Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.10.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0217	0.977
27DAP/17DAP	0.97216	1
39DAP/27DAP	0.88934	0.482
41DAP/39DAP	1.37999	0.118
42DAP/41DAP	1.07076	1
43DAP/42DAP	1.04054	1
47DAP/43DAP	1.11927	0.576
52DAP/47DAP	1.25089	0.67
57DAP/52DAP	1.1075	0.987

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13717	0.04
17DAP/reference	0.9082	0.097
27DAP/reference	0.89522	0.106
39DAP/reference	0.91448	0.247
41DAP/reference	0.86538	0.018
42DAP/reference	0.9269	0.01
43DAP/reference	0.93108	0.08
47DAP/reference	0.89263	0.002
52DAP/reference	0.93759	0.172
57DAP/reference	0.94076	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29194	0.319
27DAP/17DAP	0.85723	0.724
39DAP/27DAP	0.69236	0.126
41DAP/39DAP	1.53281	0.612
42DAP/41DAP	1.06494	1
43DAP/42DAP	0.96698	0.729
47DAP/43DAP	0.93413	0.597
52DAP/47DAP	0.93713	0.801
57DAP/52DAP	0.73997	0.076
57DAP/7DAP	0.49464	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.47487	0.032
17DAP/reference	1.38938	0.006
27DAP/reference	1.13333	0.246
39DAP/reference	1.02275	0.601
41DAP/reference	0.94278	0.223
42DAP/reference	0.98528	0.554
43DAP/reference	1.10704	0.14
47DAP/reference	0.98687	0.671
52DAP/reference	1.01191	0.802
57DAP/reference	0.85737	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12238	0.491
17DAP/reference	0.90663	0.106
27DAP/reference	0.97343	0.519
39DAP/reference	0.87105	0.036
41DAP/reference	0.97198	0.373
42DAP/reference	0.9233	0.081
43DAP/reference	0.84276	0.135
47DAP/reference	0.88965	0.022
52DAP/reference	0.76752	0.004
57DAP/reference	0.68972	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.96577	0.02
17DAP/reference	1.00795	0.886
27DAP/reference	1.09688	0.143
39DAP/reference	1.40011	0.038
41DAP/reference	1.04028	0.777
42DAP/reference	1.13163	0.364
43DAP/reference	1.13494	0.233
47DAP/reference	0.98063	0.525
52DAP/reference	1.10937	0.89
57DAP/reference	0.88402	0.053

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.30005	0.966
26DAP/20DAP	1.26424	0.567
34DAP/26DAP	1.0496	1
51DAP/34DAP	0.98335	0.927
52DAP/51DAP	1.34561	0.117
53DAP/52DAP	1.08961	0.901
55DAP/53DAP	1.16931	0.366
57DAP/55DAP	0.70503	0.051
62DAP/57DAP	1.01044	1
68DAP/62DAP	0.94233	0.787
68DAP/14DAP	1.15967	0.469

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.68733	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.71681	0.212
Mature Green Tomato/Ripe Tomato	0.96108	0.66
Immature Eggplant/Mature Eggplant	2.24016	0.05
Ripe Pepper/Ripe Tomato	19.2578	1
Mature Eggplant/Ripe Tomato	11.5845	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.86825	0.944
1-1-2/M82	0.8428	0.958
12-2/M82	0.71672	0.955
12-4/M82	1.0432	1
1-3/M82	0.76622
2-1-1/M82	1.16134
2-1/M82	N/A	N/A
2-6/M82	1.19318	0.505
3-2/M82	0.85955
4-1-1/M82	1.03768	1
4-1/M82	0.96189	1
4-3-2/M82	0.7956
4-3/M82	0.96959
5-3/M82	1.10084	0.572
6-2/M82	0.95147
6-3/M82	1.30898
7-1/M82	0.98618
7-2/M82	N/A	N/A
9-3-2/M82	0.78264	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87914	0.321
IL2-6/WTpooled	0.70346	1
IL7-5/WTpooled	0.65458
IL7-3/WTpooled	1.00998	1
IL12-4/WTpooled	0.50225	0.71
IL1-4/WTpooled	1.03023	1
WT/WTpooled	0.90407	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	1.17716	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93835	1
DC3000/delta hrp 6h	0.95812	0.95
DC3000/delta hrp 12h	0.99692	1
DC3000/delta hrp 24h	0.64107	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.31806	0.032
DC3000 delta B/DC3000 delta AB	1.22961	0.304

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92004	1
Exp 36h	0.8881	0.749
Exp 60h	1.01906	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01197	1
Var 0h	0.43415	0.261
Var 12h I row2-row1	1.12617	0.544
Var 12h NI row2-row1	1.12966	0.649
Var 36h I row2-row1	0.87581	1
Var 36h NI row2-row1	1.34906	0.482
Var 60h I row2-row1	0.86752	0.374
Var 60h NI row2-row1	1.11014	0.904
Time course 0hI-0hNI	0.79931	0.08
Time course 12hI-12hNI	1.086	0.403
Time course 36hI-36hNI	0.80248	0.112
Time course 60hI-60hNI	0.61788	0.009

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)	1.04608	0.36
transgenic ySAMdc/azygous control (breaker)	0.83245	0.142
transgenic ySAMdc/azygous control (red)	0.94258	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01365	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05375	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.10211	0.105
Manapal/WT (break)	1.50309	0.14
Manapal/WT (red)	4.02935	0.164