Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.16.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28182	0.83
27DAP/17DAP	1.11891	0.902
39DAP/27DAP	1.26425	0.59
41DAP/39DAP	1.04554	0.939
42DAP/41DAP	0.91593	1
43DAP/42DAP	1.00576	0.937
47DAP/43DAP	1.12965	0.926
52DAP/47DAP	0.90941	0.685
57DAP/52DAP	0.96925	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84281	0.033
17DAP/reference	0.90916	0.18
27DAP/reference	1.0193	0.847
39DAP/reference	0.9531	0.424
41DAP/reference	0.93336	0.012
42DAP/reference	0.88377	0.02
43DAP/reference	0.89534	0.084
47DAP/reference	0.91619	0.025
52DAP/reference	0.95568	0.33
57DAP/reference	1.06161	0.724

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03113	1
27DAP/17DAP	1.15882	0.658
39DAP/27DAP	1.05169	0.603
41DAP/39DAP	1.20199	0.817
42DAP/41DAP	0.74936	0.017
43DAP/42DAP	1.34724	0.699
47DAP/43DAP	1.03224	0.954
52DAP/47DAP	1.6225	0.116
57DAP/52DAP	1.20069	0.378
57DAP/7DAP	1.03486	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10389	0.534
17DAP/reference	1.36152	0.015
27DAP/reference	1.36399	0.015
39DAP/reference	1.24332	0.073
41DAP/reference	1.23567	0.064
42DAP/reference	1.33768	0.059
43DAP/reference	1.56648	0.012
47DAP/reference	1.19824	0.229
52DAP/reference	1.52017	0.007
57DAP/reference	1.42266	0.023

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01987	0.951
17DAP/reference	0.77202	0.022
27DAP/reference	0.86896	0.173
39DAP/reference	0.74994	0.013
41DAP/reference	0.89028	0.188
42DAP/reference	0.91762	0.261
43DAP/reference	0.84611	0.144
47DAP/reference	0.91069	0.097
52DAP/reference	0.92785	0.06
57DAP/reference	0.83734	0.019

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.85224	0.18
17DAP/reference	1.035	0.918
27DAP/reference	1.27095	0.035
39DAP/reference	1.22754	0.055
41DAP/reference	1.5511	0.017
42DAP/reference	1.2936	0.287
43DAP/reference	1.33241	0.418
47DAP/reference	0.95495	0.315
52DAP/reference	1.34552	0.1
57DAP/reference	1.25529	0.378

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06125	0.966
26DAP/20DAP	0.43779
34DAP/26DAP	0.82743	0.653
51DAP/34DAP	0.96871	0.856
52DAP/51DAP	0.93382	1
53DAP/52DAP	1.45054	0.623
55DAP/53DAP	1.19194	0.848
57DAP/55DAP	0.85377	0.322
62DAP/57DAP	1.00598	0.994
68DAP/62DAP	0.97604	0.769
68DAP/14DAP	1.1451	0.615

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.69466	0.102

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.97108
Mature Green Tomato/Ripe Tomato	0.61574	0.021
Immature Eggplant/Mature Eggplant	1.59269
Ripe Pepper/Ripe Tomato	0.65249
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.58062
12-2/M82	N/A	N/A
12-4/M82	0.90671	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	N/A	N/A
3-2/M82	1.10813
4-1-1/M82	N/A	N/A
4-1/M82	1.03049
4-3-2/M82	0.93752
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	1.03103
7-2/M82	0.14888
9-3-2/M82	0.87367	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.00741

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.16682	0.921
DC3000/delta hrp 6h	1.83975
DC3000/delta hrp 12h	1.10815	1
DC3000/delta hrp 24h	1.02123	0.821

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	0.71094	1
Exp 36h	1.23178	1
Exp 60h	1.19082	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.86702	1
Var 0h	0.94219
Var 12h I row2-row1	0.88202	0.627
Var 12h NI row2-row1	1.09079	1
Var 36h I row2-row1	1.11068	1
Var 36h NI row2-row1	1.43909
Var 60h I row2-row1	0.95453	0.285
Var 60h NI row2-row1	0.72931	0.932
Time course 0hI-0hNI	0.99763	0.958
Time course 12hI-12hNI	1.22964	0.756
Time course 36hI-36hNI	1.46416	0.147
Time course 60hI-60hNI	3.77716	0.022

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)	1.09286	0.325
transgenic ySAMdc/azygous control (breaker)	0.81675	0.173
transgenic ySAMdc/azygous control (red)	1.10824	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03592	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01617	1

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)	0.98849	1
Manapal/WT (red)	0.83228	0.36