Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.9.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95078	0.664
27DAP/17DAP	1.03933	1
39DAP/27DAP	0.85331	0.495
41DAP/39DAP	1.24997	0.708
42DAP/41DAP	1.12895	0.877
43DAP/42DAP	1.0946	0.957
47DAP/43DAP	1.01619	0.959
52DAP/47DAP	1.10339	0.828
57DAP/52DAP	0.97788	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9814	0.503
17DAP/reference	0.97351	0.503
27DAP/reference	0.94393	0.24
39DAP/reference	1.04029	0.465
41DAP/reference	0.9877	0.814
42DAP/reference	0.91689	0.002
43DAP/reference	1.02196	0.678
47DAP/reference	0.95682	0.098
52DAP/reference	0.87109	0.096
57DAP/reference	0.89995	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98244	0.732
27DAP/17DAP	0.98467	0.821
39DAP/27DAP	1.05255	0.565
41DAP/39DAP	1.06882	0.748
42DAP/41DAP	0.96578	0.721
43DAP/42DAP	1.02561	0.627
47DAP/43DAP	0.97763	0.75
52DAP/47DAP	1.0486	0.851
57DAP/52DAP	1.03271	0.79
57DAP/7DAP	1.07953	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94861	0.091
17DAP/reference	0.9108	0.021
27DAP/reference	0.87795	0.01
39DAP/reference	0.96366	0.109
41DAP/reference	0.94545	0.174
42DAP/reference	1.05132	0.233
43DAP/reference	0.87818	0.018
47DAP/reference	0.87071	0.057
52DAP/reference	0.96378	0.278
57DAP/reference	0.95696	0.083

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02458	0.894
17DAP/reference	0.99342	0.693
27DAP/reference	1.02917	0.834
39DAP/reference	0.96607	0.428
41DAP/reference	0.93549	0.226
42DAP/reference	0.88064	0.108
43DAP/reference	0.99766	0.814
47DAP/reference	0.84999	0.023
52DAP/reference	1.01448	0.838
57DAP/reference	1.02185	0.868

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90544	0.048
17DAP/reference	0.93932	0.313
27DAP/reference	0.91324	0.039
39DAP/reference	0.87458	0.012
41DAP/reference	0.91648	0.167
42DAP/reference	0.7993	0.036
43DAP/reference	0.86468	0.044
47DAP/reference	0.88755	0.191
52DAP/reference	0.88575	0.368
57DAP/reference	0.70643	0.025

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03433	0.966
26DAP/20DAP	1.00781	1
34DAP/26DAP	1.03421	1
51DAP/34DAP	0.99558	0.957
52DAP/51DAP	0.98659	1
53DAP/52DAP	0.997	1
55DAP/53DAP	0.98928	0.864
57DAP/55DAP	1.05147	0.927
62DAP/57DAP	1.07464	0.158
68DAP/62DAP	1.02151	1
68DAP/14DAP	1.00906	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92051	0.269

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.33154	0.058
Mature Green Tomato/Ripe Tomato	0.95707	0.569
Immature Eggplant/Mature Eggplant	0.82926	0.072
Ripe Pepper/Ripe Tomato	1.86701	0.256
Mature Eggplant/Ripe Tomato	1.58967	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95639	0.69
1-1-2/M82	0.91075	1
12-2/M82	0.9276	0.955
12-4/M82	0.96674	1
1-3/M82	1.06976	1
2-1-1/M82	1.08447
2-1/M82	0.98404
2-6/M82	1.07706	0.405
3-2/M82	0.94506
4-1-1/M82	0.98854	1
4-1/M82	1.01603
4-3-2/M82	0.78079
4-3/M82	1.06178	1
5-3/M82	1.0224	1
6-2/M82	0.96108
6-3/M82	0.92731	1
7-1/M82	1.41711
7-2/M82	0.95872	0.881
9-3-2/M82	0.81148

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.96572	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95345	1
IL12-4/WTpooled	1.27179	0.673
IL1-4/WTpooled	0.95686
WT/WTpooled	1.02593	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	1.12119	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05705	0.692
DC3000/delta hrp 6h	1.34819	1
DC3000/delta hrp 12h	1.01818	1
DC3000/delta hrp 24h	1.07087	0.411

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03017	0.515
DC3000 delta B/DC3000 delta AB	1.01888	0.655

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88546	1
Exp 36h	1.19767	1
Exp 60h	1.04483	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99437	1
Var 0h	0.86943	1
Var 12h I row2-row1	1.16394	0.222
Var 12h NI row2-row1	1.03358	1
Var 36h I row2-row1	0.97754	1
Var 36h NI row2-row1	0.91315	0.61
Var 60h I row2-row1	1.11393	1
Var 60h NI row2-row1	1.08887	1
Time course 0hI-0hNI	1.05357	0.867
Time course 12hI-12hNI	1.05102	0.777
Time course 36hI-36hNI	1.14023	0.056
Time course 60hI-60hNI	1.26448	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)	0.84008	0.289
transgenic ySAMdc/azygous control (breaker)	0.93234	0.49
transgenic ySAMdc/azygous control (red)	1.08041	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98382	0.286

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82841	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89913	1
Manapal/WT (break)	0.91675	1
Manapal/WT (red)	1.02448	1