Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02871	0.975
27DAP/17DAP	1.04935	0.911
39DAP/27DAP	0.82249	0.328
41DAP/39DAP	1.34186	0.32
42DAP/41DAP	1.07451	0.962
43DAP/42DAP	1.0322	1
47DAP/43DAP	1.04719	0.889
52DAP/47DAP	1.03361	0.957
57DAP/52DAP	0.99573	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94222	0.277
17DAP/reference	0.96499	0.503
27DAP/reference	1.02357	0.559
39DAP/reference	1.00316	1
41DAP/reference	0.85554	0.114
42DAP/reference	0.89069	0.038
43DAP/reference	0.93586	0.394
47DAP/reference	0.99545	0.636
52DAP/reference	0.9648	0.438
57DAP/reference	1.02333	0.724

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00138	0.871
27DAP/17DAP	0.99944	1
39DAP/27DAP	0.96883	0.737
41DAP/39DAP	1.03584	1
42DAP/41DAP	0.86596	0.538
43DAP/42DAP	1.27594	0.273
47DAP/43DAP	0.9839	0.93
52DAP/47DAP	0.92435	0.797
57DAP/52DAP	0.64656	0.137
57DAP/7DAP	1.383	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11238	0.625
17DAP/reference	0.87234	0.192
27DAP/reference	0.99409	0.656
39DAP/reference	1.27326	0.21
41DAP/reference	1.01316	0.741
42DAP/reference	0.98199	0.554
43DAP/reference	1.01378	0.727
47DAP/reference	1.02077	1
52DAP/reference	0.99803	0.679
57DAP/reference	0.99438	0.589

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97276	0.475
17DAP/reference	0.99114	0.673
27DAP/reference	1.01932	0.765
39DAP/reference	0.97517	0.469
41DAP/reference	0.92925	0.218
42DAP/reference	0.96148	0.289
43DAP/reference	1.05692	0.655
47DAP/reference	1.00292	1
52DAP/reference	1.06073	0.021
57DAP/reference	1.06783	0.06

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07918	0.644
17DAP/reference	1.0758	0.675
27DAP/reference	0.73717	0.14
39DAP/reference	1.2008	0.182
41DAP/reference	1.03966	1
42DAP/reference	0.95937	0.671
43DAP/reference	0.96341	0.568
47DAP/reference	1.06079	0.461
52DAP/reference	0.97701	0.747
57DAP/reference	0.89831	0.18

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97288	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.14472	1
51DAP/34DAP	1.30582	0.164
52DAP/51DAP	1.35924	0.171
53DAP/52DAP	0.97709	0.868
55DAP/53DAP	0.87133	0.663
57DAP/55DAP	1.58553	0.865
62DAP/57DAP	1.12025
68DAP/62DAP	N/A	N/A
68DAP/14DAP	0.93693

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.06404	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.04629	0.666
Mature Green Tomato/Ripe Tomato	0.94282	0.569
Immature Eggplant/Mature Eggplant	1.15015	0.13
Ripe Pepper/Ripe Tomato	0.6534	0.293
Mature Eggplant/Ripe Tomato	0.39343

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.82091
12-2/M82	N/A	N/A
12-4/M82	0.77692	0.358
1-3/M82	N/A	N/A
2-1-1/M82	0.80637
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.77912
4-1-1/M82	0.84216
4-1/M82	0.71958
4-3-2/M82	0.81606	0.487
4-3/M82	1.01811
5-3/M82	0.76105	0.49
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.92018
7-2/M82	N/A	N/A
9-3-2/M82	0.83612	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.64278	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.09766	1
IL12-4/WTpooled	0.85396	0.71
IL1-4/WTpooled	0.71982	0.562
WT/WTpooled	1.10786	0.686

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	0.81762

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96626	1
DC3000/delta hrp 6h	1.03545	0.95
DC3000/delta hrp 12h	0.94974	1
DC3000/delta hrp 24h	0.64675	0.039

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	1.13027

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05589	1
Exp 36h	1.17396	1
Exp 60h	1.29572	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97476	1
Var 0h	0.83406	1
Var 12h I row2-row1	1.09709	0.736
Var 12h NI row2-row1	1.33096	0.235
Var 36h I row2-row1	0.87014	0.805
Var 36h NI row2-row1	1.05159	1
Var 60h I row2-row1	1.09608	0.562
Var 60h NI row2-row1	1.00333	1
Time course 0hI-0hNI	0.84635	0.142
Time course 12hI-12hNI	0.79939	0.033
Time course 36hI-36hNI	0.74869	0.05
Time course 60hI-60hNI	0.25015	0.006

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)	0.98718	0.567
transgenic ySAMdc/azygous control (breaker)	1.14896	1
transgenic ySAMdc/azygous control (red)	1.07331	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99448	0.651

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89904	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76028	0.172
Manapal/WT (break)	0.80876	1
Manapal/WT (red)	2.22191	0.15