Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.13.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03088	0.77
27DAP/17DAP	1.05305	1
39DAP/27DAP	0.80643	0.529
41DAP/39DAP	1.53071	0.225
42DAP/41DAP	1.11476	1
43DAP/42DAP	1.08992	1
47DAP/43DAP	1.06446	0.966
52DAP/47DAP	1.5468	0.367
57DAP/52DAP	1.05677	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99035	0.756
17DAP/reference	0.77834	0.342
27DAP/reference	0.94919
39DAP/reference	0.88051	0.554
41DAP/reference	1.24787
42DAP/reference	1.07041	0.366
43DAP/reference	1.08948
47DAP/reference	0.9327	0.345
52DAP/reference	1.24018	0.038
57DAP/reference	1.3842	0.564

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89819	0.289
27DAP/17DAP	0.96173	0.782
39DAP/27DAP	1.12319	0.285
41DAP/39DAP	1.1612	0.315
42DAP/41DAP	0.93606	0.456
43DAP/42DAP	1.05602	0.273
47DAP/43DAP	1.02916	0.892
52DAP/47DAP	0.99397	0.962
57DAP/52DAP	1.02804	0.825
57DAP/7DAP	1.03994	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.4347	0.066
17DAP/reference	0.32337	0.011
27DAP/reference	0.68434	0.013
39DAP/reference	0.56966	0.011
41DAP/reference	0.44649	0.013
42DAP/reference	0.63553	0.017
43DAP/reference	0.40722	0.009
47DAP/reference	0.6432	0.128
52DAP/reference	0.26867	0.009
57DAP/reference	0.21133	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93344	0.532
17DAP/reference	1.0284	0.613
27DAP/reference	0.87751	0.144
39DAP/reference	0.8487	0.047
41DAP/reference	0.85859	0.07
42DAP/reference	0.94148	0.261
43DAP/reference	0.90062	0.336
47DAP/reference	1.02777	0.775
52DAP/reference	0.88594	0.037
57DAP/reference	1.07591	0.477

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.37447	0.034
17DAP/reference	0.93154	0.305
27DAP/reference	0.54542	0.035
39DAP/reference	0.58045	0.014
41DAP/reference	0.40486	0.019
42DAP/reference	0.63825	0.019
43DAP/reference	0.7453	0.052
47DAP/reference	1.03618	0.585
52DAP/reference	1.44399	0.17
57DAP/reference	3.3109	0.167

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02068	1
26DAP/20DAP	0.83747	0.244
34DAP/26DAP	1.05534	1
51DAP/34DAP	0.85653	0.104
52DAP/51DAP	1.03876	0.704
53DAP/52DAP	1.09446	0.517
55DAP/53DAP	1.01709	0.994
57DAP/55DAP	1.03187	0.997
62DAP/57DAP	1.02002	1
68DAP/62DAP	0.98039	0.787
68DAP/14DAP	0.8413	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90754	0.239

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.69317
Mature Green Tomato/Ripe Tomato	0.48616	0.022
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.31386	0.224
Mature Eggplant/Ripe Tomato	0.06884	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04013	1
1-1-2/M82	0.99335	1
12-2/M82	1.12378	1
12-4/M82	0.76509	0.619
1-3/M82	1.37657	0.255
2-1-1/M82	1.20698	0.375
2-1/M82	1.05638
2-6/M82	1.007	1
3-2/M82	0.68248	0.455
4-1-1/M82	1.03236	1
4-1/M82	0.79948	1
4-3-2/M82	0.48522	1
4-3/M82	1.07301	1
5-3/M82	1.00641	1
6-2/M82	0.76431	0.497
6-3/M82	1.03787	1
7-1/M82	0.94706	0.509
7-2/M82	1.12194	1
9-3-2/M82	0.90945	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.78425	0.243
IL2-6/WTpooled	1.20609	0.788
IL7-5/WTpooled	1.05068	1
IL7-3/WTpooled	0.77565	0.259
IL12-4/WTpooled	0.7514	0.581
IL1-4/WTpooled	1.04058	1
WT/WTpooled	1.07125	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	2.15401	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03992	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.23965	1
DC3000/delta hrp 24h	1.38369	0.082

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.31019	0.055
DC3000 delta B/DC3000 delta AB	1.13679	0.225

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	2.20063	0.254
Exp 36h	3.6081	0.326
Exp 60h	2.76902	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.88201	1
Var 0h	0.59866	0.325
Var 12h I row2-row1	1.10235	0.263
Var 12h NI row2-row1	0.85527	0.627
Var 36h I row2-row1	1.03495	1
Var 36h NI row2-row1	0.73108	0.522
Var 60h I row2-row1	1.37995	0.562
Var 60h NI row2-row1	1.05862	1
Time course 0hI-0hNI	1.10313	0.799
Time course 12hI-12hNI	0.96709	0.82
Time course 36hI-36hNI	1.50608	0.005
Time course 60hI-60hNI	1.81883	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)	1.72481	0.931
transgenic ySAMdc/azygous control (breaker)	0.5364	0.134
transgenic ySAMdc/azygous control (red)	0.67023	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04237	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.33039	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.29332	0.172
Manapal/WT (break)	1.27529	1
Manapal/WT (red)	0.74359	0.274