Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.11.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72698	0.162
27DAP/17DAP	1.01942	0.926
39DAP/27DAP	1.03536	0.949
41DAP/39DAP	1.53976	0.208
42DAP/41DAP	1.08506	1
43DAP/42DAP	0.89839	0.841
47DAP/43DAP	0.80587	0.41
52DAP/47DAP	2.5371	0.116
57DAP/52DAP	0.83201	0.81

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98332	0.55
17DAP/reference	0.95837	0.342
27DAP/reference	0.95473	0.471
39DAP/reference	1.01417	0.828
41DAP/reference	1.00803	0.91
42DAP/reference	1.03891	0.113
43DAP/reference	1.0968	0.095
47DAP/reference	0.96257	0.207
52DAP/reference	0.90983	0.167
57DAP/reference	0.95793	0.165

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99692	0.782
27DAP/17DAP	1.04898	0.842
39DAP/27DAP	1.08697	0.526
41DAP/39DAP	0.90992	0.662
42DAP/41DAP	1.11602	0.763
43DAP/42DAP	0.94263	0.466
47DAP/43DAP	1.20931	0.286
52DAP/47DAP	1.10449	0.724
57DAP/52DAP	0.91552	0.352
57DAP/7DAP	1.11442	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84199	0.058
17DAP/reference	0.78951	0.013
27DAP/reference	0.8426	0.042
39DAP/reference	0.80236	0.021
41DAP/reference	0.90831	0.174
42DAP/reference	0.83918	0.058
43DAP/reference	0.88282	0.202
47DAP/reference	0.81253	0.079
52DAP/reference	0.77127	0.03
57DAP/reference	0.58385	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11374	0.41
17DAP/reference	1.01569	1
27DAP/reference	0.9457	0.34
39DAP/reference	0.83129	0.009
41DAP/reference	0.90106	0.096
42DAP/reference	0.93939	0.212
43DAP/reference	0.85345	0.236
47DAP/reference	1.00432	1
52DAP/reference	0.94509	0.203
57DAP/reference	1.25059	0.182

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99022	0.699
17DAP/reference	0.82112	0.205
27DAP/reference	0.79345	0.031
39DAP/reference	0.79537	0.01
41DAP/reference	0.84203	0.05
42DAP/reference	0.82206	0.087
43DAP/reference	0.72811	0.033
47DAP/reference	0.89013	0.224
52DAP/reference	0.96777	0.637
57DAP/reference	0.70159	0.026

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07139	0.966
26DAP/20DAP	0.9123	1
34DAP/26DAP	0.99619	0.991
51DAP/34DAP	1.35751	0.387
52DAP/51DAP	0.95931	1
53DAP/52DAP	1.14672	0.662
55DAP/53DAP	1.27221	0.131
57DAP/55DAP	1.13073	0.407
62DAP/57DAP	1.08892	0.303
68DAP/62DAP	0.95557	0.747
68DAP/14DAP	0.77564	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0131	0.607

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.70816	0.132
Immature Eggplant/Mature Eggplant	1.57044	0.3
Ripe Pepper/Ripe Tomato	0.02647
Mature Eggplant/Ripe Tomato	1.78981	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.1174
1-1-2/M82	0.94317	1
12-2/M82	1.32626	0.327
12-4/M82	0.97165	1
1-3/M82	0.9693
2-1-1/M82	0.9419
2-1/M82	N/A	N/A
2-6/M82	0.97937	1
3-2/M82	0.92344	1
4-1-1/M82	1.03435	1
4-1/M82	0.57358	1
4-3-2/M82	0.92226	1
4-3/M82	0.8753	1
5-3/M82	0.89529	0.642
6-2/M82	0.83219
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.01884	1
9-3-2/M82	0.80113	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.4222
IL2-6/WTpooled	1.16202	0.659
IL7-5/WTpooled	1.17645
IL7-3/WTpooled	0.88097	0.31
IL12-4/WTpooled	1.15524	0.557
IL1-4/WTpooled	0.96267	1
WT/WTpooled	1.03002	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	1.40985	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99918	1
DC3000/delta hrp 6h	1.04702	1
DC3000/delta hrp 12h	0.78059	1
DC3000/delta hrp 24h	0.85777	0.166

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	1.29928	0.212

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.25946	0.254
Exp 36h	1.31693	0.693
Exp 60h	1.60491	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97231	1
Var 0h	1.13044	0.782
Var 12h I row2-row1	1.09559	0.204
Var 12h NI row2-row1	0.78552	0.488
Var 36h I row2-row1	1.04609	1
Var 36h NI row2-row1	1.28118	1
Var 60h I row2-row1	0.9792	1
Var 60h NI row2-row1	1.05615	1
Time course 0hI-0hNI	1.02168	1
Time course 12hI-12hNI	1.04745	0.684
Time course 36hI-36hNI	1.24034	0.013
Time course 60hI-60hNI	1.63591	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)	0.98301	0.722
transgenic ySAMdc/azygous control (breaker)	0.98592	1
transgenic ySAMdc/azygous control (red)	1.23804	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00225	0.958

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.41026	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86967	1
Manapal/WT (break)	0.93251	1
Manapal/WT (red)	0.54917	0.181