.76018	0.032
39DAP/reference	0.67873	0.01
41DAP/reference	0.69383	0.008
42DAP/reference	0.65939	0.001
43DAP/reference	0.78015	0.043
47DAP/reference	0.72295	0.001
52DAP/reference	0.85225	0.016
57DAP/reference	0.85393	0.049

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.14328	0.196
27DAP/17DAP	0.86162	0.684
39DAP/27DAP	0.89283	0.529
41DAP/39DAP	1.11315	0.727
42DAP/41DAP	0.7296	0.036
43DAP/42DAP	1.00062	0.902
47DAP/43DAP	1.06413	0.833
52DAP/47DAP	1.22609	0.568
57DAP/52DAP	1.20818	0.699
57DAP/7DAP	1.17379	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65296	0.059
17DAP/reference	0.72629	0.02
27DAP/reference	0.72199	0.012
39DAP/reference	0.70217	0.012
41DAP/reference	0.77385	0.044
42DAP/reference	0.68905	0.015
43DAP/reference	0.59561	0.011
47DAP/reference	0.76225	0.168
52DAP/reference	0.74993	0.022
57DAP/reference	0.6996	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.59978	0.006
17DAP/reference	0.52129	0.003
27DAP/reference	0.60416	0.009
39DAP/reference	0.59134	0.011
41DAP/reference	0.66608	0.01
42DAP/reference	0.80806	0.108
43DAP/reference	0.71019	0.009
47DAP/reference	0.71153	0.022
52DAP/reference	0.59352	0.003
57DAP/reference	0.53385	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.63903	0.02
17DAP/reference	0.82838	0.198
27DAP/reference	0.74551	0.052
39DAP/reference	0.65787	0.008
41DAP/reference	0.81086	0.077
42DAP/reference	0.85697	0.087
43DAP/reference	0.75958	0.043
47DAP/reference	0.61354	0.004
52DAP/reference	1.05526	0.637
57DAP/reference	0.98681	0.564

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.32991	0.945
26DAP/20DAP	0.85804	1
34DAP/26DAP	1.0007	1
51DAP/34DAP	1.34183	0.059
52DAP/51DAP	1.07913	1
53DAP/52DAP	1.43797	0.144
55DAP/53DAP	1.12612	0.842
57DAP/55DAP	0.87012	0.508
62DAP/57DAP	0.86712	0.871
68DAP/62DAP	1.10212	0.858
68DAP/14DAP	0.9662	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96928	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.45659	0.17
Mature Green Tomato/Ripe Tomato	0.72305	0.033
Immature Eggplant/Mature Eggplant	11.9393	0.05
Ripe Pepper/Ripe Tomato	8.79682
Mature Eggplant/Ripe Tomato	3.844

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	1.0307
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	1.03918	0.695
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	0.67956	0.487
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	1.41153
7-1/M82	1.0766
7-2/M82	N/A	N/A
9-3-2/M82	0.736

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.2011	0.365
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.31983	0.792
IL7-3/WTpooled	1.28354	1
IL12-4/WTpooled	0.92803	0.71
IL1-4/WTpooled	1.16842	1
WT/WTpooled	1.11457	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	1.2836

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01989	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.97619	1
DC3000/delta hrp 24h	2.23607	0.107

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	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.12788	1
Var 0h	1.22415
Var 12h I row2-row1	1.00514	1
Var 12h NI row2-row1	0.87398
Var 36h I row2-row1	0.84204	1
Var 36h NI row2-row1	0.90717	0.743
Var 60h I row2-row1	0.75618	0.285
Var 60h NI row2-row1	0.93065	0.866
Time course 0hI-0hNI	0.93449	0.675
Time course 12hI-12hNI	0.86347	0.375
Time course 36hI-36hNI	0.77586	0.22
Time course 60hI-60hNI	2.37545	0.06

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	2.2674	0.166
transgenic ySAMdc/azygous control (red)	1.36353	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08604	0.077

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96183	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.61111	1
Manapal/WT (red)	N/A	N/A