Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.4.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7513	0.169
27DAP/17DAP	0.8931	0.754
39DAP/27DAP	1.04343	0.82
41DAP/39DAP	0.81111	0.317
42DAP/41DAP	1.06957	0.958
43DAP/42DAP	1.09434	0.976
47DAP/43DAP	0.70122	0.197
52DAP/47DAP	1.05813	0.902
57DAP/52DAP	1.02928	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0475	0.685
17DAP/reference	0.91756	0.224
27DAP/reference	0.93441	0.304
39DAP/reference	0.8564	0.17
41DAP/reference	0.82793	0.009
42DAP/reference	0.90514	0.019
43DAP/reference	1.0271	0.838
47DAP/reference	1.03017	0.495
52DAP/reference	0.99653	0.73
57DAP/reference	1.16767	0.105

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12036	0.515
27DAP/17DAP	0.85014	0.279
39DAP/27DAP	1.06969	0.718
41DAP/39DAP	1.15998	0.753
42DAP/41DAP	1.03408	0.991
43DAP/42DAP	0.65048	0.022
47DAP/43DAP	1.16766	0.389
52DAP/47DAP	0.99052	0.917
57DAP/52DAP	1.64205	0.059
57DAP/7DAP	1.03493	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.93734	0.025
17DAP/reference	1.75833	0.008
27DAP/reference	1.81087	0.009
39DAP/reference	1.79485	0.006
41DAP/reference	1.75933	0.013
42DAP/reference	1.61478	0.009
43DAP/reference	1.48055	0.007
47DAP/reference	1.33366	0.259
52DAP/reference	1.54919	0.007
57DAP/reference	1.41692	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0113	0.965
17DAP/reference	0.91039	0.195
27DAP/reference	1.0797	0.583
39DAP/reference	1.04487	1
41DAP/reference	0.97425	0.412
42DAP/reference	1.00311	1
43DAP/reference	0.69981	0.019
47DAP/reference	1.07412	0.621
52DAP/reference	0.7868	0.007
57DAP/reference	0.78207	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.73615	0.024
17DAP/reference	1.12721	0.887
27DAP/reference	1.29267	0.041
39DAP/reference	1.28524	0.035
41DAP/reference	1.08084	0.818
42DAP/reference	1.2636	0.074
43DAP/reference	1.37731	0.123
47DAP/reference	0.88005	0.103
52DAP/reference	1.46701	0.061
57DAP/reference	1.27313	0.072

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96196	1
26DAP/20DAP	2.26441	0.097
34DAP/26DAP	0.58703	0.05
51DAP/34DAP	1.34866	0.159
52DAP/51DAP	1.07441	0.776
53DAP/52DAP	0.98614	0.938
55DAP/53DAP	0.79093	0.058
57DAP/55DAP	1.21597	0.87
62DAP/57DAP	1.00444	1
68DAP/62DAP	1.56334	0.23
68DAP/14DAP	1.65113	0.034

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.51532	0.034

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03039	1
Mature Green Tomato/Ripe Tomato	1.62628	0.119
Immature Eggplant/Mature Eggplant	1.3475	0.058
Ripe Pepper/Ripe Tomato	1.65736	0.258
Mature Eggplant/Ripe Tomato	3.01621	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.72026
1-1-2/M82	1.10429	1
12-2/M82	0.94791
12-4/M82	0.70453	0.282
1-3/M82	N/A	N/A
2-1-1/M82	0.78802	0.784
2-1/M82	1.09369
2-6/M82	0.92968	1
3-2/M82	1.06105	1
4-1-1/M82	0.81747	0.959
4-1/M82	N/A	N/A
4-3-2/M82	1.35728
4-3/M82	1.58702	0.268
5-3/M82	1.20129	1
6-2/M82	1.07726	1
6-3/M82	1.11954	1
7-1/M82	0.89642	0.803
7-2/M82	1.46828	0.324
9-3-2/M82	1.19902	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.97607	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.99407	1
IL12-4/WTpooled	1.04719	0.673
IL1-4/WTpooled	1.05938
WT/WTpooled	0.93086	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	1.11895	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01181	1
DC3000/delta hrp 6h	1.01667	0.95
DC3000/delta hrp 12h	0.93045	1
DC3000/delta hrp 24h	1.16582	0.136

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.27994	0.055
DC3000 delta B/DC3000 delta AB	1.30441	0.237

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.7695	1
Exp 36h	1.29146	0.693
Exp 60h	1.05809	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.13757	0.98
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.11716	0.321
transgenic ySAMdc/azygous control (breaker)	1.57555	0.248
transgenic ySAMdc/azygous control (red)	1.18898	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03397	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72085	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8812	1
Manapal/WT (break)	0.95385	1
Manapal/WT (red)	1.34135	0.164