Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.18.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97424	0.77
27DAP/17DAP	1.02374	0.922
39DAP/27DAP	1.00377	0.899
41DAP/39DAP	1.25947	0.223
42DAP/41DAP	0.94982	1
43DAP/42DAP	1.01925	1
47DAP/43DAP	0.94452	0.799
52DAP/47DAP	1.15996	0.651
57DAP/52DAP	1.11892	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19985	0.121
17DAP/reference	1.08506	0.138
27DAP/reference	1.11169	0.069
39DAP/reference	1.16387	0.122
41DAP/reference	1.32629	0.018
42DAP/reference	1.35624	0.001
43DAP/reference	0.9789	0.728
47DAP/reference	1.24034	0.001
52DAP/reference	1.35744	0.026
57DAP/reference	1.21937	0.291

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00443	1
27DAP/17DAP	0.99119	0.943
39DAP/27DAP	0.98084
41DAP/39DAP	1.02639	0.827
42DAP/41DAP	0.95621	0.635
43DAP/42DAP	0.99805	1
47DAP/43DAP	0.98231	0.909
52DAP/47DAP	0.99278
57DAP/52DAP	1.0005	0.913
57DAP/7DAP	1.08975

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83192	0.1
17DAP/reference	0.81968	0.064
27DAP/reference	1.00984	0.698
39DAP/reference	1.03835	0.819
41DAP/reference	1.04655	0.614
42DAP/reference	0.94712	0.355
43DAP/reference	0.93476	0.252
47DAP/reference	1.04464	0.915
52DAP/reference	0.80237	0.035
57DAP/reference	0.76475	0.031

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20414	0.217
17DAP/reference	1.34836	0.024
27DAP/reference	1.18924	0.323
39DAP/reference	1.28728	0.034
41DAP/reference	1.37541	0.043
42DAP/reference	1.3094	0.016
43DAP/reference	1.35777	0.027
47DAP/reference	1.12915	0.108
52DAP/reference	1.26037	0.01
57DAP/reference	1.27809	0.017

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87861	0.183
17DAP/reference	1.0417	0.792
27DAP/reference	0.9236	0.165
39DAP/reference	0.85945	0.037
41DAP/reference	1.0024	0.754
42DAP/reference	1.07386	0.47
43DAP/reference	1.17943	0.375
47DAP/reference	1.00287	0.731
52DAP/reference	0.79835	0.142
57DAP/reference	1.18874	0.196

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99921	1
26DAP/20DAP	1.10424	0.718
34DAP/26DAP	1.04513	1
51DAP/34DAP	1.06304	0.55
52DAP/51DAP	0.96719	1
53DAP/52DAP	1.03664
55DAP/53DAP	0.94489	0.698
57DAP/55DAP	1.23634	0.793
62DAP/57DAP	0.93946	0.871
68DAP/62DAP	0.81489	0.722
68DAP/14DAP	0.89949	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.07376	0.663

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.96893	0.673
Mature Green Tomato/Ripe Tomato	1.06467	0.814
Immature Eggplant/Mature Eggplant	1.01418	0.58
Ripe Pepper/Ripe Tomato	1.02703	1
Mature Eggplant/Ripe Tomato	1.48393	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93393	0.944
1-1-2/M82	1.03423	1
12-2/M82	0.95865	0.955
12-4/M82	1.01262	1
1-3/M82	0.92333	0.501
2-1-1/M82	0.82009	0.465
2-1/M82	1.59054
2-6/M82	0.94124	1
3-2/M82	0.95756	1
4-1-1/M82	0.98366	1
4-1/M82	1.11986	1
4-3-2/M82	0.88802	0.698
4-3/M82	1.00427	1
5-3/M82	1.00437	1
6-2/M82	0.95498	1
6-3/M82	0.96911	1
7-1/M82	1.02415	0.598
7-2/M82	0.87904	0.578
9-3-2/M82	0.83875	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.81135
WT/WTpooled	N/A	N/A

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	0.79211	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05451	0.846
DC3000/delta hrp 6h	1.09641	0.857
DC3000/delta hrp 12h	0.97816	1
DC3000/delta hrp 24h	1.01437	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91722	0.273
DC3000 delta B/DC3000 delta AB	1.01085	0.726

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.4197	0.228
Exp 36h	1.22046	1
Exp 60h	1.85391	0.215

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00469	1
Var 0h	0.89964	0.933
Var 12h I row2-row1	1.27064	0.204
Var 12h NI row2-row1	1.02155	1
Var 36h I row2-row1	0.90331	1
Var 36h NI row2-row1	0.85275	0.478
Var 60h I row2-row1	1.16617	0.562
Var 60h NI row2-row1	1.08787	1
Time course 0hI-0hNI	1.03295	1
Time course 12hI-12hNI	1.03527	0.842
Time course 36hI-36hNI	1.04413	0.316
Time course 60hI-60hNI	1.10735	0.137

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)	0.95618	0.614
transgenic ySAMdc/azygous control (breaker)	1.21782	1
transgenic ySAMdc/azygous control (red)	0.90482	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87171	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.19287	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86362	1
Manapal/WT (break)	0.80108	1
Manapal/WT (red)	0.95409	0.503