Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.18.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89865	0.551
27DAP/17DAP	0.78692	0.609
39DAP/27DAP	1.06715	1
41DAP/39DAP	1.03818	0.964
42DAP/41DAP	0.93911	1
43DAP/42DAP	1.15163	0.954
47DAP/43DAP	1.15495	0.889
52DAP/47DAP	1.2229	0.69
57DAP/52DAP	1.19171	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01201	0.743
17DAP/reference	0.93332	0.63
27DAP/reference	0.96958	0.623
39DAP/reference	1.01189	0.874
41DAP/reference	0.89817	0.341
42DAP/reference	0.96043	0.315
43DAP/reference	0.80291	0.098
47DAP/reference	0.94077	0.392
52DAP/reference	1.05706	1
57DAP/reference	1.01144	0.767

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14448	0.271
27DAP/17DAP	0.94868	0.854
39DAP/27DAP	0.89286	0.405
41DAP/39DAP	1.05139	0.807
42DAP/41DAP	1.06803	0.8
43DAP/42DAP	0.98363	0.875
47DAP/43DAP	0.97242	0.87
52DAP/47DAP	0.9442	0.848
57DAP/52DAP	1.009	1
57DAP/7DAP	1.03833	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75414	0.088
17DAP/reference	0.88966	0.039
27DAP/reference	0.832	0.013
39DAP/reference	0.80202	0.049
41DAP/reference	0.81075	0.032
42DAP/reference	0.62086	0.01
43DAP/reference	0.77306	0.034
47DAP/reference	0.61148	0.057
52DAP/reference	0.67717	0.028
57DAP/reference	0.78583	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95294	0.623
17DAP/reference	0.87236	0.214
27DAP/reference	1.00683	0.735
39DAP/reference	1.12511	0.746
41DAP/reference	0.96558	0.459
42DAP/reference	1.0076	1
43DAP/reference	1.33744	0.532
47DAP/reference	1.02385	0.79
52DAP/reference	0.93365	0.351
57DAP/reference	1.12005	0.827

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00954	1
17DAP/reference	1.02864	0.854
27DAP/reference	0.90353	0.126
39DAP/reference	0.7981	0.009
41DAP/reference	0.8521	0.119
42DAP/reference	0.73187	0.015
43DAP/reference	0.78507	0.025
47DAP/reference	1.13701	0.847
52DAP/reference	0.8253	0.25
57DAP/reference	0.87328	0.048

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.82062	1
26DAP/20DAP	0.97204	1
34DAP/26DAP	1.00831	1
51DAP/34DAP	1.05532	0.946
52DAP/51DAP	0.95575	1
53DAP/52DAP	0.92668	0.79
55DAP/53DAP	1.06062	0.927
57DAP/55DAP	1.00369	0.94
62DAP/57DAP	1.04231	1
68DAP/62DAP	0.98498	0.914
68DAP/14DAP	0.62801	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.11639	0.527

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	2.84421	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92463
1-1-2/M82	1.00252
12-2/M82	0.8922
12-4/M82	1.00612
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.16425	0.505
3-2/M82	N/A	N/A
4-1-1/M82	1.06607
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.00682	1
6-2/M82	N/A	N/A
6-3/M82	0.95764	0.68
7-1/M82	N/A	N/A
7-2/M82	1.10693	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.88536	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.62592	0.31
IL12-4/WTpooled	0.87644	0.71
IL1-4/WTpooled	1.21867
WT/WTpooled	0.89194	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	2.44388	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11537	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.91624	1
DC3000/delta hrp 24h	1.1465	0.322

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.56475	0.025
DC3000 delta B/DC3000 delta AB	0.41204	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97364	1
Var 0h	0.85562	0.457
Var 12h I row2-row1	0.77115	0.418
Var 12h NI row2-row1	1.02273	1
Var 36h I row2-row1	0.9338	0.805
Var 36h NI row2-row1	1.75051	1
Var 60h I row2-row1	1.43256	0.543
Var 60h NI row2-row1	1.0018	1
Time course 0hI-0hNI	1.0291	1
Time course 12hI-12hNI	0.99133	0.972
Time course 36hI-36hNI	0.86017	0.169
Time course 60hI-60hNI	0.08469	0.005

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)	1.71471	0.699
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	1.05081	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91606	0.149

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88439	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9373	1
Manapal/WT (break)	1.22752	1
Manapal/WT (red)	0.90159	0.607