Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.4.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23084	0.588
27DAP/17DAP	1.46958	0.544
39DAP/27DAP	1.28082	0.372
41DAP/39DAP	0.97986	0.883
42DAP/41DAP	0.89045	1
43DAP/42DAP	0.95229	0.867
47DAP/43DAP	1.37897	0.193
52DAP/47DAP	1.38582	0.63
57DAP/52DAP	1.12362	0.96

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12304	0.139
17DAP/reference	1.13677	0.229
27DAP/reference	1.29997	0.01
39DAP/reference	1.0845	0.403
41DAP/reference	0.97606	0.667
42DAP/reference	1.14026	0.004
43DAP/reference	1.21088	0.008
47DAP/reference	1.33223	0.001
52DAP/reference	1.5335	0.008
57DAP/reference	1.44089	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19801	0.278
27DAP/17DAP	1.30828	0.413
39DAP/27DAP	1.36026	0.343
41DAP/39DAP	1.48104	0.612
42DAP/41DAP	0.94898	0.599
43DAP/42DAP	0.88489	0.466
47DAP/43DAP	1.37408	0.601
52DAP/47DAP	1.48475	0.258
57DAP/52DAP	0.9002	0.566
57DAP/7DAP	0.90085	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.092	0.6
17DAP/reference	1.27067	0.025
27DAP/reference	1.17973	0.301
39DAP/reference	1.49376	0.011
41DAP/reference	1.63566	0.011
42DAP/reference	1.50064	0.008
43DAP/reference	1.44849	0.023
47DAP/reference	1.47384	0.014
52DAP/reference	1.36215	0.017
57DAP/reference	1.59704	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65569	0.02
17DAP/reference	0.99205	0.51
27DAP/reference	1.09977	0.595
39DAP/reference	1.48255	0.021
41DAP/reference	1.5483	0.007
42DAP/reference	1.31093	0.008
43DAP/reference	0.86579	0.181
47DAP/reference	1.28885	0.009
52DAP/reference	1.29666	0.008
57DAP/reference	1.12677	0.64

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08701	0.588
17DAP/reference	0.86215	0.217
27DAP/reference	1.13596	0.111
39DAP/reference	1.07188	0.227
41DAP/reference	0.92391	0.293
42DAP/reference	1.03659	0.943
43DAP/reference	1.20531	0.237
47DAP/reference	1.06983	0.82
52DAP/reference	1.22996	0.158
57DAP/reference	1.73809	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93597	1
26DAP/20DAP	1.1548	1
34DAP/26DAP	0.83861
51DAP/34DAP	0.5013
52DAP/51DAP	0.89462	1
53DAP/52DAP	0.85728	0.581
55DAP/53DAP	0.9612	0.746
57DAP/55DAP	2.19124	0.87
62DAP/57DAP	1.28944	0.217
68DAP/62DAP	2.20631	0.039
68DAP/14DAP	1.89201	0.026

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89903	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.76596	0.058
Mature Green Tomato/Ripe Tomato	0.88904	0.2
Immature Eggplant/Mature Eggplant	1.75524	0.05
Ripe Pepper/Ripe Tomato	1.18268	0.258
Mature Eggplant/Ripe Tomato	1.74056	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0406	1
1-1-2/M82	1.07804	1
12-2/M82	1.04912
12-4/M82	0.77655	0.33
1-3/M82	1.68292
2-1-1/M82	0.83028	1
2-1/M82	N/A	N/A
2-6/M82	0.72592	1
3-2/M82	1.22263	0.426
4-1-1/M82	0.70105	1
4-1/M82	N/A	N/A
4-3-2/M82	1.43847
4-3/M82	1.24415	0.268
5-3/M82	1.39678	1
6-2/M82	N/A	N/A
6-3/M82	1.02645
7-1/M82	1.33949	1
7-2/M82	0.82582	0.527
9-3-2/M82	0.82674

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.53257
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.5006
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.53391
IL1-4/WTpooled	1.27713	1
WT/WTpooled	2.59115	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	3.14948	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03667	0.921
DC3000/delta hrp 6h	1.04519	1
DC3000/delta hrp 12h	1.29708	1
DC3000/delta hrp 24h	0.92062	0.464

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.23146	1
Exp 36h	1.1903	1
Exp 60h	1.38525	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.05738	0.782
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.05831	0.36
transgenic ySAMdc/azygous control (breaker)	0.8566	0.251
transgenic ySAMdc/azygous control (red)	0.82011	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.16027	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71987	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86647	1
Manapal/WT (break)	0.90524	1
Manapal/WT (red)	0.67409	0.181