Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.16.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82776	0.31
27DAP/17DAP	3.57186	0.27
39DAP/27DAP	3.76854	0.02
41DAP/39DAP	1.32132	0.38
42DAP/41DAP	1.26976	0.654
43DAP/42DAP	1.25432	0.875
47DAP/43DAP	1.70018	0.229
52DAP/47DAP	1.11474	0.883
57DAP/52DAP	2.36076	0.521

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74071	0.027
17DAP/reference	0.77547	0.009
27DAP/reference	0.88851	0.275
39DAP/reference	1.20736	0.514
41DAP/reference	0.92898	0.434
42DAP/reference	1.02408	1
43DAP/reference	1.17612	0.038
47DAP/reference	1.74026	0.001
52DAP/reference	1.37857	0.033
57DAP/reference	1.58628	0.021

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12597	0.56
27DAP/17DAP	1.31118	0.116
39DAP/27DAP	1.89982	0.062
41DAP/39DAP	1.02466	1
42DAP/41DAP	0.84906	0.298
43DAP/42DAP	1.21969	0.554
47DAP/43DAP	1.35472	0.094
52DAP/47DAP	1.1905	0.799
57DAP/52DAP	1.33002	0.438
57DAP/7DAP	1.44844	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11452	0.534
17DAP/reference	0.85833	0.017
27DAP/reference	1.09444	0.246
39DAP/reference	1.12943	0.096
41DAP/reference	1.44636	0.009
42DAP/reference	1.55447	0.007
43DAP/reference	1.28087	0.026
47DAP/reference	1.43621	0.112
52DAP/reference	1.79569	0.007
57DAP/reference	2.14314	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.52587	0.009
17DAP/reference	0.44887	0.003
27DAP/reference	0.67105	0.029
39DAP/reference	0.80485	0.079
41DAP/reference	1.09304	0.301
42DAP/reference	0.9913	0.594
43DAP/reference	0.66727	0.044
47DAP/reference	1.96285	0.02
52DAP/reference	0.93965	0.121
57DAP/reference	0.97278	0.46

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85096	0.147
17DAP/reference	0.73931	0.105
27DAP/reference	0.99167	0.691
39DAP/reference	1.33011	0.084
41DAP/reference	1.15969	0.034
42DAP/reference	1.42784	0.033
43DAP/reference	1.33695	0.172
47DAP/reference	1.56275	0.01
52DAP/reference	1.81763	0.031
57DAP/reference	2.02408	0.025

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.23911	0.966
26DAP/20DAP	1.1949	0.629
34DAP/26DAP	0.99596	0.954
51DAP/34DAP	3.39332	0.036
52DAP/51DAP	0.7462	1
53DAP/52DAP	1.49274	0.047
55DAP/53DAP	0.54899	0.018
57DAP/55DAP	0.64219	0.099
62DAP/57DAP	12.6543	0.081
68DAP/62DAP	1.97319	0.062
68DAP/14DAP	5.61454	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86403	0.145

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.00828	0.036
Mature Green Tomato/Ripe Tomato	0.41568	0.096
Immature Eggplant/Mature Eggplant	34.4147	0.05
Ripe Pepper/Ripe Tomato	3.15866	0.256
Mature Eggplant/Ripe Tomato	0.42765	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87092	0.841
1-1-2/M82	1.35942	1
12-2/M82	1.05994	1
12-4/M82	1.10676	1
1-3/M82	3.7884	0.277
2-1-1/M82	1.10471	0.764
2-1/M82	0.97092	1
2-6/M82	1.56414	0.374
3-2/M82	1.22368	0.463
4-1-1/M82	1.99923	1
4-1/M82	1.07825	1
4-3-2/M82	2.78195	0.284
4-3/M82	1.23567	1
5-3/M82	0.37591	0.395
6-2/M82	0.64868	0.444
6-3/M82	0.97032	1
7-1/M82	0.86284	0.803
7-2/M82	3.29208	0.324
9-3-2/M82	2.63027	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.10487	0.419
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.24423	1
IL12-4/WTpooled	1.10203	0.695
IL1-4/WTpooled	0.98979
WT/WTpooled	0.90947	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	2.16876	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.67955	0.637
DC3000/delta hrp 12h	0.5997	1
DC3000/delta hrp 24h	0.98804	0.818

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.1278	0.042
DC3000 delta B/DC3000 delta AB	4.025	0.043

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1086	1
Exp 36h	1.15721	1
Exp 60h	0.96458	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06026	1
Var 0h	1.45758	0.339
Var 12h I row2-row1	0.93377	0.856
Var 12h NI row2-row1	2.03108	0.281
Var 36h I row2-row1	1.21476	0.908
Var 36h NI row2-row1	0.67837	0.584
Var 60h I row2-row1	0.53984	0.285
Var 60h NI row2-row1	0.51878	0.292
Time course 0hI-0hNI	1.25936	0.227
Time course 12hI-12hNI	2.04077	0.031
Time course 36hI-36hNI	5.11649	0.004
Time course 60hI-60hNI	28.6785	0.008

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)	0.57154	0.314
transgenic ySAMdc/azygous control (breaker)	0.92985	0.49
transgenic ySAMdc/azygous control (red)	1.36513	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.63635	0.063

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88644	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	8.88266	0.084
Manapal/WT (break)	6.43276	0.13
Manapal/WT (red)	1.76819	0.137